MOLECULAR SPECTROSCOPY

SPECTRUM SOFTWARE

Users Guide

2 . Spectrum
Release History

Released Date Software Version

March 2009
Release 6.3
Any comments about the documentation for this product should be addressed to:
User Assistance
PerkinElmer Ltd
Chalfont Road
Seer Green
Beaconsfield
Bucks HP9 2FX
United Kingdom
Or emailed to: info@[Link]
Notices
The information contained in this document is subject to change without notice.
Except as specifically set forth in its terms and conditions of sale, PerkinElmer makes
no warranty of any kind with regard to this document, including, but not limited to, the
implied warranties of merchantability and fitness for a particular purpose.
PerkinElmer shal not be liable for errors contained herein for incidental consequential damages in
connection with furnishing, performance or use of this material.
Copyright Information
This document contains proprietary information that is protected by copyright.
All rights are reserved. No part of this publication may be reproduced in any form whatsoever or
translated into any language without the prior, written permission of PerkinElmer, Inc.
Copyright 2009 PerkinElmer, Inc.
Produced in the UK.
Trademarks
Registered names, trademarks, etc. used in this document, even when not specifically marked as
such, are protected by law.
PerkinElmer is a registered trademark of PerkinElmer, Inc.
Spectrum, Spectrum 100, Spectrum 100N, and Spectrum 400 are trademarks of PerkinElmer, Inc.

Spectrum . 3

Table Of Contents
Introduction ............................................................................................. 11
About This Manual ...........................................................................................12
Welcome to Spectrum ......................................................................................13
Displaying Spectra ................................................................................... 15
Adding, Deleting or Moving Spectra ...................................................................17
Copying a Graph to another Windows Application
..............................19
Cutting, Copying and Pasting Spectra .........................................................19
Using the Mouse to Copy or Move Spectra ..................................................20
Spectrum Browser
...........................................................................21
Selecting Spectra on a Graph .....................................................................22
Changing the Appearance of the Graph .............................................................23
Changing the Appearance of a Graph ..........................................................23
Ranges .....................................................................................................24
Annotations ...............................................................................................24
Scale ........................................................................................................26
Fonts ........................................................................................................26
Graph Colors .............................................................................................26
Spectrum Colors ........................................................................................27
Changing the View of the Spectrum ..................................................................28
Optimize
..........................................................................................29
Using the Mouse to Zoom in on a Region of Interest in a Spectrum ..............30
Using the Autorange Commands to Rescale the Graph .................................31
Autoscale Y ...............................................................................................31
Offsetting Spectra ......................................................................................32
Panning and Expanding..............................................................................33
Display Modes for Graphs

................................................................35

Radar Display
..................................................................................36
Previous Range and Full Scale ....................................................................36
Adding and Editing Text on a Graph

........................................................37

Copying and Pasting Text

.................................................................38
Removing Text from a Graph .....................................................................39
Cursors ............................................................................................................40
Horizontal Cursor

.............................................................................40

Vertical Cursor
.................................................................................40
Displaying the Vertical Cursor or Changing Its Mode ....................................40
Label Cursor
....................................................................................41
Moving a cursor:........................................................................................41
Moving both the horizontal and vertical cursors: ..........................................41
Labelling Peaks
......................................................................................42
Clearing peak labels ...................................................................................42
Moving Peak Labels ...................................................................................42
Removing individual peak labels .................................................................42

4 . Spectrum
.................................................................. 43
Copying a Graph to a Report
To copy graphs into a report: .................................................................... 43
Which graph holder is the graph copied into? ............................................. 43
Which report template is used? .................................................................. 43
Report Template ....................................................................................... 43
Working with Spectra .............................................................................. 45
Selecting a Spectrum Name for the Result of a Process Command ...................... 47
Correcting Spectra ........................................................................................... 48
Data Tune-up
................................................................................. 48
Baseline Correction ................................................................................... 49
Changing the form of data ............................................................................... 52
Changing the Form of Data ........................................................................ 52
Absorbance
Transmittance

.................................................................................... 53
.................................................................................. 53

Convert X

....................................................................................... 54

Difference

...................................................................................... 55

Derivative

....................................................................................... 57

Interpolate
ATR Correction
Kubelka-Munk

..................................................................................... 59
............................................................................... 60
................................................................................. 63

Kramers-Kronig
............................................................................... 64
Extracting Information from Spectra ................................................................. 68
Compare
........................................................................................ 68
Setting up a Comparison ........................................................................... 71
IR Search
....................................................................................... 74
Setting up a Search ................................................................................... 76
Interactive Interpretation

................................................................ 79

Peak Table
..................................................................................... 81
Peak Options ............................................................................................ 84
Quant Prediction
............................................................................. 85
Setting up a Quant Prediction .................................................................... 87
Peak/Area Height
............................................................................ 89
Setting Defaults for a Peak Area/Height Measurement ................................. 93
Peak Area / Height Options

.............................................................. 94

Spectrum . 5
Preparing Spectra .............................................................................................95
Deconvolution

.................................................................................95

Spectral Calculator
Normalize

...........................................................................99

..................................................................................... 100

Abex

............................................................................................. 101

Blank

............................................................................................ 103

Status Information
............................................................................... 105
Displaying the Status Information ............................................................. 105
General Tab ............................................................................................ 105
Instrument Tab ....................................................................................... 106
Accessories Tab ....................................................................................... 106
History Tab ............................................................................................. 107
Quality Checks Tab .................................................................................. 107
Process History .............................................................................................. 108
Abex History............................................................................................ 108
Absorbance History .................................................................................. 108
ATR Correction History ............................................................................. 109
Baseline Correction History ....................................................................... 109
Blank History ........................................................................................... 110
Convert X History .................................................................................... 110
Deconvolution History .............................................................................. 111
Derivative History .................................................................................... 111
Difference History .................................................................................... 112
Interpolate History ................................................................................... 113
Kramers-Kronig History ............................................................................ 113
Kubelka-Munk History .............................................................................. 114
Normalize History .................................................................................... 114
Smooth History........................................................................................ 115
Interactive Smooth History ....................................................................... 115
Spectral Calculator History ....................................................................... 116
Transmittance History .............................................................................. 116
Controlling the Instrument .................................................................... 117
Controlling the Spectrometer .......................................................................... 118
Collecting Spectra .......................................................................................... 119
Sample tab.............................................................................................. 121
Multiple Sample tab ................................................................................. 122
Scan tab ................................................................................................. 125
Instrument tab ........................................................................................ 128
Resolution ............................................................................................... 129
Setting the Data Interval .......................................................................... 131
Apodization ............................................................................................. 132
Phase Correction ..................................................................................... 134
Scan Speed ............................................................................................. 135
Abscissa units .......................................................................................... 136
2nd Derivative ......................................................................................... 137
CO2/H2O Suppression ............................................................................... 138
AVI Correction ......................................................................................... 138
Look Ahead ............................................................................................. 139
Quality Checks......................................................................................... 140
Beam tab ................................................................................................ 141

6 . Spectrum
Source.................................................................................................... 142
Filterwheel .............................................................................................. 143
Detectors................................................................................................ 144
Beamsplitters .......................................................................................... 146
J-Stop Dialog .......................................................................................... 147
Accessory tab ......................................................................................... 148
Ranges tab ............................................................................................. 149
Changing Range (Spectrum 400 only) ...................................................... 151
Scan Progress ......................................................................................... 153
Scan Background .................................................................................... 154
Halt ........................................................................................................ 154
Monitoring..................................................................................................... 155
Monitor tab ............................................................................................. 156
Display tab ............................................................................................. 157
Stopping monitoring ................................................................................ 157
Force Gauge ........................................................................................... 158
Monitoring toolbar ................................................................................... 158
Controlling Accessories................................................................................... 159
Controlling Accessories ............................................................................ 159
Sample Shuttle
HATR

............................................................................. 160

........................................................................................... 161

Universal ATR

............................................................................... 162

Diffuse Reflectance
NIRA

....................................................................... 163

............................................................................................ 164

NIR Tablet Autosampler

NIR Fiber Optic Probe
Liquid Sipper

................................................................ 166
................................................................... 168

................................................................................ 170

Setting Up the Instrument

.................................................................... 171
Menus .................................................................................................... 172
Toolbar .................................................................................................. 173
Instrument Settings Files ......................................................................... 174
Sampling Configuration ........................................................................... 175
Data Collection Setup .............................................................................. 177
Adjustments Toolbox ..................................................................................... 178
Using the Adjustments Toolbox ................................................................ 179
Maintenance

................................................................................. 180

Wavenumber Calibration
Aligning the Instrument
Relocating the Centerburst

............................................................... 181
................................................................. 183
............................................................ 183

AVI Calibration
.............................................................................. 184
Instrument Display .................................................................................. 185
Calibrate LCD .......................................................................................... 186
Fiber Probe Display ................................................................................. 187

Spectrum . 7
Instrument Validation ..................................................................................... 188
To perform a test: ................................................................................... 188
System Suitability
Validate Instrument
ASTM 0

.......................................................................... 189
....................................................................... 193

......................................................................................... 197

USP
.............................................................................................. 200
Validation Errors ...................................................................................... 204
Validation Reports ................................................................................... 205
Routine Access and Standard Access Users ...................................................... 209
Routine Access Users ............................................................................... 209
Standard Access Users ............................................................................. 209
Working with Files and Windows .......................................................... 211
Working with Files and Windows ..................................................................... 212
Opening or Closing Files ................................................................................. 213
Opening a File
............................................................................... 213
Selecting Files in the File Selector ............................................................. 213
To close a file: ......................................................................................... 213
To close all the open windows .................................................................. 213
Printing
............................................................................................... 214
Printing a text window ............................................................................. 214
Printing a graph window .......................................................................... 214
Changing the Page Layout ....................................................................... 214
Printing a Graph using a Report Template ................................................. 215
Changing the Print Setup ......................................................................... 215
Print Spectra Colors ................................................................................. 216
Black and White Printing .......................................................................... 216
Working with Graphs ...................................................................................... 217
Creating a New Graph

.................................................................... 217

Saving Graphs
............................................................................... 217
Creating a New Graph Template ............................................................... 218
Saving and Renaming Spectra ......................................................................... 219
Saving Spectra

.............................................................................. 219

Renaming Spectra
......................................................................... 219
Arranging Windows and Icons ......................................................................... 220
Changing the Way Windows are Displayed ................................................ 220
Arranging Icons ....................................................................................... 220
Exiting Spectrum
.................................................................................. 221
Exiting from Spectrum ............................................................................. 221
Unsaved data .......................................................................................... 221
Closing the Data Server ........................................................................... 221
Viewing Spectrum Information in Windows Explorer ......................................... 222

8 . Spectrum
Customizing Spectrum ........................................................................... 225
Customizing Spectrum ................................................................................... 226
IR Assistant
......................................................................................... 227
Starting the IR Assistant .......................................................................... 227
Using the IR Assistant ............................................................................. 228
Performing a Task ................................................................................... 229
Tools ............................................................................................................ 230
Using the Toolbox ................................................................................... 231
The Options Dialog ........................................................................................ 232
Options .................................................................................................. 232
File Options ............................................................................................ 233
View Options .......................................................................................... 234
Process Options ...................................................................................... 235
Instrument Options ................................................................................. 236
Peak Options .......................................................................................... 237
Other Options ......................................................................................... 238
Learn Mode
......................................................................................... 239
Learn Mode ............................................................................................ 239
Recording a New Learn Mode Script

............................................... 241

Playing a Learn Mode Script

........................................................... 242
Editing a Learn Mode script ..................................................................... 243
Commands that Cannot be Added to a Learn Mode Script.......................... 247
Using Interactive Commands in a Learn Mode Script ................................. 248
Spectrum Administration ....................................................................... 251
Administration Menu ...................................................................................... 252
Administration for Spectrum .................................................................... 252
Administration for Spectrum ES................................................................ 252
Setting up Users, Groups and Passwords......................................................... 253
Default Users .......................................................................................... 254
Default Groups........................................................................................ 255
Adding a New User ................................................................................. 256
Creating or Deleting a Group ................................................................... 257
Assigning Users to, and Removing Users from, a Group............................. 258
Assigning Instruments to a Group ............................................................ 258
Disabling, or Deleting, a User................................................................... 259
Passwords .............................................................................................. 260
Changing a Password .............................................................................. 260
Maximum and Minimum Password Age ..................................................... 262
Password Length..................................................................................... 263
Re-using Passwords ................................................................................ 263
Limiting failed Login attempts using Lockout ............................................. 264
Reinstating Locked Out Users .................................................................. 265
Windows Login ....................................................................................... 266
Logging in to Spectrum using a Windows Login ........................................ 269
Removing a User from the PKIUsers Windows Group ................................ 270
User Configuration in Spectrum ...................................................................... 271
Configuring Menu items in Spectrum ........................................................ 271
Configuring the Toolbox & Toolbar in Spectrum ........................................ 272
Group Configuration in Spectrum ES ............................................................... 274
Configuring Menu items in Spectrum ES ................................................... 274
Important Menu Configuration Considerations .......................................... 275
Configuring the Toolbar & Toolbox in Spectrum ES ................................... 277
Applying other Configuration settings in Spectrum ES ................................ 279

Spectrum . 9
Administration Audit Trail................................................................................ 283
Login History ........................................................................................... 284
Summary ................................................................................................ 286
Spectrum Audit Trail ....................................................................................... 287
Archiving the Active database ................................................................... 288
Displaying an Active database stored elsewhere ........................................ 288
Printing an Audit database ....................................................................... 289
Exporting an Audit database..................................................................... 290
Creating & Using a new Active database ................................................... 290
Instrument and Accessory Configuration .......................................................... 291
Installing an Instrument ........................................................................... 291
Removing an Instrument .......................................................................... 293
Adding Accessories .................................................................................. 293
Legacy File Converter ..................................................................................... 295
Importing and exporting Quant methods ......................................................... 296
Spectrum Menus .................................................................................... 299
Menus ........................................................................................................... 300
File Menu ....................................................................................................... 301
Edit Menu ...................................................................................................... 302
View Menu ..................................................................................................... 303
Process Menu................................................................................................. 304
Instrument Menu ........................................................................................... 305
Setup Menu ................................................................................................... 306
Administration Menu....................................................................................... 307
Administration for Spectrum ..................................................................... 307
Administration for Spectrum ES ................................................................ 307
Procedures Menu ........................................................................................... 308
Window Menu ................................................................................................ 309
Help Menu ..................................................................................................... 310
Index ............................................................................................................ 311

10 . Spectrum

I ntroduction

12 . Spectrum

About This M anual

Spectrum is the main PerkinElmer software package for collecting, viewing and
processing IR spectra. This manual is divided into seven areas:

Displaying Spectra - Topics on how to display spectra and change the way graphs
and spectra are displayed.

Working with Spectra - Topics on how to manipulate and process spectra to get the
information you want, the way you want it.

Controlling the Spectrometer - Topics on how to use your instrument to collect

spectra and how to set up, adjust and validate your instrument.

Working with Files and Windows - Topics on general manipulation of windows within
the main application window, including the use of templates and how to save or
print in Spectrum.

Customizing Spectrum - Topics on different ways to adapt Spectrum for the way you
want it, including details of the IR Assistant, Learn Mode, using logins, and changing
the toolbar and toolbox tools.

Spectrum Administration - Topics on setting up users and groups; how to examine

audit trails; configuring instruments and accessories; and using legacy files and
methods.

Spectrum Menus - A quick way to get help about a particular menu command.

This manual is derived from the on-screen HTML help file accessed from the Spectrum
software:

To display on-screen HTML help, select Contents and Index from its Help menu, or
click Help on a dialog.

To display this version (which can be printed in its entirety) from the on-screen
HTML help, click the [Link] icon.

Introduction . 13

W elcom e to Spectrum
Spectrum can be used to set up and collect data from a range of PerkinElmer
spectrometers, including the:

Spectrum 100 FT-IR / Spectrum 100N FT-NIR

Spectrum One FT-IR / Spectrum One NTS FT-NIR

Spectrum 400

The Spectrum View menu contains commands that enable you to change the way you
view the spectrum, while the Process menu contains commands to manipulate the data
including the ability to extract qualitative and quantitative information from the spectrum.
Spectrum is a very powerful software package, to familiarize yourself with its abilities we
suggest you work through the on-screen tutorials by choosing Learning Spectrum on
the Help menu.
There is a multimedia introduction to the instruments, which you can access directly off
the Spectrum Multimedia CD. This CD also contains multimedia tutorials for each of the
main sampling accessories.

14 . Spectrum

Displaying Spectra

16 . Spectrum
This chapter includes topics on how to display spectra and change the way graphs and
spectra are displayed:

Adding, Deleting or Moving Spectra - This section tells you how to change which
spectra are displayed on a graph.

Changing the Appearance of the Graph - This section tells you how to customize the
graph and how spectra look when displayed on the graph.

Changing the View of the Spectrum - This section tells you how to manipulate
spectra to see the details of interest to you.

Adding and Editing Text on a Graph - This section tells you how to work with text
that you can add to a graph.

Cursors - This topic tells you all about using cursors to get information from the
graph.

Labelling Peaks - This topic tells you how to label the peaks in the spectrum.

Copying a Graph to a Report - This topic tells you about transferring graphs to
Report Builder.

Displaying Spectra . 17

Adding, Deleting or M oving Spectra

A spectrum is a set of data than can be displayed on a graph. In Spectrum, the term
spectrum also includes interferograms, chromatograms, and time drives. The filename of
a spectrum is displayed in the information pane at the bottom of the graph window.

When you have collected your spectra or opened spectrum files, they are displayed on a
graph.
Spectrum enables you to display several spectra on a graph.
You can add extra spectra to a graph in two ways:

using the Open command on the File menu;

moving or copying spectra from another application using the mouse.

Spectrum Browser enables you to preview the spectra that are in the memory of your PC
and add them to your graph.
You can also cut or copy spectra from a graph and paste them onto another graph,
remove spectra from a graph and copy spectra to other Windows applications, for
example to include them in a document or copy the graph to a report.
If you want to perform an action, for example correct a spectrum's baseline, on only
some of the spectra on a graph, you must select the spectra before you perform the
action.

18 . Spectrum

Adding Spectra to a Graph

1. Display the File menu and choose Open.
The Open dialog opens. The directory that contains your spectral (.sp) files is
specified by the File tab accessed by displaying the Setup menu and choosing
Options.
2. Click on the filename of the spectrum that you want to display.
If you want to add another type of spectrum file, choose the appropriate file
extension from the List of Files of Type box.
3. Choose OK.
The spectrum is displayed on the graph.

R em oving Spectra from a Graph

4. Select the spectrum or spectra that you want to remove from the graph.
When a spectrum is selected, its filename is underlined.
NOTE: If you want to remove the spectra from the graph but not the labels, make sure
none of the text labels displayed are selected. The Cut command is active on
selected text labels above anything else.
5. Display the Edit menu and choose Cut.
The selected spectra are removed from the graph. You can now use the Paste
Spectra command to add the cut spectra to another graph or you can paste the
spectra into another Windows application.

Deleting Spectra
The Delete command on the Edit menu allows information to be removed from the
spectra. The information that has been removed is not permanently deleted from
Spectrum ES - it has just been erased.
NOTE: If you want to use the Delete command on a spectrum displayed on a graph,
make sure none of the text labels displayed are selected. The Delete command is
active on selected text labels above anything else.
1. Make sure no text labels are selected.
2. Select the spectra on the graph that you want to delete.
The spectrum name is underlined when it has been selected.
3. Display the Edit menu and choose Delete or press DEL.
The spectra disappear. If Confirm Deletes has been enabled, a warning dialog is
displayed before the selected spectra are deleted. Choose OK to confirm the
deletion.
See also
Copying a Graph to another Windows Application
Cutting, Copying and Pasting Spectra
Using the Mouse to Copy or Move Spectra Between Graphs and Applications
Spectrum Browser
Selecting Spectra on a Graph

Displaying Spectra . 19

Copying a Graph to another W indow s Application

When a graph window is active, and no text has been selected on that window, the Copy
command copies the whole graph on to the clipboard. The graph can then be pasted into
another Windows application. If you paste the graph back into Spectrum, only the
spectra will be pasted on to the current graph.
Graphs are copied as Windows metafiles. You can paste graphs only into Windows
applications that can support metafiles.

Copying a graph
Make sure that the text window that you want to copy is the active window and that no
text has been selected on the chosen graph.

Display the Edit menu and choose Copy.

The graph is copied to the clipboard. The graph is now available to be pasted into
another Windows application.

NOTE: If you copy a graph with vertical text to another Windows application and then
print the graph, the orientation of the text may change. This depends on the
printer and print driver used. This does not happen if you print a graph directly
from Spectrum.

Cutting, Copying and P asting Spectra

The Cut command on the Edit menu cuts information from its current position, and
places it on the Windows clipboard ready for pasting back into a different position, either
in the same application or within a different Windows application. The Paste Spectra
command on the Edit menu enables you to paste spectra on to the active graph that
have been copied or cut from another graph.

Cutting spectra
1. If there are text labels on the graph, make sure that none of them is selected.
The Cut command cuts selected text labels in preference to spectra.
2. Select the spectrum or spectra that you want to remove from the graph.
When a spectrum is selected, its filename is underlined.
3. Display the Edit menu and choose Cut, or press CTRL + X.
The selected spectra are removed from the graph. You can now use the Paste
Spectra command to add the cut spectra to another graph or you can paste the
spectra into another Windows application. A list of the names of the spectra is kept
in memory.

20 . Spectrum

Copying spectra
1. If there are text labels on the graph, make sure that none of them is selected.
The Copy command copies selected text labels in preference to spectra.
2. Select the spectrum or spectra that you want to copy.
When a spectrum is selected, its filename is underlined.
3. Display the Edit menu and choose Copy, or press CTRL + C.
The selected spectra are copied. You can now use the Paste Spectra command to
add the spectra to another graph or you can paste the spectra into another
Windows application. A list of the names of the spectra is kept in memory.

Pasting spectra
1. Click on the graph on to which you will paste the spectra.
This ensures that this graph is the active graph.
2. Display the Edit menu and choose Paste Spectra.
The spectra on the clipboard are pasted on to the active graph..
NOTE: Graphs are copied as Windows metafiles. You can paste spectra only into
Windows applications that support metafiles.

Using the M ouse to Copy or M ove Spectra

This topic describes using the mouse to Copy or Move spectra between Graphs and
Applications.
1. Select the spectrum or spectra you want to copy from the current graph of an
application.
When a spectrum is selected, its filename is underlined.
2. Position the mouse pointer on the name of the spectrum you want to copy.
The mouse pointer changes to a hand

3. To copy the spectra, press and hold down the left mouse button, drag the spectra
to their new location and release the mouse button. To move spectra instead of
copying them, press hold down CTRL when you drag the spectra.
Dropping the spectrum on an existing graph copies or moves the spectrum to
that graph.
Dropping the spectrum on the toolbar opens a new graph containing the
spectrum.
Dropping the spectrum on the icon for an application starts the application, and
displays the spectrum in a new graph.
When spectra are copied, the mouse pointer changes shape:
indicates the spectra are being copied;
indicates the spectra are being moved.

Displaying Spectra . 21

Spectrum Brow ser

The spectrum browser enables you to browse through the spectra in memory (iconized or
displayed), select the spectra you require, and add them to a new graph or the current
graph.

Adding a Spectrum to the Current Graph

1. Display the View menu and choose Spectrum Browser.
The Spectrum Browser dialog is displayed.
2. From the list of Spectra in Memory, select the spectrum you want to add to the
graph.
The selected spectrum is displayed in the center of the dialog. Above the spectrum
are the directory path and filename of the spectrum.
Below the spectrum are the comments on the spectrum, entered when it was
collected.
NOTE: You can see more information on the selected spectrum by choosing Status. This
displays the Status Information dialog.
3. Choose Add to View.
The selected spectrum is added to the current graph.
4. Choose Close.

Adding a Spectrum to a New Graph

1. Display the View menu and choose Spectrum Browser.
The Spectrum Browser dialog is displayed.
2. Select the spectrum you want to add to the graph from the list in the Spectra in
Memory field.
3. Choose New View.
A new graph, which contains the selected spectrum, opens.
4. Choose Close.

22 . Spectrum

Selecting Spectra on a Graph

You sometimes need to select spectra on a graph, so that your next action applies only to
the selected spectra. For example, you may want to remove the spectrum from the
graph, or offset it from the other spectra.
When a spectrum is selected, its filename is underlined.

To select one spectrum :

Click on the filename of the spectrum.

The spectrum is selected and the other spectra are deselected.

To select m ore than one spectrum :

Hold down CTRL while you click on the filenames.

The spectra you click on are selected.

To select all the spectra displayed on the graph:

Display the View menu and choose Select All or press CTRL+A.

To deselect som e spectra, leaving the others selected:

Hold down CTRL, and click on the filenames of the spectra you want to deselect.
The spectra you click on are deselected, leaving the others selected.

Displaying Spectra . 23

Changing the Appearance of the Graph

Changing the Appearance of a Graph
The Format View dialog enables you to format the graph window to suit your
requirements, there are six tabs:
Ranges - Enables you to choose the range of values used on the abscissa (x axis) and
ordinate (Y axis).
Annotations - Enables you to choose the layout for the graph.
Scale - Enables you define how the scale looks and how it is labelled.
Fonts - Enables you to choose the fonts used for the graph labels and units.
Graph Colors - Enables you to choose the colors used for graph elements.
Spectrum Colors - Enables you to choose the colors used for spectra in the order that
they are added to the graph.

Saving a Graph Tem plate

Once you have changed the formatting of a graph, you can save the graph format as a
template. You can then use this template for other graphs.
1. Format the graph so that it meets your requirements.
2. Display the File menu and choose Save As (Window).
The Save As dialog is displayed.
3. Change the directory path to the directory that contains your graph templates.
4. Change the file extension to Graph Template (.gfm) by selecting it from the Save
File as Type text box.
5. Type a name for your new template.
You do not have to type the extension, .gfm - it is added automatically when the
template is saved.
6. Choose OK.
The format of the graph is saved as a template.
If there were spectra on the graph when you saved it as a template, the spectra will
not be saved as part of the template file. If you want to include the spectra, you
must save the file as a graph (.gph).
7. Display the Setup menu and choose Configuration.
The Configuration dialog is displayed.
8. Select Graph or Review Graph and change the default template to the one you
have created.
9. Choose OK.
The new template is now set as the default.

24 . Spectrum

Ranges
This tab enables you to manually change the abscissa and ordinate ranges of the
displayed graph, simply type the values that you require for the Left and Right of the
abscissa range, and for the Top and Bottom of the ordinate range.

Annotations
This tab enables you to choose the layout for the graph.
Units - You can choose to have labels saved with the spectrum file, labels entered by
you, or a combination of both. If you choose User, the text box below becomes active to
enable you to enter a label.
Ordinate Orientation - You can choose to have Y axis label displayed either horizontally
or vertically.
Grid - You can choose to have the grid displayed vertically, horizontally, neither, or both.
Scale Change - You can turn on or off the Scale Change facility,
The changes that you make apply only to the current graph. If you want the changes to
be displayed every time you use this template, you must save the changes to the
template.

Displaying the Annotations tab

1. Display the View menu and choose Format View.
The Format View dialog is displayed.
2. Choose Annotations.
The Annotations tab is displayed.

Setting the Axes Units

You can specify the abscissa and ordinate unit labels and the orientation of the ordinate
label.
You can display both the file units and/or the user units, or neither of them, if you wish.
If you display both, the file unit label is displayed after the user unit label, as shown
below.

Choose whether to use File units and/or User units for both axes.
If you choose File, Spectrum will use the units from the spectrum file displayed.
These are the units used on the graph when it was saved to disk.
If you choose User, the text box underneath the User check box becomes active,
and you can enter the label of your choice.
If you choose File and User, the two units names will be used side by side.

Displaying Spectra . 25

Setting the Orientation of the Ordinate Label

In the Ordinate Orientation field choose Horizontal or Vertical.

If you have a long label for the ordinate axis, you will probably need to display it
vertically to be able to read it on the display. If the label is short, it is purely a
matter of preference.

Grid
There is a grid of horizontal and vertical lines that you can display on your graph. You
can choose to have only the horizontal grid, only the vertical grid, neither or both
displayed.
The changes that you make apply only to this graph. If you want to choose the layout for
the grid to be displayed every time, you must save the changes to the template.

In the Grid section, choose whether on to display the horizontal and/or vertical grid
lines.
indicates that the grid lines will be displayed.

Scale Change
Scale Change is a particular feature of the abscissa scale that you can choose to switch
on or off. It is traditionally used for enhancing the finger print region of infrared spectra.
When it is switched on, the abscissa scale below 2000 cm-1 is expanded such that each
scale interval defined on the graph represents half the value it did above 2000 cm-1 (see
figure below). This enables you to see more clearly the peaks in the region
2000 to 450 cm-1.

The default setting for Scale Change is on.

26 . Spectrum

Scale
There may be times when you want to define how the scale looks and how it is labelled.
If this is the case:
1. On the Scale tab, switch Automatic off by choosing Manual.
When you choose Manual, the Interval sections become active. This enables you to
independently change the label intervals on both the abscissa and ordinate scales.
2. Type the Abscissa and/or Ordinate axes spacing for scale labels in the Label
boxes.
3. Type the Abscissa and/or Ordinate axes spacing for scale markers in the Grid
boxes.
If you switch Automatic on, Spectrum automatically sets the default scale according to
the spectra displayed on the graph.

Fonts
This tab enables you to choose the text styles used on the abscissa (x axis) and ordinate
(Y axis) for both the labels and the units.
First use the Font Selector to choose the Font, Size and Style and then click in the
relevant boxes to change the way the text for that label or unit is displayed.
Font Selector - Displays the font currently selected, and a list of all the available fonts
from which you can choose.
Size - Enables you to change the size of your chosen font.
Styles - Enables you to choose either bold, italic, neither or both for your chosen font.
Abscissa - Displays a sample of the font chosen for the labels and units used on the
abscissa.
Ordinate - Displays a sample of the font chosen for the labels and units used on the
ordinate.

Graph Colors
You can use the Graph Colors tab to change the color of the items that make up the
graph.
The changes that you make apply only to this graph. If you want the new colors to be
displayed every time you use this template, you must save the changes to the template.
1. Click on a color in the Palette.
The color is selected.
2. Click on the box next to the item whose color you want to change.
You can change the color of similar items independently.
The box to the right of the text changes to the color that you have chosen, and the
item in the example changes to the color you selected.

Displaying Spectra . 27

Spectrum Colors
You can use the Spectrum Colors tab to change colors that are used for displaying
spectra on the graph.
To choose the colors in which the spectra added to a graph are displayed:
1. Click on the color in the Palette that you want to use.
The color is selected.
2. Click in the Spectrum Order section for the spectrum you want displayed in the
chosen color.
The color changes to the palette color.
The next spectrum you add to the graph will use the new color selection. However,
spectra that are already displayed on a graph will not change color.

28 . Spectrum

Changing the View of the Spectrum

Spectrum enables you to manipulate spectra in several ways:

Using the Optimize command to automatically improve the way the spectra look;

Using the mouse to zoom in on a region of the graph;

Automatically rescaling the graph so that spectra fill the graph

Rescaling the ordinate scale of the graph so two or more spectra with different
intensities can be compared;

Offsetting one spectrum so that it is above the other spectra on the graph;

Moving the view of the spectrum up and down or left and right
, or
expanding or contracting the abscissa and ordinate scale around a fixed point

Changing the way multiple spectra are displayed.

Using a radar display.

Returning a graph to a previous range, or to full scale.

NOTE: These techniques only change the way the spectra look, they do not modify the
data in any way.

Displaying Spectra . 29

Optim ize
NOTE: The Optimize command on the View menu is only displayed if you have installed
IR Expert.
If your spectrum contains large noise spikes or peaks from atmospheric CO2 or water
vapor the unwanted features can dominate the spectrum; this means that the peaks in
the regions of the spectrum that you are interested in are difficult to see. If you use
Autorange X to rescale your spectrum, it includes the unwanted features in its
calculations and rescales the graph to include these features.
Optimize recognizes these unwanted features in your spectrum, and when it rescales the
graph the unwanted features are ignored. Optimize rescales the graph to the next whole
number.
Optimize changes the way your spectra are displayed on the screen it does not change
your data.

30 . Spectrum

Using the M ouse to Zoom in on a Region of I nterest in a

Spectrum
You can zoom in on a region of the graph, which you outline using a grow box that you
create with the mouse. The grow box can be moved and sized. You can use the Radar
Display to see which region of the spectrum you are viewing, and to zoom out. Once you
have created a grow box you can zoom in on the area marked out by the grow box. The
part of the graph outlined by the grow box is then displayed on the whole graph, and the
abscissa and ordinate ranges change scale accordingly:
1. Position the mouse pointer at the top-left corner of the region you want to enlarge.
2. Hold down the left mouse button and drag the mouse diagonally until the grow box
covers the region that you want to see in more detail.
3. Release the left mouse button.
A grow box has been created around the region of interest.
4. Double-click inside the grow box.
The graph is re-sized to the area of the grow box.

W orking w ith Grow Boxes

Once you have created a grow box you can change its size or move it.
Changing the Size of a Grow Box
1. Position the mouse pointer just inside the perimeter of the grow box.
The cursor changes to a two-headed arrow

2. You can size the box diagonally by positioning the mouse pointer at a corner, or in
one direction only by positioning it at an edge.
3. Hold down the left mouse button and drag the mouse until the grow box is the size
you require.
4. Release the mouse button.
Moving a Grow Box
1. Position the mouse pointer inside the grow box.
The cursor changes to a four- headed arrow

2. Hold down the left mouse button and drag the grow box to the required position.
3. Release the mouse button.
Removing a Grow Box

Position the mouse pointer outside the grow box and click.

Displaying Spectra . 31

Using the Autorange Com m ands to Rescale the Graph

You can use the Autorange X and Autorange Y commands to rescale the axes of a
graph so that the selected spectra fill the graph, making the features on the spectrum
easier to see.

Autorange X
1. Select the spectra that you want to be fitted on to the graph.
The names of the selected spectra are underlined.
2. Display the View menu, and choose Autorange X, or press CTRL+R.
The ordinate range stays the same, but the abscissa range increases so that the
selected spectra fill the graph.

Autorange Y
1. Select the spectra that you want to be fitted on to the graph.
The names of the selected spectra are underlined.
2. Display the View menu, and choose Autorange Y, or press CTRL+Y.
The abscissa range stays the same, but the ordinate range increases so that the
selected spectra fill the graph.

Autoscale Y
The Autoscale Y command scales the selected spectra so that they each fill the graph,
enabling you to compare spectra of different intensities, for example, an absorption
spectrum and a transmission spectrum.

Using the Autoscale Y com m and

1. Select the spectra that you want to Autoscale Y.
2. Display the View menu, and choose Autoscale Y.
The selected spectra are scaled, vertically, so that both spectra completely fill the
graph. The ordinate scale is removed because the two spectra are on different
scales.

Cancel Autoscale
After using the Autoscale Y command, to remove the Autoscaling from the graph:
1. Select the spectra whose autoscaling you want to cancel.
2. Display the View menu and choose Cancel Autoscale.
The autoscaling is removed from the selected spectra.

R edisplaying the Ordinate Scale

The ordinate scale is not only removed from the graph when spectra are autoscaled, but
also when an offset is introduced into one or more of the spectra.

32 . Spectrum
If the ordinate scale does not re-appear when you cancel the autoscaling for all the
spectra on the graph, then one or more of the spectra on the graph must contain an
offset.

R em oving the offset from all the spectra

1. Select all the spectra.
2. Display the View menu and choose Cancel Offset.
The ordinate scale is redisplayed.

Offsetting Spectra
You can vertically offset spectra from each other so that they do not overlap, enabling
you to see the shape of each spectrum more easily. You cannot offset a single spectrum.

To Offset a Spectrum
1. Select the spectrum that you want to offset.
2. Click in the graph region and then press
direction you want.

or

keys to move the spectrum in the

The numbers on the ordinate scale disappear when you introduce an offset.
NOTE: To move the selected spectrum by a smaller amount, hold down SHIFT while you
press

or

keys.

Fitting the Spectra on to the Graph

When you introduce an offset, you may find that one of the spectra has moved off the
top or bottom of the graph. You can use Autorange Y to change the range of the graph
so that all the spectra fit onto the graph (the offset is maintained):
1. Select the spectra that you want to fit onto the graph.
The spectra are underlined, indicating that they are selected.
2. Display the View menu, and choose Autorange Y.
The spectra are fitted onto the graph, and the offset is maintained.

Cancelling an Offset and Redisplaying the Ordinate Scale

To cancel an offset you use the Cancel Offset command:
1. Select the spectra whose offset you want to cancel.
2. Display the View menu and choose Cancel Offset.
The offset is removed from the selected spectra.
NOTE: If spectra are removed so that the graph contains only one spectrum, any offset
that has been applied is automatically removed and the ordinate scale is
redisplayed.

Displaying Spectra . 33

R edisplaying the Ordinate Scale

The ordinate scale is not only removed from the graph when an offset is introduced, but
also when a spectrum is autoscaled.
If the ordinate scale does not re-appear when you cancel the offset for all the spectra on
the graph, one or more of the spectra on the graph must have been autoscaled.
1. Select All the spectra.
2. Display the View menu and choose Cancel Autoscale.
The ordinate scale is redisplayed.

P anning and Expanding

There are four toolbar tools which enable you to pan along, or expand the axis of
interest.

M oving Spectra to the Left or R ight

The Pan X button on the toolbar enables you to move along the abscissa axis to view
different regions of the spectrum.

To move the spectra to the left, click on the arrow that points to the left.

To move the spectra to the right, click on the arrow that points to the right.

The abscissa start and end values for the graph change, but the abscissa scale does
not.

M oving Spectra Up or Dow n

Pan Y enables you to move along the ordinate axis to view different regions of the
spectrum.

To move the spectra up, click on the arrow that points up.

To move the spectra down, click on the arrow that points down.

NOTE: The Pan Y tool cannot be used if the spectra are displayed on the graph in split
display mode.

34 . Spectrum

Ex panding or Contracting the Abscissa Scale

Expand X enables you to either expand or contract the abscissa scale around a fixed
point on the graph. The fixed point is the abscissa or, if the vertical cursor is displayed,
the vertical cursor.

To contract the abscissa scale, click on the horizontal arrows that point towards
each other.

To expand the abscissa scale, click on the horizontal arrows that point away from
each other.

If you click on the left mouse button, the start and end values are changed by 2%.
Holding the left mouse button down continually changes the values until you release the
button.

Ex panding or Contracting the Ordinate Scale

Expand Y enables you to either expand or contract the ordinate scale around a fixed
point on the graph. The fixed point is the ordinate or, if the horizontal cursor is displayed,
the horizontal cursor.

To contract the ordinate scale, click on the vertical arrows that point towards each
other.

To expand the ordinate scale, click on the vertical arrows that point away from each
other.

When you click on the left mouse button, the start and end values are changed by 2%.
Holding the left mouse button down continually changes the values until you release the
button.
NOTE: The Expand Y tool cannot be used if the spectra are displayed on the graph in
split display mode.

Displaying Spectra . 35

Display M odes for Graphs

The Overlay/Split Display command on the View menu switches between overlay
display mode and split display mode.

Split
Split Display mode formats the graph such that all the spectra are autoscaled and
automatically offset, one above the other. Any spectra that are added to the graph later
are also autoscaled and offset.

Overlay
Overlay display mode formats the graph such that the spectra are displayed on top of
each other, on the same axes.

36 . Spectrum

Radar Display
This is a window that displays the complete range of data for every spectrum that has
been added to a graph. If you rescale a graph, you can use the radar display to see
which region of the graph you are currently viewing.
The grow box displayed in the radar display shows you which region of the graph is
currently displayed in the graph window, and enables you to zoom out.
You can size and move the grow box in the Radar Display in the same way as a grow box
in the graph window.
The Radar Display command on the View menu toggles the Radar Display on and off:

Displaying the radar display

Display the View menu and choose Radar Display.

When the radar display is active, a check mark
is displayed in the View menu,
next to the Radar Display command, and the button in the toolbar or toolbox
remains pressed down (if the Radar Display toolbar button is displayed).

R em oving the radar display

Display the View menu and choose Radar Display.

The radar display is removed.

P revious Range and Full Scale

R eturning to the Previous R ange
The Previous Range command returns a graph to its previous range, that is, changes
the abscissa and ordinate ranges back to the values that they had before you last
changed them. The ranges may have been changed by zooming in using a grow box, by
typing new values in the Format View dialog, or by using the Autorange X or Autorange Y
commands.

Display the View menu and choose Previous Range.

The graph is redisplayed with its previous range.

R eturning to the Full Scale

The Full Scale rescales both the ordinate and abscissa of the graph to the maximum and
minimum of the selected spectra.

Display the View menu and choose Full Scale.

The graph is redisplayed with its full scale.

Displaying Spectra . 37

Adding and Editing Tex t on a Graph

When you have collected your spectra or opened spectrum files, they are displayed on a
graph.
Spectrum enables you to add text to the graph, for example you could add the batch
number that the sample was from. You can then edit the text and change its appearance,
move it or remove it from the graph.
When you save your graph as a .gph file the text is saved with the file.
Text is not saved when you save a spectrum (.sp) file.

Adding and Editing Tex t

To add text to a graph:
1. Display the View menu and choose Add/Edit Text.
The Add/Edit Text dialog is displayed.
2. Type the required text in the Text Label text box.
You can enter several lines of text, if you want the text to wrap you must press
RETURN at the end of each line.
3. Choose the Orientation of the text label.
You can choose from horizontal left to right, or vertically upwards or vertically
downwards. Multi-line text can only be horizontal.
4. Choose OK.
The text that you typed appears in the middle of the graph. The position of the text
is fixed, not in relation to the screen, but in relation to the graph coordinates. If you
position text next to a particular peak, the text stays with the peak when you
rescale the axes. You can, however, reposition the text.

Changing the Appearance of the Tex t

1. Select the text on the graph that you want to edit or format by positioning the
mouse pointer on the text and clicking with the left mouse button.
The text is surrounded by a box.
2. Display the View menu and choose Add/Edit Text.
The Add/Edit Text dialog is displayed with the selected text already in the Text
Label field. If required the text can be edited.
3. Choose Fonts.
The Font dialog is displayed.
4. Choose the font, font style, size, effects and color.
A sample of text is displayed in the Sample box.
5. Choose OK.
The Font dialog closes leaving the Add/Edit Text dialog displayed.
6. Choose OK.
The Add/Edit Text dialog closes.

38 . Spectrum

M oving Tex t
When you have added text to a graph you can move it as follows:
1. Position the mouse pointer on the text that you want to move.
2. Click the left mouse button.
A box is displayed around the text and the pointer changes to a 4-headed arrow
.
3. Drag the box to the required position for the text.
The text is not displayed in the text box while the left mouse button is held down
and the text box is being moved.
4. When the text box is correctly positioned, release the left mouse button.
The text moves to its new position.

Copying and P asting Text

You can copy and paste text labels on graphs, and the text from text windows such as
reports.

Copying tex t labels

1. Use the mouse to choose the text on the graph that you want to copy.
A text box surrounds the text when it has been selected.
2. Display the Edit menu and choose Copy, or press CTRL + C.
The text is placed on the clipboard and is therefore available to paste back on to
another graph or into another Windows application.

Copying tex t w indow s

1. Make sure that the text window that you want to copy is the active window.
To make a window active, click on it, or choose its name from the Window menu.
Suitable windows are those that contain processing results in text format.
2. Display the Edit menu and choose Copy, or press CTRL + C.
The contents of the window are copied to the clipboard, and can be pasted back to
a location of your choice.

Pasting Tex t

Display the Edit menu and choose Paste, or press CTRL+V.

The text on the clipboard appears in the middle of the graph. It can now be moved
to the required position.

Displaying Spectra . 39

Rem oving Text from a Graph

Cutting Tex t
The Cut command on the Edit menu is a standard Windows command. Information is
removed from its current position, and is copied on to the clipboard ready for pasting
back into a different position, either in the same application or within a different Windows
application.
1. Click on the text that you want to remove.
A box is displayed around the text.
2. Display the Edit menu and choose Cut or press CTRL + X.
The text is removed. It has been placed on to the clipboard and is therefore
available to paste onto another graph or into another Windows application using the
Paste command.

Deleting Tex t
The Delete command on the Edit menu is a standard Windows Delete command. When
you use the Delete command information is erased. You can use the Delete command on
text or spectra.
NOTE: If you want to use the Delete command on a spectrum displayed on a graph,
make sure none of the text labels displayed are selected. The Delete command is
active on selected text labels above anything else.
1. Use the mouse to choose the text on the graph that you want to delete.
A text box surrounds the text when it has been selected.
2. Display the Edit menu and choose Delete or press DEL.
The chosen text disappears.

40 . Spectrum

Cursors
The vertical and horizontal cursors are vertical or horizontal lines that are displayed on
your graph. You can move the cursors using the mouse pointer. The cursors enable you
to compare the position and/or intensities of features in a spectrum.
The vertical cursor can be used in continuous or peak mode, peak mode enables you to
easily move cursor from one peak to the next.
When the vertical cursor is displayed you can label points on a spectrum.

Horizontal Cursor
The horizontal cursor is a horizontal line that you can move vertically on the graph. As
the cursor moves, the ordinate value corresponding to the cursor position on the graph is
displayed in the graph information pane.
NOTE: The horizontal cursor will be removed from the graph if you choose Split Display
Mode.

To display or remove the cursor, display the View menu, point to Cursor and choose
Horizontal.
When the horizontal cursor is displayed, a check mark
Horizontal command.

is displayed next to the

When the horizontal cursor is displayed. The ordinate value at the horizontal cursor
is displayed in the information pane at the bottom of the active graph.

Vertical Cursor
The vertical cursor is a vertical line that you can move horizontally across a graph. It can
operate in one of two different modes: as a continuous cursor or as a peak cursor. In
continuous mode, the cursor moves smoothly across the graph; in peak mode, it jumps
from peak to peak, or snaps to the nearest peak. As the cursor moves, the abscissa and
ordinate values are displayed in the graph information pane.

Displaying the Vertical Cursor or Changing I ts M ode

To display or remove the cursor, display the View menu, point to Cursor and choose
Vertical - Continuous or Vertical-Peak.
is displayed next to the
When the vertical cursor is displayed, a check mark
Vertical - Continuous or Vertical - Peak command, and a C or P is displayed in
the status line.
When the vertical cursor is displayed, the abscissa value at the vertical cursor is
displayed in the information pane at the bottom of the graph.

When you switch to Vertical - Peak, a peak table is generated automatically for all the
selected spectra, enabling you to label individual peaks.

Displaying Spectra . 41

Label Cursor
You can label the vertical cursor in Peak or Continuous mode. In Peak mode, the
vertical cursor snaps to the nearest peak or base, so you will be labeling a peak. In
Continuous mode you can label the cursor in any position.
Display the vertical cursor.
1. Move the vertical cursor to the position you want to label.
In Peak mode the cursor snaps to the nearest peak when you release the mouse
button.
2. Display the View menu and choose Label Cursor.
OR
Place the mouse pointer over the vertical cursor and doubleclick.
The peak is labeled with either the abscissa value, the ordinate value, or both, depending
on the settings in the Options command Peak tab.

M oving a cursor:
1. Position the mouse pointer on the cursor.
The mouse pointer changes shape to a two headed arrow

2. Hold down the left mouse button and drag the horizontal cursor up or down.
3. Release the mouse button.
When the vertical cursor is in peak cursor mode, the vertical cursor jumps to the nearest
peak when you release the mouse button. When it is in peak cursor mode, the vertical
and
arrow keys:
cursor can be moved using the
The peaks that the cursor jumps to are defined by the Peak Option. If the cursor misses
out a peak that you required, execute the Peak Table command using a smaller
threshold.

M oving both the horizontal and vertical cursors:

If your graph contains a horizontal and a vertical cursor, you can move both together:
1. Position the mouse pointer on the intersection of the horizontal and vertical cursors.
The mouse pointer changes shape to a four headed arrow,

2. Hold down the left mouse button and drag the intersection to a new position.
3. Release the mouse button.

42 . Spectrum

Labelling Peak s
1. Select the spectrum whose peaks you want to label.
2. Display the View menu and choose Label Peaks.
Peaks are labelled with red lines, and bases are labelled with green lines.

Clearing peak labels

If you want to remove all the peak labels from the selected spectrum, you can do so
using the Clear All Peak Labels command.
1. Select the spectra whose peaks you want to remove.
2. Display the View menu and choose Clear All Peak Labels.
All the peak labels are removed from the selected spectra.

M oving P eak Labels

When you label peaks with the Label Peaks command, the labels may at first seem
rather crowded. You can move peak labels, or remove them if you do not need them,
until they are spaced as you require.
1. Position the mouse pointer over the peak label and hold down the left mouse
button.
The peak label is selected; this is indicated by a green box surrounding it. The
mouse pointer changes to a four headed arrow

2. Drag the peak label to a new position, and release the mouse button.
The line connecting the peak label to the peak is automatically repositioned.

Rem oving individual peak labels

1. Click on the peak label that you want to remove.
The peak label is selected; this is indicated by a green box surrounding it.
2. Display the Edit menu and choose Delete.
The selected peak label is removed.

Displaying Spectra . 43

Copying a Graph to a R eport

When you copy a graph into a report, you copy it into a report template. A report
template contains the layout for a report page, enabling you to standardize the layout for
reports.
Report templates are created using Report Builder, a separate PerkinElmer application
that is supplied with Spectrum. It enables you to create a report containing the spectra
that you have worked on using Spectrum (or any other PerkinElmer application).

To copy graphs into a report:

1. Make sure that the graph that you want to copy into Report Builder is the active
graph.
To make a graph active, click on it, or choose its name from the Window menu.
2. Display the File menu and choose Copy to Report
The graph is displayed in Report Builder. Report Builder is started if it was closed.

W hich graph holder is the graph copied into?

The graph is displayed in the report, in the selected graph holder. If this already contains
a graph, you are asked if you want to replace this graph with the new one or to cancel
the operation. If none of the graph holders is selected (for example, if Report Builder was
closed), the graph is displayed in the graph holder that was first added to the report.
If no graph holder is available, an error message is displayed and the graph is not copied.
Choose OK to clear the error message, and use the Report Builder Add Graph Holder
command to create a graph holder.

W hich report tem plate is used?

If Report Builder was closed, the default report template is used. If Report Builder is
already running, the graph or text is copied into the template that is currently being
used. For more information refer to the Help in Report Builder.

Report Tem plate

A report template contains the layout for a report page. You can create a report template
using Report Builder, a separate PerkinElmer application that is supplied with Spectrum,
and which helps you to produce reports from the results of your analyses.
To start Report Builder from within Spectrum, display the Setup menu and choose
Report Template. Report template files have .pfm extensions.
For information on how to use Report Builder to create, format, and print your reports,
see the Report Builder on-screen help.

44 . Spectrum

W orking w ith Spectra

46 . Spectrum
This chapter includes topics on how to manipulate and process spectra to get the
information you want, the way you want it. The sub-sections are on:

Correcting the spectrum, to improve the quality of your spectrum;

Changing the form of the data to a more useful form, or so that you can perform
further processing;

Extracting Information from Spectra using Compare, Search, Interactive

Interpretation, the Quants, Peak Area/Height or a Peak Table;

Prepare the spectrum so that it can be compared with other spectra;

Viewing the Status Information for a spectrum to see what processing has been
performed on it.

Working with Spectra . 47

Selecting a Spectrum Nam e for the R esult of a

Process Com m and
When you select a Process command from the Process menu, a dialog may be displayed,
allowing you to change the name of the processed spectrum:
Result Spectrum displays the name of the current spectrum. To keep this name,
overwriting the current spectrum with a processed one, choose OK.
To use a new name for the processed spectrum, type a new name in the Name text box,
or choose Auto Name. If you choose Auto Name, a new spectrum name is generated
automatically. When you are satisfied with the new name, choose OK.
To choose whether or not this dialog is displayed, see Process Options.

48 . Spectrum

Correcting Spectra
When you have collected your sample spectrum it may contain a lot of noise or have a
sloping baseline, Spectrum enables you to:

perform data tune-up;

reduce the amount of noise;

flatten a sloping baseline.

Data Tune-up
NOTE: The Data Tune-up command on the View menu is only displayed if you have
installed IR Expert.
Data Tune-up enables you to perform three processing operations on your spectra. You
use the Process tab of the Options dialog to select which options are performed, but
using the full options, four steps are performed:

Spectrum identifies regions of your spectrum that contain only noise;

The whole spectrum is smoothed to reduce the amount of noise;

The baseline of the spectrum is corrected for any slope;

Any regions of noise that were identified in the first step are blanked from the
spectrum.

These steps can, of course be performed manually using the other items in the Process
menu.

Working with Spectra . 49

Baseline Correction
W hat does Baseline Correction do to a spectrum ?
Baseline correction removes baseline features, for example those caused by scattering
from your spectrum.

W hat can I use Baseline Correction for ?

You can use Baseline Correction to remove slopes in the baseline of your spectrum; these
may have been caused by scattering of the infrared beam by your sample.
You may want to correct the baseline of a sample spectrum before you compare your it
with reference spectra, or measure peak intensities.

Without baseline correction

With baseline correction

There are two ways to apply baseline correction:

Automatic

A baseline correction is automatically applied across the whole spectrum.

Interactive

You apply the baseline correction based on selected points, view the results
and modify the correction as required.

50 . Spectrum

Interactive Baseline Correction

In the interactive mode, the Baseline Correction dialog enables to you to use the vertical
cursor or by typing values in a text box, to specify where the BasePoints of your
spectrum lie. You can correct the baseline over the whole of the spectrum or the
correction can be applied to a limited range of the spectrum. You select a number of
points in the spectrum. A curve intersecting the spectrum at these points is constructed
using a cubic spline, and this curve is subtracted from the original spectrum.
If only one point is selected, a horizontal baseline is used; and if two points are selected,
the baseline is a linear slope connecting them. The calculations are carried out in
absorbance.
If the baseline is corrected over a limited range, an offset equal to the absorbance at the
highest selected frequency is subtracted from the region between the start of the
spectrum and the start of the selected region.
An offset equal to the absorbance at the last selected frequency is applied to the region
between the end of the selected range and the end of the spectrum.

Using Interactive Baseline Correction

1. Display and select the spectrum or spectra that you wish to process.
2. Display the Process menu and choose Baseline Correction and then Interactive
Correction.
The Baseline Correction dialog is displayed.
3. If you want to have the baseline flattened automatically, choose Automatic. If not,
go to step 4.
If you have selected Automatic, the flattened spectrum is displayed.
4. To select the baseline points to be used for the correction, move the cursor to the
first point you want to use or type the first abscissa in the BasePoint text box.
The abscissa value appears in the BasePoint text box.
5. To accept this value, double-click on the cursor or choose BasePoint.
The value is added to the list box and the new baseline is added to the display. A vshaped marker is placed on the spectrum to indicate a BasePoint.
To remove a base point, highlight the point you want to remove in the BasePoint
text box and press the DEL key.
The base point is removed from the baseline.
6. Repeat steps 4 and 5 and identify as many baseline points as you require.
The baseline is updated on the display, and another marker added, each time a new
value is selected.
7. If you are satisfied with the spectrum after the baseline correction has been applied,
choose OK to accept the result.
The Baseline Correction dialog closes. If you had originally selected more than one
spectrum for Baseline Correction, the dialog is displayed with the next spectrum.
Resume the process at step 3 (Automatic Baseline Correction) or 4 (selecting the
BasePoints).

Working with Spectra . 51

Correcting a Lim ited R ange of the Baseline

1. If you want to correct only part of the spectrum, choose Limited Range.
The baseline display changes to show the start and end of the spectrum.
NOTE: The Limited Range option is only available if you have selected two or more
BasePoints.
2. When you are satisfied with the baseline to be used for the calculation, choose
Calculate.
The baseline is corrected and the result displayed.
The status line shows the baseline points used for the calculation.
To remove a base point, highlight the point you want to remove in the BasePoint
text box and press the DEL key.
3. If you are satisfied with the spectrum after the baseline correction has been applied,
choose OK to accept the result.
The Baseline Correction dialog closes. If you had originally selected more than one
spectrum for Baseline Correction, the dialog is displayed with the next spectrum.

Autom atic Baseline Correction

The automatic correction first identifies baseline regions by calculating a smoothed first
derivative and then adjusts the baseline over the complete range using these points as
reference.
1. Display and select the spectrum or spectra that you wish to process.
2. Display the Process menu and choose Baseline Correction and then Automatic
Correction.
Baseline correction is performed.

Theory
The aim of Baseline Correction is to correct the spectrum without distorting the band
intensities in the final spectrum or introducing discontinuities.

In the automatic mode, a quadratic function is fitted to the spectrum and

subtracted. For the automatic operation to be successful, there must be significant
regions of the spectrum that can be regarded as baseline. Quadratic fitting will
remove slope and bow from the spectrum, but not more complex baseline features.

Alternatively, you can select a number of points in the spectrum where there are no
absorption bands. A smooth curve is constructed through these points and
subtracted. You can correct the baseline over the full abscissa range, or over a
limited range. In the latter case, an offset equal to the absorbance at the highest
selected frequency is subtracted from the region between the start of the spectrum
and the start of the selected region. An offset equal to the absorbance at the lowest
selected frequency is applied to the region between the end of the selected range
and the end of the spectrum.

In both modes, the calculations are performed in absorbance to preserve band

intensities.

52 . Spectrum

Changing the form of data

Changing the Form of Data
The commands in this part of the Process menu enable you to change the form of your
spectrum so that it can be processed further or can be meaningfully compared with other
data. The available commands are:
Absorbance - Converts a spectrum with transmittance (%T) as its ordinate to absorbance
units (A).
Transmittance - Converts a spectrum with absorbance (A) as its ordinate to transmittance
units (%T).
Convert X - Converts the abscissa units of a spectrum to the units that you choose.
Difference - Performs a weighted subtraction one spectrum from another.
Derivative - Calculates a derivative spectrum of your spectrum.
Interpolate - Copies a spectrum, and changes the number of points that make up the
spectrum.
ATR Correction - Makes a spectrum collected with the ATR (Attenuated Total Reflectance)
accessory similar to a transmittance spectrum so that you can compare the two types of
spectrum.
Kubelka-Munk - Converts a spectrum with reflectance as its ordinate to Kubelka-Munk
units.
Kramers-Kronig - Calculates an absorbance spectrum from a specular reflectance
spectrum.

Working with Spectra . 53

Absorbance
W hat does Absorbance do to a spectrum ?
Converts a spectrum with transmittance (%T) as its ordinate to absorbance units (A).

W hen should I use an Absorbance scale ?

You can display spectra in absorbance and transmittance ordinate scales. Traditionally
transmittance scale has been used for interpretation of spectra and absorbance has been
used for quantitative work.
When using a transmittance scale the noise level is independent of the energy level.
Therefore the influence of noise on the spectrum is greater at low transmittance levels
than at high transmittance levels.
When using transmittance scale, as you increase the concentration or thickness of the
sample, the shape of strongly absorbing bands changes. Absorbance is a logarithmic
scale, changes in concentration have less effect on the shape of peaks.
Absorbance spectra may be dominated by large, noisy bands. A transmittance scale may
be better if you want to look at detail close to the baseline of the spectrum.

Using Absorbance
To convert spectra from Transmittance to Absorbance:
1. Display and select the spectrum or spectra that you want to convert to absorbance.
2. Display the Process menu and choose Absorbance.
The selected spectrum or spectra are displayed on the absorbance scale.

Transm ittance
W hat does Transm ittance do to a spectrum ?
Converts a spectrum with absorbance (A) as its ordinate to transmittance units (%T).

W hen should I use an Transm ittance scale ?

You can display spectra in absorbance and transmittance ordinate scales. Traditionally
transmittance scale has been used for interpretation of spectra and absorbance has been
used for quantitative work.
When using a transmittance scale the noise level is independent of the energy level.
Therefore the influence of noise on the spectrum is greater at low transmittance levels
than at high transmittance levels.
When using transmittance scale, as you increase the concentration or thickness of the
sample, the shape of strongly absorbing bands changes. Absorbance is a logarithmic
scale, changes in concentration have less effect on the shape of peaks.
Absorbance spectra may be dominated by large, noisy bands. A transmittance scale may
be better if you want to look at detail close to the baseline of the spectrum.

54 . Spectrum

Using Transm ittance

1. Display and select the spectrum or spectra that you want to convert to
transmittance.
2. Display the Process menu and choose Transmittance.
The spectra selected are displayed on the transmittance scale.

Convert X
W hat does Convert X do to a spectrum ?
Converts the abscissa units of a spectrum to the units that you choose.

W hen should I use Convert X ?

When you want to convert the abscissa units of your infrared spectrum to and from
wavenumbers, microns or nanometers.

When you want to convert the abscissa units of your chromatogram to and from
minutes or seconds.

When you want to convert the abscissa units of your Raman spectrum to and from
Raman shift spectrum units or absolute wavenumbers.

W hat do the param eters do ?

The Data Interval enables you to change the data interval of your spectrum when you
change the abscissa scale.

Using Convert X
1. Display and select the spectrum or spectra that you want to convert.
2. Display the Process menu and choose Convert X.
The Convert X dialog is displayed.
3. Choose the Abscissa Units you want to convert to.
The current abscissa unit option is unavailable.
4. If you do not want to use the default Data Interval, type the required value.
The default data interval maintains the number of points in the spectrum.
5. Choose OK or OK All.
The spectra are converted and displayed.
OK If you have selected more than one spectrum, the named spectrum is processed
and displayed. Then the dialog is redisplayed for the next spectrum.
OK All If you have selected more than one spectrum, all the spectra are processed
and displayed without further interaction.

Working with Spectra . 55

Theory
For most applications in chemistry, mid infrared spectra are displayed on an abscissa
scale that is linear in wavenumber. Fourier Transform interferometers generate data
points at equally-spaced intervals, so that a linear wavenumber scale is natural.
However, for some applications a linear wavelength scale is preferred. Wavenumbers,
microns and nanometers are the abscissa units available. Near infrared spectra often
have a nanometer abscissa scale.
When chromatograms are displayed, conversion between minutes and seconds is
available.
A direct conversion between scales may be unsatisfactory because it results in an uneven
distribution of data points that is not readily handled by data processing and display
routines.
To avoid this uneven distribution, Convert X uses interpolation to produce a spectrum
with data points at equally-spaced wavelengths. However, if the conversion maintains the
smallest spacing of data points in wavelength found in the original, the number of
interpolated points can become large.

Difference
W hat does Difference do to a spectrum ?
The Difference command performs a weighted subtraction of one spectrum from another.

W hen should I use Difference ?

When you want to calculate the difference between two spectra, you can remove the
contribution of some components and see what remains. For example, you can use it to:

find the spectrum of a solute by subtracting the solvent spectrum from the solution
spectrum;

find the spectrum of an unknown component of a mixture by subtracting the spectra

of the known components;

subtract the background spectrum of a sampling accessory.

NOTE: The difference is only calculated and displayed for the range that data exist in
both spectra. For example, if one spectrum has a range of 4400 to 600 cm-1 and
the other from 4000 to 400 cm-1, the resultant difference spectrum will be from
4000 to 600 cm-1.

56 . Spectrum

W hat do the param eters do ?

The parameter Factor enables you to multiply the spectrum you are subtracting from the
first spectrum by a factor.
For example:
Difference = (spectrum 1) - (spectrum 2) x Factor + c
where c is a constant that is calculated by Spectrum, to minimize baseline shift in
the Difference.
Instead of defining the factor, you can choose to have it calculated automatically by
clicking on Auto; the automatic difference calculation performs a least squares fit of the
two spectra.
By default, the factor is calculated over the full range of the data displayed. If you want
the factor to be calculated over a limited range, select and expand the region of interest
using a grow box or the Format View command.

Using Difference
1. Display and select the two spectra whose difference you want to calculate.
Note that if either or both of the selected spectra are displayed in Absorbance, then
both of the spectra and the result will be displayed in Absorbance in the Difference
dialog. If both of the selected spectra are displayed in %T, the result is also
displayed in %T.
The calculation is always performed in Absorbance.
2. Display the Process menu and choose Difference.
The Difference dialog is displayed: it contains two graphs; the top graph contains
the two spectra, whose difference is to be calculated; the bottom graph contains the
difference spectrum, which has an initial scaling factor of 1.0. You can change the
relative sizes of the two graphs by dragging the bar separating them. The mouse
pointer changes to a two-headed arrow when it is positioned over the bar.
NOTE: The difference is only calculated and displayed for the range that data exist in
both spectra. For example, if one spectrum has a range of 4400 to 600 cm-1 and
the other from 4000 to 400 cm-1, the resultant difference spectrum will be from
4000 to 600 cm-1.
3. Choose the difference Factor you want.
The factor that is being applied to the spectrum that is being subtracted is reported
in the Factor text box; you can type a value in this field or use the touchpad control
to change the factor. Each time you change this factor, the difference spectrum is
recalculated and displayed.
Note that when you click on the touchpad, the spectrum is immediately recalculated
and redisplayed. If you select a different factor by typing a number into the Factor
text box, the new difference spectrum is displayed when you choose Calculate.
As the scaling factor is changed, an offset is applied to the resultant spectrum in
order to compensate for any baseline shift introduced by the subtraction.

Working with Spectra . 57

Swap If you want to swap the order of the two spectra, choose Swap;
spectrum1 - (spectrum2 x factor) becomes
spectrum2 - (spectrum1 x factor)
You can choose Swap again to reverse this. The status line at the bottom of the
window shows the equation that is currently being used to calculate the result
spectrum.
Auto
Instead of defining the factor, you can choose to have it calculated automatically by
clicking on Auto; the automatic difference calculation performs a least squares fit of
the two spectra.
By default, this is done over the full range of the data displayed. If you want to use
a limited range, select and expand the region of interest using a grow box.
The factor is applied to the complete spectrum, if you have zoomed in on the
spectra, zoom out to see the complete spectra.
4. Choose OK to accept the result.
This dialog is closed and the difference spectrum displayed.

Theory
You can optimize the elimination of particular bands by varying a scaling factor that is
applied to one of the spectra. This enables you to overcome, for example, the effect of
different concentrations or sample thicknesses for the two spectra.
The Difference calculation is performed in absorbance because it is the absorbance that
varies linearly with concentration or path length. If the spectra contain regions where the
absorbance is very high, the noise level in these regions of the difference spectrum will
be high.
Difference spectra are very sensitive to small changes in the shapes and positions of
bands; you should use identical instrument conditions for the two spectra involved in any
subtraction.

Derivative
W hat does Derivative do to a spectrum ?
Calculates a derivative spectrum of your spectrum.

W hen should I use Derivative ?

Derivative spectra usually have sharper features than the original spectra. In quantitative
analysis, they are sometimes used to reduce the effects of overlapping bands. You can
use the amplitudes of features in derivative spectra in the same way as peak
absorbances. The elimination of some baseline effects in derivative spectra can be useful
in quantitative methods.
You can use the Derivative command to take the first, second, third or fourth order
derivative of a spectrum.
The first derivative removes any baseline offset and the second derivative removes any
linear slope also.

58 . Spectrum
Second-derivative spectra have sharp minima where there are maxima in the original
spectrum and so can be used to identify band positions in complex regions.

First derivative

Second derivative

Third Derivative

Fourth derivative
[1300 - 1100 cm-1, 9 points]

Working with Spectra . 59

W hat do the param eters do ?

The Number of Points sets the number of data points used to calculate the derivative.
As you increase the number of data points used in the calculation, the contributions of
broader features increases relative to narrow features.

Using Derivative
1. Display and select the spectrum or spectra that you wish to process.
2. Display the Process menu and choose Derivative.
The Derivative dialog is displayed.
3. Select the Order of the derivative, and the Number of Points to provide the
required degree of smoothing.
4. Choose OK or OK All.
OK - If you have selected more than one spectrum, the named spectrum is
processed and displayed. Then the dialog is redisplayed for the next spectrum.
OK All - If you have selected more than one spectrum, all the spectra are
processed and displayed without further interaction.

Theory
Derivative uses the Savitzky-Golay procedure to estimate the derivative of a smooth
curve, constructed through the original data points of your original spectrum. It uses a
number of neighboring data points to estimate the curve. As the number of data points
used in the calculation is increased, the contributions of broader features increases
relative to narrow features.
Derivative spectra have both negative and positive features, which make them difficult to
interpret. Because of this, deconvolution is now often preferred for separating
overlapping bands. However, deconvolution is a more subjective procedure.
Derivative spectra emphasize narrow features, including noise, relative to broad ones.
You can control this to some extent by varying the width of the derivative function. This
is equivalent to applying some smoothing to the derivative spectrum.

I nterpolate
W hat does Interpolate do to a spectrum ?
Interpolate copies a spectrum, and changes the number of points that make up the
spectrum.

W hen should I use Interpolate ?

You can use Interpolate to:

give incompatible spectra the same data interval, for example before you use
Compare;

save part of a spectrum;

reduce the number of data points in a file to save storage space, or to reduce the
time needed to process or print it.

60 . Spectrum

W hat do the param eters do ?

The parameters Start, End, and Interval change the range of the new spectrum, and the
interval between points in the new spectrum.
NOTE: You can find out how many points there are in a spectrum by displaying the File
menu and choosing Status.

Using Interpolate
1. Display and select the spectrum or spectra that you wish to copy or interpolate.
2. Display the Process menu and choose Interpolate.
The Interpolate dialog is displayed. If you have selected more than one spectrum,
the name of the first one is shown.
3. Enter the Start and End values for the interpolated spectrum.
4. Enter the Data Interval for the interpolated spectrum.
5. Choose OK or OK All.
OK - If you have selected more than one spectrum, the named spectrum is
processed and displayed. Then the dialog is redisplayed for the next spectrum.
OK All - If you have selected more than one spectrum, all the spectra are
processed and displayed without further interaction.

Theory
Interpolation adds points to a spectrum by adding new points between the points that
already exist. Interpolation removes points from a spectrum by selecting every nth point
of a spectrum and removing it.
The number of data points needed in a spectrum depends on the width of the features in
the spectrum. If the separation of the data points is smaller than that needed to define
the features in the spectrum, the number of points can be reduced without reducing the
amount of information in the spectrum.
Increasing the number of data points in a spectrum cannot increase the amount of
information in the spectrum.

ATR Correction
NOTE: The use of ATR correction is NOT appropriate for spectra collected in the near
infrared.

W hat does ATR Correction do to a spectrum ?

ATR correction makes a spectrum collected with an ATR (Attenuated Total Reflectance)
accessory similar to a transmittance spectrum so that you can compare the two types of
spectrum.

W hen should I use ATR Correction ?

For processing spectra that have been collected with an ATR accessory.

Working with Spectra . 61

W hat do the param eters do ?

The ATR correction calculation assumes that the degree of contact between your sample
and the ATR crystal is perfect. The Contact function enables you to correct for less than
perfect contact between the sample and the ATR crystal.
If the contact is perfect, for example a liquid sample the penetration depth is proportional
to the wavelength and the contact factor is 0. The value of the Contact function is
usually decided by visual inspection of the spectrum.

62 . Spectrum

Using ATR Correction

NOTE: The use of ATR correction is NOT appropriate for spectra collected in the near
infrared region.
1. Display and select the spectrum or spectra that you wish to correct.
2. Display the Process menu and choose ATR Correction.
The ATR Correction dialog is displayed.
3. Choose a Contact correction factor if necessary.

See Parameters to understand the use of this factor.

4. Choose OK or OK All to process the spectrum or spectra.
OK - If you have selected more than one spectrum, the named spectrum is
processed and displayed. Then the dialog is redisplayed for the next spectrum.
OK All - If you have selected more than one spectrum, all the spectra are
processed and displayed without further interaction.

Theory
The penetration depth of the infrared beam into the sample varies with the wavelength
of the radiation, the longer the wavelength, the deeper the penetration. The effective
pathlength of the spectrum collected therefore varies with the wavelength of the
radiation.
ATR correction corrects for the variation in effective pathlength. Absorbance values at the
shortest wavelength (highest wavenumber value) are unchanged, but as the wavelength
increases the absorbance is increasingly attenuated.
ATR correction also enables you to correct for less than perfect contact between your
sample and the ATR crystal.

Working with Spectra . 63

Kubelka-M unk
W hat does the K ubelka-M unk transform do to a spectrum ?
Converts a spectrum with reflectance as its ordinate to Kubelka-Munk units.

W hen should I use a K ubelka-M unk scale ?

This transform is used with the diffuse reflectance spectra of powders. In theory, after KM (Kubelka-Munk) transformation, the band intensities vary linearly with concentration
(obey Beer's Law). So, you would use K-M for diffuse reflectance spectra just as you
would use absorbance for spectra measured in transmittance.
You will find most mid infrared diffuse reflectance spectra in the literature presented in KM units.
However, it has been very difficult to obtain good quantitative results from diffuse
reflectance spectra in the mid infrared region. The main reason is that absorption in this
region is very strong, whereas the K-M theory is strictly applicable only to very weak
absorption.

Using Kubelka-M unk

1. Display and select the diffuse reflectance spectrum or spectra that you wish to
convert to K-M units.
The spectrum shown is in reflectance units.
2. Display the Process menu and choose Kubelka-Munk.
The spectrum is displayed in K-M units.
NOTE: Performing the Kubelka-Munk transform on a spectrum that is already in K-M
units will convert it to Reflectance units.

Theory
The K-M command converts a reflectance spectrum, R, to K-M units, using the
relationship:

where R is the reflectance spectrum and F(R) is the K-M spectrum.

If the reflectance spectrum has any totally absorbing bands, they are truncated at
0.0655% to avoid division by zero.

64 . Spectrum

Kram ers-Kronig
NOTE: The use of the Kramers-Kronig transform is NOT appropriate for spectra collected
in the near infrared.

W hat does the K ram ers-K ronig transform do to a spectrum ?

The Kramers-Kronig transform calculates an absorbance spectrum from a specular
reflectance spectrum.

W hen should I use an K ram ers-K ronig scale ?

The Kramers-Kronig scale is suitable if your spectrum was collected from a smooth, shiny
sample.
This scale is not suitable for diffuse reflectance spectra, for diffuse reflectance spectra
you should use Kubelka-Munk as the ordinate scale.

W hat do the param eters do ?

Start

The starting wavenumber for the region you want to transform.

End

The end wavenumber for the region you want to transform.

Absorbance The name for the absorbance spectrum.

N-Index

The name for the refractive index spectrum, if it is required.

K-Index

The name for the absorption index spectrum, if it is required

Working with Spectra . 65

The three spectra that can be derived by the Kramers-Kronig transform are:

Original reflanctance spectrum

Absorbance spectrum

Absorption index (k-index) spectrum

66 . Spectrum

Using Kram ers-K ronig

NOTE: The use of the Kramers-Kronig transform is NOT appropriate for near infrared
spectra.
1. Display and select the specular reflectance spectrum or spectra that you wish to
process.
2. Display the Process menu and choose Kramers-Kronig.
The Kramers-Kronig dialog is displayed.
3. Set the wavenumber range, and the Calculate / Destination spectrum name
options.
Start The starting wavenumber for the region you want to transform.
End The end wavenumber for the region you want to transform.
Absorbance The name for the absorbance spectrum.
N-Index The name for the refractive index spectrum, if it is required.
K-Index The name for the absorption index spectrum, if it is required.
NOTE: The time taken to perform the transform increases proportional to the square of
the number of points used.
4. Choose OK to process the spectrum.
The calculated spectra are displayed.
OK - If you have selected more than one spectrum, the named spectrum is
processed and displayed. Then the dialog is redisplayed for the next spectrum.
OK All - If you have selected more than one spectrum, all the spectra are
processed and displayed without further interaction.

Working with Spectra . 67

Theory
The Kramers-Kronig transform calculates an absorbance spectrum from a specular
reflectance spectrum.
You can also display an absorption index and/or a refractive index spectrum calculated
from the specular reflectance spectrum. Specular reflectance spectra typically have
derivative-like features rather than symmetrical absorption bands.
This is because not only does the absorption of a sample change with wavelength, but
also its refractive index. A typical specular reflectance spectrum is shown below.

Very often, reflectance spectra are a mixture of specular and diffuse reflection. The
Kramers-Kronig transform may help qualitative interpretation in such spectra if the
contribution from surface reflection is dominant, but you will find distorted band shapes
and intensities.
NOTE: For best results, there should be baseline regions free from bands at each end of
the region of the spectrum that you wish to transform.

68 . Spectrum

Ex tracting I nform ation from Spectra

When you have collected your sample spectrum, Spectrum enables you to extract
information from the spectrum. This information may be to identify your sample, or
quantify how much of a substance is present in it:

Identify your sam ple:

Compare your spectrum with other spectra;
Search libraries or interpret your spectrum;
Interpret your spectrum interactively to identify PSUs (Possible Structural Units) that may
be present;
Generate a Peak Table for your spectrum.

Quantify how m uch of a substance is in your sam ple:

Perform a Quant analysis on your spectrum;
Measure Peak Areas and Heights for your spectrum.

Com pare
W hat can I use Com pare for ?

To compare one spectrum with another spectrum.

To compare one spectrum with a directory of spectra.

To compare one spectrum with a spectrum in memory.

W hat does Com pare do ?

Compare estimates the similarity between two spectra, it emphasizes those features in
the spectrum that relate to the chemical composition of the sample, and ignores, or
reduces the influence of, those features that have other causes.
This is achieved by using a number of mathematical filters: these can be applied in order
to emphasize or reduce the contribution of various features. As well as the correlation
coefficient, Compare reports a factor that represents the average ratio of the
absorbances in the spectra being compared.
NOTE: Before you use the Compare command you must set up the comparison by using
the Setup Compare command.
In each case the results are displayed in a window, or series of windows. You can save
each window as a text file, or copy its contents to the clipboard (see Copying and Pasting
Text).
NOTE: While the comparisons are being processed a progress bar is displayed, together
with a Cancel button. You may stop the process at any time: the results already
obtained are displayed.

Working with Spectra . 69

The reference spectra can be in one, or several directories (see Setting Up a Comparison
to understand how to prepare this).

W hen should I use Com pare and w hen should I use Search ?
If you know that your sample is one of a range of materials or if you want to measure
how similar your spectrum is to another spectrum, you should use Compare; this
compares your sample spectrum with one other spectrum or several spectra and reports
the degree of similarity between the spectra.
You should use IR Search when you do not know the identity of your sample, a search
compares your sample spectrum with libraries that can contain many spectra, or
compares the peaks in your spectrum with many Possible Structural Units to identify your
sample. Even if your sample is not in the libraries, an interpretation will give you
information on what functional groups are present in your sample, and provide clues as
to what it is.

W hat do the Results M ean ?

A correlation of 1.0 indicates that there is a perfect match between the two spectra. In
practice this is extremely unlikely, and probably means that the two spectra are copies of
the same spectrum.
A correlation of zero indicates that the two spectra are wholly unrelated. This is also
unlikely because there are almost always some small similarities between spectra.

Using Com pare

NOTE: Before you use the Compare command you must set up the comparison by using
the Compare Setup command.
1. Display and select the spectra you want to compare.
NOTE: While the comparisons are being processed a progress bar is displayed, together
with a Cancel button. You may stop the process at any time: the results already
obtained are displayed.
2. Display the Process menu and choose Compare.
If you are comparing one unknown with one reference spectrum, the result is
displayed.
If you are comparing one unknown with several reference spectra, the results are
listed in order of decreasing correlation of the reference spectra to the sample
spectrum.
If you are comparing several unknowns with one reference spectrum, the results are
listed in order of decreasing similarity of unknown spectra to the reference
spectrum.

70 . Spectrum

Perform ing Com parisons w ith Spectra in M em ory

See Setting Up a Comparison to understand how to select the comparison to be with
spectra in memory.
1. Display and select the spectrum or spectra you want to compare.
2. Display the Process menu and choose Compare.
The Compare dialog is displayed.
3. Build the list of reference spectra.
Add

Adds the selected Spectrum in Memory to the Spectra to Compare list.

Add All Adds all the Spectra in Memory to the Spectra to Compare list.
Delete

Deletes the selected spectrum from the Spectra to Compare list.

4. Choose OK or OK All to perform the comparison.

OK - If you have selected more than one spectrum, the named spectrum is
processed and the results displayed. Then the dialog is redisplayed for the next
spectrum.
OK All - If you have selected more than one spectrum, all the spectra are
processed and the results displayed without further interaction.

Theory
Compare uses the absorbance spectra so that differences in concentration or pathlength
are overcome. Two numbers are reported: correlation and factor. The correlation
coefficient is calculated by the following expression:

Correlation =

where Ai and Bi are the absorbance values in spectra A and B at frequency i, and wi
is a weighting that depends on the filters selected. When more than one filter is
used, the total weighting is the product of the weightings of the individual filters.
See Setting Up a Comparison for a description of the filters, and how to set them
up.
A correlation of one is a perfect match. It is unlikely to occur unless the comparison
spectrum is a copy of the sample spectrum.
A correlation of zero indicates that the two spectra are wholly unrelated. This too is
unlikely in practice, because all absorption spectra have at least the similarity that
absorption bands reduce the transmittance.
Factor = least squares fit factor of B on A.

Working with Spectra . 71

Setting up a Com parison

Before you use the Compare command on the Process Menu to perform a comparison,
you must set up the compare parameters as follows:
To display the Compare Setup dialog:
1. Display the Setup menu and choose Compare.
2. Click on the tabs to display the settings.

Com pare Setup - Type

You can compare your sample spectrum against a single spectrum, a directory of spectra,
or a spectrum in the memory of the PC. The Type tab enables you to choose the type of
comparison that will be performed.
Spectra vs Directory

Spectra are compared with all the spectra in a directory that

you specify. Choose Add to add a directory to the list of
directories.

Reference vs Spectra

Spectra are compared with a reference spectrum. Choose

Browse to select the reference spectrum.

Spectra vs Memory

You will be prompted for the names of the reference spectra

when you are performing the comparison (see Performing
Comparisons with Spectra in Memory)

Proceed on Error

The comparison will continue even if errors occur, for example

if spectra have incompatible data intervals.

Com pare Setup - Filters

When you collect spectra with different instruments, on different days or under different
conditions, there may be differences in the spectra that are not due to differences in your
sample. These filters reduce or eliminate the differences from these sources.
Some regions of a spectrum contain information that is more reliable than other regions
of the same spectrum. These filters reduce the influence of the less reliable information
on the comparison.
When more than one filter is used, the total weighting is the product of the weightings of
the individual filters.
Resolution
Weighting

This filter emphasizes the influence of features with widths of

approximately 8 to 16 cm-1 in mid infrared spectra, and 16 to 32 cm-1
in near infrared spectra. Bands with widths in this range tend to be
the bands that correspond to real features in your spectrum.
Bands with widths below this are often high frequency noise, and
bands with widths broader than this are often baseline features.
This option is separately selectable.

Intensity
Weighting

The signal-to-noise ratio of the spectrum varies with the abscissa

scale, data with a low signal-to-noise ratio is less reliable than data
with a high signal-to-noise ratio. This option applies a black body filter
that reduces the influence of data in the regions at the ends of the
spectrum where the signal-to-noise ratio is lower.
This option is only selectable with Noise Weighting.

72 . Spectrum
Noise Weighting The noise level in a region of a spectrum that is near to totally
absorbing is greater than other regions. This option applies a black
band filter that reduces the influence of regions where the
transmission is low because they have high noise in absorbance.
This option is only selectable with Intensity Weighting.
CO2 Blanking,
H2O Weighting
and H2O
Blanking

Spectra collected on different days, and under different conditions will

show the influence of different amounts of carbon dioxide and water
vapor. These are not a valid differences between spectra, these filters
reduce or eliminate these differences.
The CO2 Blanking filter removes the influence of carbon dioxide on
your spectrum, it excludes all data between 2390 and 2280 cm-1.
This filter is only selectable if Intensity and Noise Weighting are
selected. Note that this filter is not appropriate for near infrared
spectra.
The H2O Weighting filter reduces the influence of data between
7450 and 6950 cm-1, 5600 and 5100 cm-1, 4000 and 3500 cm-1, and
1900 and 1300 cm-1 Data in these regions is de-weighted by a factor
of 8.
This option is only selectable if Intensity and Noise Weighting are
selected.
The H2O Blanking filter excludes all data between 7450 and
6950 cm-1, 5600 and 5100 cm-1, 4000 and 3500 cm-1, and 1900 and
1300 cm-1.
This filter is only selectable if Intensity and Noise Weighting are
selected.

Com pare Setup - Regions

You may want to compare spectra over a limited wavenumber range because you are
particularly interested in a region or because you want to exclude regions of a spectrum.
Range enables you to limit the regions of the spectra that are compared.

Com pare Setup - Display

When a comparison has finished the results are displayed on the screen. The Display tab
enables you to choose the items that are displayed.
Text Report

Specifies the Number of Hits that are reported for each hit list for
each sample.

Graph Window

Select Display if you want to view the sample spectrum and

reference spectra when the comparison has finished.
Select Overlay if the spectra are to be displayed in overlay display
mode.
Select Split if the spectra are to be displayed in split display mode.
The Number of Hits is the number of spectra from the hit list that are
displayed for each sample.

Working with Spectra . 73

Com pare Setup - Output

The Output tab enables you to choose whether a report is printed after the comparison
has finished, and how the results are printed.
To Printer

The compare report (a text file) is automatically printed after each

comparison.

To Printer with
Template

The compare report is automatically printed after each comparison

using the selected report template.

Include Graph

The graph is printed with the report.

You may find it useful to print both types of report, because although a report printed
using a template will have a better layout, if the Compare report is a large one, it may
not fit into the space provided in the template. You can type the path and filename of the
template, or select one by clicking on Browse.

Com pare Setup - Threshold

You can enter two Threshold values to further define the Compare function. These are
called the Correlation Threshold and the Discrimination Threshold.
Correlation

Allows you to set the required degree of similarity between the two
spectra.
Enter a value between 0.00 (no similarity) and 1.00 (identical). The
default value is 0.98.
The higher the Correlation Threshold, the lower the chance of incorrect
identification. But this also gives an increased chance of a false negative
result which lowers the efficiency of accurate identification. If the
Correlation Threshold is exceeded, the result is reported in the results
window as Pass.
In most cases the Correlation Threshold will be sufficient to identify a
material, but sometimes you may also wish to enter a Discrimination
Threshold. Note that Correlation and Discrimination are linked. If you
enter values in both the Correlation and Discrimination fields, both of
these conditions must be satisfied to return a Pass.

Discrimination Provides an additional test to ensure that you discriminate between

materials in your library.
Enter a value between 0.00 and 1.00. The default value is 0.05.
The Discrimination Threshold is used to ensure that the closest match is
sufficiently separated from the next closest match. Its value is equal to
the difference in the Correlation coefficients of the first two spectra
reported in the results window. As an example, let's take the case when
the Discrimination Threshold is 0.05. The result is pass when the
Discrimination value is greater than 0.05. If the Correlation Threshold is
also exceeded, the result is reported in the results window as Pass. If
the Discrimination value is less than 0.05, the result is fail. In this case,
even if the Correlation Threshold is exceeded, the result is Fail.
The Threshold you use depends on the materials in your library. If the
other materials are very different from the selected material, you should
set the Discrimination Threshold high. If the materials are very similar to
the selected material you will need to set the Discrimination Threshold
low. The Discrimination field is not available unless the Correlation check
box is selected.

74 . Spectrum

I R Search
W hat can I use Search for ?
IR Search helps you to identify an unknown material. It will search through a library or
libraries to find the spectra that best match your unknown sample. It can also interpret
your unknown spectrum directly by determining from the pattern of peaks (and absences
of peaks) which Possible Structural Units (functional groups) are likely to be present.
NOTE: This command is only available if Expert Search version 1.3 or Spectrum Search
Plus is installed. If IR Search is not available on your PC, this command is grayed.

W hen should I use Com pare and w hen should I use Search ?
You should use IR Search when you do not know the identity of your sample, a search
compares your sample spectrum with libraries that can contain many spectra, or
compares the peaks in your spectrum with many Possible Structural Units to identify your
sample.
Even if your sample is not in the libraries, an interpretation will give you information on
what functional groups are present in your sample, and provide clues as to what it is.
If you know that your sample is one of a range of materials or if you want to measure
how similar your spectrum is to another spectrum, you should use Compare; this
compares your sample spectrum with one other spectrum or several spectra and reports
the degree of similarity between the spectra.

W hat do the Different Search Types do ?

There are three types of search available:

Interpretation - an interpretation compares the peaks in your sample spectrum with

the peaks that correspond to 896 PSUs (Possible Structural Units). A list of the PSUs
in your sample spectrum is displayed. You do not need to have a search library to
perform an interpretation.

Euclidean - a Euclidean search compares every point in your sample spectrum with
the points in spectra in a search library.

Library search - a library search compares the position of the peaks in your sample
spectrum with the position of peaks in the spectra in a search library.

W hat Type of Search should I use ?

An interpretation is useful:

if you think that your sample spectrum will not be present in a search library, the
interpretative search will indicate what PSUs are present in the sample.

A library search is useful because:

it is faster than a Euclidean search - it is comparing a relatively small number of

peak positions whereas a Euclidean search compares a much larger number of
points in the spectra;

if you know that your sample contains a mixture of materials you can set up the
search so that additional peaks from the other components are ignored.

Working with Spectra . 75

A Euclidean search is useful where the search library spectra are not distinguishable
from each other, for example:

within classes of chemically-similar complex compounds where bands overlap

strongly, the Euclidean search compares all the points in the spectrum and hence
identifies peaks that are less-well separated;

when you are searching for mixtures that are different in the proportions of their
components, a Euclidean search takes account of peak intensity as well as position;

when the signal-to-noise ratio of your spectrum is poor, a Euclidean search

effectively ignores the noise in the spectrum.

if you are searching for near infrared or Raman spectra, only a Euclidean search is
available.

a Euclidean search compares every point in a spectrum with spectra in a search

library, the results from a Euclidean search are more reliable than a library search.

If you are using near infrared or Raman spectra only a Euclidean search is available.
If your spectra does not have an ordinate axis in %T, %R or A only a Euclidean search is
available.

Search Libraries
Several search libraries are supplied with Spectrum Search Plus. When Spectrum Search
Plus is installed on your PC they are installed in the directory c:\pel_data\libs. Spectrum
Search Plus also enables you to create libraries of your own, or to use libraries supplied
by other manufacturers; for information on this see the Spectrum Search Plus on-sceen
help. You cannot create search libraries using Spectrum. Additional libraries are available
from PerkinElmer.

W hat do the Search Results M ean ?

When a search finishes the results are displayed as hit lists. If you have chosen Display
in the Graph Window section of the Display tab, a graph window displaying your
sample spectrum and spectra of the top items in the hit list are also displayed.
The hit lists give the compounds that most closely match your sample spectrum. There
are six different hit lists that use different methods for scoring.
Euclidean

A hit list of the best spectrum shape matches.

PSU/peak

A hit list based primarily on the PSU score. The peak match score is used
only to rank those hits with identical PSU scores.

PEAK/psu

A hit list based primarily on the peak match score. The weight given to
PSU matches is lower for high peak match scores.

MIX PSU

A hit list based on the PSU score, but allowing for the spectrum being
that of a mixture of compounds.

MIX PEAK

A hit list based on peak matches, but allowing for the spectrum being
that of a mixture of compounds.

Peak Match

A hit list based on the peak match score only.

76 . Spectrum
The hit lists are a useful aid to identification. However, we recommend that you make a
visual comparison of the sample and library spectra before accepting the identification.
To display the sample spectrum and an item in the hit list:

Double-click on an item in a hit list.

Starting a Search
1. Display and select the spectrum or spectra that you want to identify.
2. Display the Process menu and choose IR Search.
The hit lists are displayed.
We advise you not to select several spectra and several hit lists simultaneously, because
the display can become overcrowded and confusing.

Displaying unknow n and library spectra

You can see how well the unknown spectrum matches a library spectrum by doubleclicking on the spectrum name in a hit list. The two spectra are displayed.
For further information about the format and meaning of the hit lists, see the IR Search
Setup or the Spectrum Search Plus on-screen help.

Setting up a Search
Before you use the IR Search command on the Process Menu to perform a Search, you
must set up the search parameters as follows:
NOTE: If you are using near infrared spectra, you must build the search libraries
yourself, and you can perform only a Euclidean Search. To use near infrared
spectra, you must have Spectrum Search version 1.6 or later.
1. Display the Setup menu and choose IR Search.
The Search Setup dialog is displayed. You can set up the format of the results that
are output, and choose which libraries are to be used for the Search. You can start
it by choosing Search on this dialog. This command is available only if Expert
Search version 1.3 or Spectrum Search is installed. If IR Search is not available on
your PC, this command is grayed.
2. Click on the tabs to display the settings.
Choosing Search will start the Spectrum Search application. You can do this at any
stage in the process.
NOTE: If the Search Libraries listed are NIR libraries, only the Report Options for a
Euclidean search are enabled.

Working with Spectra . 77

IR Search Setup - Libraries

Before you perform a search you must choose the libraries you are going to search to
identify your sample. The Library tab enables you to select the libraries.
NOTE: If you are using near infrared spectra, you can only perform a Euclidean Search,
and you must build the search libraries yourself. To use near infrared spectra,
you must have Spectrum Search version 1.6 or later.

Search

Enables you to select the libraries that are to be searched. To add a

library to the list, choose Add, and use the file selector to select a library
file. To delete a library file, select the library and choose Delete.

Format

Enables you to choose a library format. Sadtler libraries and Nicolet /

Aldrich libraries cannot be altered in any way. If you want to generate
your own libraries, you must use PerkinElmer format libraries.

IR Search Setup - Report

The Report tab enables you to choose what type of search is performed, and how the
results of your search are displayed on screen:
Hit Lists
Euclidean

A hit list of the best spectrum shape matches is displayed. This is the
only search type available for near infrared or Raman spectra or any
spectrum with an ordinate type that is not %T, %R or A.

These items refer to hit lists generated by a library search. When you choose a hit list
that includes PSU, an interpretation is also performed.
PSU/peak

A hit list based primarily on the PSU score is generated. The peak match
score is used only to rank those hits with identical PSU scores.

PEAK/psu

A hit list based primarily on the peak match score is generated. The
weight given to PSU matches is lower for high peak match scores.

MIX PSU

A hit list based on the PSU score, but allowing for the spectrum being
that of a mixture of compounds, is displayed.

MIX PEAK

A hit list based on peak matches, but allowing for the spectrum being
that of a mixture of compounds, is displayed.

Peak Match

A hit list based on the peak match score only is generated.

Others

Peak Table

A peak table is generated for each sample. For more information about
the layout of the peak table generated, see Peak Table.

Interpretation An interpretation is performed, a list of Possible Structural Units based

on the peaks and absences for each unknown sample is generated. For
more information about the Interpretation option, see Interpretation in
the Spectrum Search Plus on-screen help.

78 . Spectrum

IR Search Setup - Regions

You may want to search for your spectra over a limited abscissa range or to exclude
specific regions of your spectrum from the search, the Regions tab enables you to specify
the abscissa range and to exclude regions.
Range

If you choose Full Overlap, the entire range that overlaps is used in the
search.
If you choose Manual, you can enter your own Start and End abscissa
values for the region to be searched.

Blanks

Specifies regions to be excluded from the search.

IR Search Setup - Display

The Display tab enables you to choose the items that are displayed when a Search has
finished.
Text Report

Specify the Number of Search Hits that are reported for each hit list for
each sample.

Graph
Window

Select Graph if you want to view the sample spectrum and spectra found
in the search library when the Search has finished.
NOTE: if more than one hit list is selected on the Results tab the spectra
will be displayed from the first hit list on the Results tab.
Select Overlay if the spectra are to be displayed in overlay display
mode.
Select Split if the spectra are to be displayed in split display mode.
The Number of Graph Hits is the number of spectra that are displayed
from the search library for each sample.

IR Search Setup - Output

The Output tab enables you to choose whether a report is printed after the search has
finished, and how the results are printed.
To Printer

Prints the results on the default printer.

Include Graph Select Include Graph to include the graph in the report. The graph is
specified on the Display tab.
To Printer with Prints the results on the default printer using the report template
Template
chosen.
Report
Template

Enables you to choose the report template used for the report, choose
Browse to use a file selector.

To Text File

Saves the results as a text (.txt) file.

Auto
Overwrite

When To Text File is chosen, automatically overwrites the existing text

file without warning.

Working with Spectra . 79

I nteractive I nterpretation
W hat can I use Interactive Interpretation for ?
Interactive Interpretation helps you identify the PSUs (Possible Structural Units) that may
be present in your sample. It is particularly useful if you think that your sample spectrum
will not be present in a search library.

W hat Does Interactive Interpretation do ?

Before your spectrum is compared with the PSUs it is processed:

a peak table is generated;

the spectrum is normalized;

the baseline is adjusted and then scaled so that the strongest peak becomes 3% T.

The peak heights used in the interpretation may therefore be different to those displayed
in the spectrum.
NOTE: This command is only appropriate for mid infrared spectra and libraries that have
%R, %T or A ordinate types.
During an Interactive Interpretation the peak table of the unknown compound is
compared with an index of 896 functional units, and those units that characterize the
sample are determined.

Starting an Interactive Interpretation

1. Select the spectrum that you want to interpret.

2. Display the Process menu and choose Interactive Interpretation or click on

The interpretation is performed on the peak table of the selected spectrum, and the
Interactive Interpretation window is displayed.
A list of PSU (Possible Structural Units) for the sample compound is displayed. If the
list is longer than one page, a scroll bar appears.
To the left of each PSU is a number referencing it to the corresponding entry in the PSU
structural diagram file. The PSUs enable you to assess the chemical nature of your
sample. However, the PSU structural diagram file may indicate other functional groups
that could generate a similar interpretation.
NOTE: You can display the PSU Structure Diagrams only if they were installed when
Spectrum Search Plus was installed.
The index of PSUs is divided into 49 groups that include for example, aromatic esters and
alkenes. When a library search is performed, it is these groups rather than the individual
PSUs that are compared with the library compounds.

80 . Spectrum

View ing the Regions of a Spectrum for a PSU

The Interactive Interpretation command enables you to view the regions of the spectrum
that correspond to the PSUs. When you perform an Interactive Interpretation the region
of the spectrum for the first region in the Region List text box is highlighted.
Viewing another region for the same PSU

Click on another item in the Region List text box.

The region of the spectrum for the new region is highlighted.

Viewing regions for another PSU

Click on another PSU in the Interpretation Result text box.

The region of the spectrum for the first item in the Region List is highlighted.

Viewing all the PSUs

In the Interactive Interpretation dialog, click on

The Complete list of standard and user PSUs is displayed.

Working with Spectra . 81

P eak Table
W hat can I use a Peak Table for ?
You can use the Peak Table command to generate a peak table that can be printed or
saved.
You can display a peak table within Windows Notepad, Wordpad or any other suitable
text editor.

W hat do the param eters do ?

A peak table is a list of the peak positions, the peak threshold used, the abscissa and
ordinate ranges, and other status information. Peak positions are listed as abscissa and
ordinate values for each peak.
Algorithm

By default, peak positions are calculated using the Interpolated Peak

algorithm, which calculates peak position from maximum intensities.
Alternatively, you can select the Center of Gravity algorithm, as used by
NIST, which calculates peak position from the shape of the area under a
peak. Refer to the thresholds set in the Peak Options dialog.

Threshold

Defines the threshold that defines the number of peaks that will be
found. The thresholds used will depend on the type of spectrum, and the
Algorithm used. Refer to the Peak Options dialog.

Start

Defines the start of the range of the peak table.

End

Defines the end of the range of the peak table.

Find

When using the Interpolated Peak algorithm, enables you to record

Peaks or Bases or both in your peak table.
When using the Center of Gravity algorithm, Peaks are always recorded.
If you choose to record Bases as well, real data points are recorded,
rather than interpolated values.

82 . Spectrum

W hat is a Peak Table ?

From left to right, the first line of the peak table includes the Spectrum filename;
Number of points in the spectrum; Start and End of the range of the spectrum;
Minimum ordinate value; Maximum ordinate value; ordinate units; Number of scans
collected; and the Data interval.

Next, any comments added to the spectrum are included.

The following line contains reference information about background intensity values.

Then, the peak or base positions in the spectrum are listed.

The footer contains the number of peaks or bases found in the spectrum.

Generating a Peak Table

1. Display and select the spectrum or spectra for which you wish to generate peak
tables.
2. Display the Process menu and choose Peak Table.
The Peak Table dialog is displayed.
3. Set the Peak Table Parameters.
See Parameters for more information
4. Choose OK or OK All.
OK - If you have selected more than one spectrum, the named spectrum is
processed and the Peak Table displayed. Then the dialog is redisplayed for the next
spectrum.
OK All - If you have selected more than one spectrum, all the spectra are
processed and Peak Tables displayed without further interaction.
The Peak Table is displayed in a scrolling window.
NOTE: The Peak Table can be saved or printed, or the data can be copied to the
clipboard for use in another application.
The algorithms used to generate a peak table when you use the Peak Table command
and the IR Search command are not the same. Therefore, the peak tables generated
may not be identical.

Working with Spectra . 83

Looking at a Peak Table
You can use any text editor to look at peak tables such as Notepad or WordPad.
Click Start within Windows and select either Notepad or WordPad from the Accessories
menu.
1. Display the File menu, and choose Open.
The Open dialog is displayed.
2. Use the file selector to select the required peak table file.
Peak tables are usually stored in the pel_data\pktables directory.
3. Choose OK.
The peak table is displayed.
Saving a Peak Table
When you have generated peak tables using the Peak Table command, you can save
them.
1. Display the File menu and choose Save As.
The Save As dialog is displayed.
2. Change the filename if you want to, and choose OK.
If you choose OK without changing anything, the peak table is saved with the same
name as the spectrum, but with a .pk extension. You can, however, change the
name of the peak table if you wish.

84 . Spectrum

P eak Options
The Peak Table and the Peak Cursor commands both use the Peak Options to
determine their behavior.
1. Display the Setup menu and choose Options
The Options tabs are displayed.
2. Choose the Peak tab.
The Peak tab is displayed.
3. Choose the settings you require.
Find

When using the Interpolated Peak algorithm, enables you to find Peaks
or Bases or both in your spectrum.
When using the Center of Gravity algorithm, Peaks are always found. If
you choose to find Bases as well, the bases found will be real data
points, rather than interpolated values.

Label

Enables you to choose whether the Abscissa value, Ordinate value, or

both are used when labelling peaks.

Algorithm

By default, the peak positions are calculated using the Interpolated

Peak algorithm, which derives peak position from maximum intensities.
Alternatively, you can select the Center of Gravity algorithm, as used by
NIST, which derives peak position from the shape of the peak.

Thresholds

Enables you to choose the thresholds used when detecting peaks or

bases.
The threshold used for the Interpolated Peak algorithm is %T (or %R);
Abs (or Log 1/R); and Units (for any other units) - depending on the
type of spectrum examined.
The Pk Ht threshold defines how much of a peak is used when
calculating its center of gravity. Where peaks are well defined a Pk Ht
threshold of 0.8 could be appropriate. However, where two poorlydefined peaks overlap to produce a shoulder, and Pk Ht is set to include
the overlap, the Center of Gravity algorithm will calculate a peak
position shifted towards the shoulder.
For example: This effect will cause an NIR Abscissa check using the
Center of Gravity algorithm (refer to Instrument Validation) at the 5669
cm-1 peak to fail unless the Pk Ht threshold is set to 0.2 or less.

Reset

Click Reset to return to the default threshold values: 2.00%T, 0.0088

Abs, 10.00 Units, 0.20 Pk Ht.

4. Choose OK.
NOTE: Any peak tables in memory are recalculated with the new settings.

Working with Spectra . 85

Quant P rediction
Spectrum Beer's Law, Spectrum QuantC and Spectrum Quant+ enable you to determine
the concentrations of the components in a mixture by analyzing its spectrum.
NOTE: Before you perform a quantitative analysis, you first need to create a method
using the appropriate application (Beer's law, QuantC, Quant+). You must also
set up the analysis by using the Setup Quant command.

NOTE: The applications used to develop Quant methods are not 21 CFR Part 11
compliant, so it not likely that they are installed on the same PC as Spectrum ES.
To use Quant Methods in a 21 CFR Part 11 compliant environment, you must
export the method from the Quant PC as a zip file, and then import the method
into Spectrum ES.

W hich Quant Package Should I Use ?

You can use Quant for a simple measurement of the concentration of an unknown by the
application of Beers Law, and analyze mixtures of compounds; either by curve-fitting, or
by more complex chemometric methods.
Beer's law predicts the concentration of each component in a mixture, by plotting
concentration against peak height or area for a set of standard spectra collected from
standard samples. The straight line graph is in the form y = mx + c. Comparing the peak
height or area in the sample spectrum with the graph gives the predicted concentration
in the sample.
For information on the different Quant packages, see the on-screen help for the
individual packages.
The online Help for this topic includes an interactive quiz that helps you decide whether
to use Spectrum Beers Law Quant, and the Spectrum Quant+ and Spectrum QuantC
packages.

86 . Spectrum
What Results are Displayed ? - Spectrum Beer's Law Quant
The Prediction Report gives the following information:
Date and Time

The date and time of the prediction.

Analyst and Comment

The details entered before the prediction.

Sample Name

The name of the sample that was predicted.

Method Name and Version

The name and version number of the Spectrum Beer's

Law method used for the prediction.

Description and Comments

The details entered when the method was built.

Created

The date and time the method was built.

Last Modified

The date and time the method was last edited.

Component concentration

The result of the prediction.

Component Error of
Prediction

A statistical evaluation of the predicted result. The result

tends to zero for a good prediction.

What Results are Displayed ? - Spectrum Quant+ and Spectrum QuantC

The results of the predictions are displayed in scrolling windows; one window for each
sample.
NOTE: The detailed meanings of the individual items in the results window, and the
mathematical basis of the calculations, are described in full in the manuals
supplied with the Quant applications. A brief summary of each is given below:
Sample information
Sample name and description.
Method name, Version, ID and Algorithm Type.
Comment (if you have selected to include one).
Statistical summary
The statistical summary of the result comprises:
RMS Error
Peak to Peak Error
%Variance (QuantC only)
F value (or Residual Ratio)
Total M-Distance (Quant+ only)

Working with Spectra . 87

Results for each component or property
The sample description and statistical summary are followed by the predictions for each
Component (or Property) in the sample. R Error and M-Distance are only displayed if you
have selected Statistics in the Quant Setup dialog.
Component1, Calc value,R Error,M-Distance (Quant+ only)
Component2, Calc value, R Error, M-Distance
The status bar at the bottom of the window shows the total number of components.
Displaying the Residuals Spectrum

Double-click on the results window.

The Residuals spectrum is displayed.

Setting up a Quant P rediction

Before you use the Quant Prediction command on the Process Menu to perform a Quant
prediction, you must set up the parameters as follows:
To display the Quant Setup dialog:
1. Display the Setup menu and choose Quant.
2. Click on the tabs to display the settings.
Choosing Quant at any stage will start the selected Quant application (Spectrum
Beer's Law, Spectrum QuantC or Spectrum Quant+) if it is installed on the PC.

Quant Setup - Type

Spectrum enables you to use Spectrum Beer's Law, Spectrum QuantC or Spectrum
Quant+ to determine the concentrations of the components in a mixture by analyzing its
spectrum. For information on which package see Which Quant Package Should I Use ?
Method

Enables you to choose the quantative analysis application that was

used to build the method. For details about these applications, refer
to the help that is provided with it.

Method Name

Enables you to choose or type the filename and path of the method
that will be used for the Quant prediction. Quant+ and QuantC
methods have .md extensions, while Beers Law methods have .uqm
extensions. Clicking on Browse displays an Open dialog to help you
find the method file.
Choose Add Comments if you want to add a comment to the report
for each of the samples you analyze. You will be prompted to add the
comment as each sample is processed.
NOTE: The applications used to develop Quant Methods are not 21
CFR Part 11 compliant, so it not likely that they are installed on the
same PC as Spectrum ES. To use Quant Methods in a 21 CFR Part 11
compliant environment, you must export the method from the Quant
PC as a zip file, and then import the method into Spectrum ES. Only
users able to perform administration tasks can import Quant methods.

88 . Spectrum

Quant Setup - Display

Text Report

If you choose Prediction Report, a prediction report is generated.

If you choose Prediction with Statistics, the R-Error and
Mahalanobis Distance values are included in the prediction report
(see Beer's Law Results or Quant+ and QuantC Results). Report
options are not available for Beer's Law predictions.

Graph Window

Select Display if you want to view the spectra when the prediction is
finished.
Select Overlay if the spectra are to be displayed in overlay display
mode, or Split if the spectra are to be displayed in split display
mode.
Choose whether to display the unknown spectrum, the residual
spectrum and the calculated spectrum.

Quant Setup - Output

To Printer

Prints the results on the default printer. The prediction report (a text
file) is automatically printed after each prediction.

Include Graph

Select Include Graph to include the graph in the report. The graph is
specified on the Display tab.

To Printer with
Template

The prediction report is automatically printed after each prediction

using the layout of the selected report template. The default report
template is [Link]. To select a different template, type the
path and filename of the template, or select one by clicking on
Browse.

Report Template Enables you to choose the report template used for the report, choose
Browse to use a file selector.

NOTE: You may find it useful to print To Printer and To Printer with Template,
because although a report printed using a template will have a better layout, if
the Quant report is a large one, it may not fit into the space provided in the
template.

Working with Spectra . 89

P eak/ Area Height

W hat can I use Peak Area/ Height for ?
You can use it to measure:

Peak areas relative to a linear baseline, between two baseline points, or between
two other points on the spectrum.

Peak heights from a peak maximum to a baseline or to zero absorbance.

The maximum height in the selected region.

W hat do the param eters do ?

You can change the default settings for Peak Area/Height using the Area/Height
command on the setup menu. See Setting Defaults for a Peak Area/Height Measurement.
Area parameters
An area is defined by a start and end abscissa value and two base points.

The Total Area is the area between the spectrum and zero absorbance or 100%
transmittance that lies within the marker bar limits.
The Corrected Area is the area between the spectrum and the marked baseline, within
the marker bar limits.

90 . Spectrum
Height parameters
A height is defined by a start and end abscissa value and two base points.

The Total Height is the height from the curve to zero absorbance.
The Corrected Height is the height from the curve to the baseline.
Max height parameters
Max height is defined by a start and end abscissa value and two base points.

The Maximum Height is the maximum peak height between the start and end abscissa
values, where the peak height is measured from the curve to zero absorbance.
The Corrected Height is the height from the curve to the baseline.

Working with Spectra . 91

M oving Area and Height M arkers w ith the M ouse

To move a base point:

Drag the base point to its new position.

To change the start and end values:

1. Double-click on the marker bar.
A shaded area is displayed.

2. Drag the sides of the shaded areas to their new positions, or move the shaded area
by dragging it from its center.
3. Double-click on the shaded area again when you have finished editing it.

92 . Spectrum

M easuring a Peak Area or Height

You can change the default settings for Peak Area/Height using the Area/Height
command on the setup menu. See Setting Defaults for a Peak Area/Height Measurement.
1. Display and select the spectrum or spectra which have areas or heights you want to
measure.
Areas and heights are calculated in the same units as the spectrum. If you want to
use units different from the current units of the spectrum, you must convert the
spectrum to the correct units first.
2. Display the Process menu and choose Peak Area/Height.
The Peak Area/Height dialog is displayed.
3. In the Calculate section, choose whether to calculate an Area, a Height or a
Maximum Height.
4. Move the vertical cursor to the peak whose height or area you want to measure.
You can switch the vertical cursor to peak mode by right-clicking on the vertical
cursor button.
5. If necessary, expand the region of interest using a grow box, (see Using the Mouse
to Zoom in on a Region of Interest).
6. Double-click on the vertical cursor.
The height or area is calculated, and the total values displayed on the graph.
The parameter values used in the calculation are displayed in the Parameters
section, beneath the graph. If you want to change any of these parameters, refer to
Area Parameters, Height Parameters or Max Height Parameters.
7. If necessary, drag the text to a new position.
The number of decimal places displayed depends on the setting in the Peak Area /
Height Options.
8. When you have finished measuring an area or height, you can print the graph or
copy it to the clipboard using the toolbar buttons.
Both the graph and the text labels are copied or printed.
9. To repeat the calculation for another area, position the cursor within the new area
of interest and double-click on it.
A new marker bar and baseline are displayed.
10. When you have finished measuring the area or height, choose OK.
If you have selected other spectra to be processed, the next one is displayed.
The results of the area/height calculation are displayed in a report.
11. To save the report as a text file, display the File menu and choose Save.

Working with Spectra . 93

Setting Defaults for a P eak Area/ Height M easurem ent

The settings on the Area/Height tabs define the settings that are used when the Peak
Area/Height dialog is first displayed. To change the settings:

Display the Setup menu and choose Area/Height.

The Area/Height tabs are displayed.

You can change all of these options from the Peak Area / Height dialog, either in the
dialog itself (see Peak Area / Height), or in the dialog that is displayed when you click on
(see Peak Area / Height Options).

Peak Area/ Height-Setup - Start Up

The Start Up tab defines the options that are selected when you first display the Peak
Area / Height dialog.
Calculate

Enables you to choose to calculate Area, Height or Max Height.

Parameters

Enables you to choose parameters that you want to set up in advance

Start and End for the area calculation and Base 1 and Base 2 for the
height calculation.

Clear

Clears the Parameter text boxes.

Smooth

Select Smooth to smooth your spectrum.

Width

Enables you to set the smoothing width.

Peak Area/ Height Setup - Display

The Display tab specifies the items that are displayed when a Peak Area/Height
measurement has finished.
Screen Labels

Enables you to specify which labels are added to the graph when a
height or area is calculated.

Decimal Places

Enables you to specify the number of decimal places used in the

labels that are added to the graph and displayed in the text results
window.

Peak Area/ Height Setup - Output

The Output tab specifies how the results are printed.
To Printer

Prints the results on the default printer.

Include Graph

Select Include Graph to include the graph in the report. The graph
is specified on the Display tab.

To Printer with
Template

Prints the results on the default printer using the report template
chosen.

Report Template Enables you to choose the report template used for the report, choose
Browse to use a file selector.

94 . Spectrum

P eak Area / Height Options

While the Peak Area / Height dialog is displayed, you can change settings for the
current calculation.

Choose

The Area / Height Options dialog is displayed. The items that are active in this
dialog depend on whether the current calculation is an area, a height or a maximum
height.

Base Width

Selecting Smooth enables you to specify the number of points over

which to apply the base point smooth.

Decimal Places

The number of decimal places that are shown in the results that are
displayed on the graph.

Display

Specifies the information that is displayed on the graph when a height

or area is calculated. All the information is available in the report.

Thresholds

Enables you to set the thresholds that are used in determining peaks
and bases.

You can also use the Area / Height command on the Setup menu to set defaults for the
Peak Area / Height command.

Working with Spectra . 95

Preparing Spectra
The commands in this part of the Process menu enable you to prepare your spectrum, so
that it can be compared with other spectra:
Deconvolve the spectrum, to improve the separation of peaks;
Perform calculations on the spectrum
Normalize the spectrum, so that a peak that you choose has a particular value;
Abex the spectrum, to simulate the effect of changing the concentration or pathlengh of
your sample;
Blank out region of the spectrum, for example a solvent peak.

Deconvolution
W hat does Deconvolution do to a spectrum ?
It applies a line-narrowing process so that interference between unresolved features is
reduced. This means that you can see peaks that are present more easily.

W hat can I use Deconvolution for ?

Deconvolution is used in estimating the positions and intensities of overlapping
absorption bands.

W hat do the param eters do ?

Gamma defines the line-narrowing and can take values between 0 and 100, with larger
values give more narrowing. The reduction in linewidth for an ideal Lorentzian line is
given by:
4 x gamma x data interval.
For spectra with a data interval of 1, typical gamma values are less than 3.
Length defines the smoothing that is applied to limit the noise generated by linenarrowing. It can take values between 0 and 95, with 95 corresponding to maximum
smoothing. The form of the smoothing is selected from Bessel or Boxcar. You should
choose Bessel for real data. For spectra of different data intervals equivalent smoothing is
achieved for equal values of (100 length) x data interval.
The example graphs below show spectra of synthetic data. These graphs show how you
can use different values of Gamma and length to distinguish overlapping bands.

96 . Spectrum
The following spectra show the effect of changing Gamma for a fixed length of 60:

Working with Spectra . 97

The following spectra show the effect of changing Length for a fixed gamma of 4:

There is no correct result for real data. For example, small negative sidelobes may be
perfectly acceptable when trying to identify band positions.

98 . Spectrum

Using Deconvolution
1. Display and select the spectrum or spectra which has bands you wish to separate.
2. Display the Process menu and choose Deconvolution.
The Deconvolution dialog is displayed. See information the parameters.
3. Select the gamma value either by clicking on the touchpad control, or by typing a
value into the Gamma field.
Note that when you click on the touchpad, the spectrum is immediately recalculated
and redisplayed. If you select a different width by typing a number into the Gamma
text box, the spectrum is only changed when you choose Calculate.
4. Select the smoothing length either by clicking on the touchpad control, or by typing
a value into the Length field.
Note that when you click on the touchpad, the spectrum is immediately recalculated
and redisplayed. If you select a different width by typing a number into the Length
text box, the spectrum is only smoothed when you choose Calculate. The
smoothing width must be less than data interval multiplied by 750.
In choosing the best combination of Gamma and Length, it is generally necessary
to change them alternately. One approach is to start by increasing the length until
distortion of the initial bands becomes apparent. Then increase Gamma until noise
or sidelobes become unacceptable. Now you need to increase length and possibly
Gamma, or to decrease both Gamma and length. This requires a trial and error
approach. There is no correct result for real data. For example, small negative
sidelobes may be perfectly acceptable when trying to identify band positions.
5. Choose OK to accept the result.
The Deconvolution dialog closes, and the resultant spectrum is displayed in the
graph. If you selected several spectra for smoothing, the next spectrum is displayed
in a new Deconvolution dialog.

Theory
Deconvolution applies a line-narrowing process so that interference between unresolved
features is reduced. This has traditionally been done by taking derivatives of the
spectrum. For example the second derivative of a band has a narrow minimum at the
frequency corresponding to the maximum of the original band. The disadvantage of
derivative spectra is that secondary maxima and minima are generated along with the
central features. Deconvolution achieves line-narrowing with minimal subsidiary features.
Deconvolution uses a method called Fourier self-deconvolution which operates on the
Fourier transform of the spectrum. It can be thought of as involving two steps. A line
narrowing filter removes broadening corresponding to a Lorentzian line shape. This filter
is characterized by a parameter called (gamma). Increasing the magnitude of gamma
produces narrower lines, but eventually leads to subsidiary features (sidelobes) around
the narrowest bands. It also increases the noise. To reduce these undesired effects a
smoothing function is applied. The degree of smoothing is controlled by a parameter
called length. Increasing the length leads to a greater degree of smoothing. This reduces
noise and sidelobes, but at the expense of some line broadening.
Deconvolution is an interactive routine to find the most appropriate combination of these
parameters. It has to be used with caution since sidelobes from large bands can be
confused with small overlapping bands.

Working with Spectra . 99

Deconvolution works best with noise-free data where all the bands are Lorentzian and
have the same width. Even with ideal data the line width cannot be reduced below the
resolution at which the spectrum was collected. With real data, the degree of narrowing
that can be achieved is limited either by noise or by the subsidiary features associated
with the sharpest bands.

Spectral Calculator
W hat does Spectral Calculator do to a spectrum ?
There is a wide selection of commands available in Spectrum to perform many of the
spectroscopic transformations you may need. If none of these is appropriate, you can
perform other arithmetical operations on spectra using the Spectral Calculator.

W hat can I use Spectral Calculator for ?

You can use the Spectral Calculator to perform calculations involving the addition,
subtraction, multiplication or division of spectra by constants or another spectrum.
You can perform several operations one after another. Calculations are performed on the
spectra as if they are pure numbers, taking no account of ordinate type. There are two
exceptions to this:
If one single-beam spectrum is divided by another single-beam spectrum, the result is
the same as happens in normal data collection
NOTE: You can use the calculator memory to store intermediate results. The spectrum is
displayed as [Link]. ?

Using the Spectral Calculator

1. Display and select the spectrum or spectra on which you want to perform a
calculation.
If you want to perform a purely numeric calculation, it does not matter which
spectrum is selected.
2. Display the Process menu and choose Spectral Calculator.
The calculator is displayed with the selected spectra shown in the upper graph, and
with a button for each spectrum shown on the calculator keypad.
3. Click the Spectral Calculator buttons to perform the calculation you require.
You can now perform any numeric calculation as on a standard calculator. However,
you can also perform calculations involving complete spectra. If you do this, the
current resultant spectrum is shown in the lower graph.
The sequence of operations leading to this result is shown in the status box at the
bottom of the window. This can be scrolled so that you can view more of the steps
in the calculation.
NOTE: You can use the calculator memory to store intermediate results. The spectrum is
displayed as [Link].
4. If you want to use another spectrum in your calculation, choose Add Spectrum
and use the file selector to choose a spectrum.

100 . Spectrum
5. Choose OK to accept the results of the calculation.
The Spectral Calculator closes, and the result spectrum, if any, is added to the
graph window.

Norm alize
W hat does Norm alize do to a spectrum ?
Normalize multiplies each point in a spectrum by a factor.

W hat can I use Norm alize for ?

Normalize enables you to compare spectra of different ordinate amplitude.
Its main use is for setting a common peak in several spectra to the same ordinate limit.
Other peaks in these spectra can then be compared. Normalize is similar to Abex, but
allows you more control over the setting of the ordinate and abscissa parameters. All
calculations are performed in absorbance.

W hat do the param eters do ?

The parameters enable you to choose:

The ordinate value to which you want the spectrum or spectra to be scaled;

The abscissa point (or range) at which this ordinate value is to be set;

Whether you want the baseline to be adjusted to zero and, if so:

Whether you want this adjustment to be automatic; or to be at a point you select.

Using Norm alize

1. Display and select the spectrum or spectra that you want to normalize.
2. Display the Process menu and choose Normalize.
The Normalize dialog is displayed.
3. Set the ordinate limit and the range in which the peak maximum is to be found.
Ordinate Limit The ordinate value to which you want the spectrum or spectra to be
scaled.
Start The start wavenumber for the region that is to include the maximum ordinate
value.
End The end wavenumber for the region that is to include the maximum ordinate
value. If End is the same as Start, that wavenumber value will be used for the
normalization.
4. You can also select a Zero Point at which the baseline is corrected.
This can be done automatically at the point of lowest absorbance, or manually at an
abscissa value you select.
Off No baseline correction is applied.
Auto Zero Automatic baseline correction is applied. The spectrum is offset so that
the minimum absorbance of the spectrum will be set to zero. Note that this abscissa
value is shown grayed in the text box.
Manual Zero Manual baseline correction is applied. Enter the abscissa value to be
used into the text box.

Working with Spectra . 101

5. Choose OK or OK All to process the spectrum or spectra.
The normalized spectrum or spectra are displayed.
OK - If you have selected more than one spectrum, the named spectrum is
processed and displayed. Then the dialog is redisplayed for the next spectrum.
OK All - If you have selected more than one spectrum, all the spectra are
processed and displayed without further interaction.

Abex
W hat does Abex do to a spectrum ?
Abex (absorbance expansion) simulates the effect of changing the concentration or
thickness of a sample.

W hat can I use Abex for ?

Abex is useful if you want to compare a spectrum with the spectrum of a reference
material. In particular, when you compare two transmittance spectra, their band
intensities must be similar otherwise the shapes of strong bands will appear different in
the two spectra.
If you are creating reference spectra, for example for use with Spectrum Search Plus, we
recommend that you use Abex to normalize them and so make future comparisons
easier. Normalize the spectra by setting the intensity of the strongest band in each
spectrum to a constant value, typically 1.5 A which is approximately 3% T.
Abex is most useful when the spectrum is weaker than you would like: if the sample is
too thick, you cannot recover information from regions where the transmittance is
essentially zero. If the maximum ordinate value of the data is greater than the Ordinate
Limit selected, only a baseline correction is applied: the data is not normalized.
You can also use Abex for simple baseline adjustment because it automatically sets the
maximum transmittance to 100%. However, you must make sure that this maximum
transmittance corresponds to a useful baseline point, and not to a negative CO2
contribution, or noise at the end of the spectrum.
Although absorbance units are used for the Abex command, the spectrum will be
displayed in the current ordinate mode, either % T or absorbance.

Theory
You can set a limit for the ordinate range. The maximum Ordinate Limit is 6.2, if a value
larger than this is entered it will be reduced to 6.2.
You can also choose whether the abscissa range on which the expansion factor is based
is the full range, or a limited range.
If you select Limited Range, the maximum and minimum ordinate values within the
selected abscissa range are used to define the parameters for the Abex process.
NOTE: There is an important difference between Abex, which processes the data; and
Autoscale Y, which is a viewing option (and has no effect on the data in
memory).

102 . Spectrum
Abex is a five-step process for transmittance data, click on the buttons below to see the
five steps:

Working with Spectra . 103

Using Abex
1. Display and select the spectrum or spectra that you want to process using Abex.
2. Display the Process menu and choose Abex.
The Abex dialog is displayed.
3. Set the Abex Options.
You can set a limit for the ordinate range. The maximum Ordinate Limit is 6.2, if a
value larger than this is entered it will be reduced to 6.2.
You can also choose whether the abscissa range on which the expansion factor is
based is the full range, or a limited range.
If you select Limited Range, the maximum and minimum ordinate values within the
selected abscissa range are used to define the parameters for the Abex process.
4. Choose OK or OK All to process the spectrum or spectra.
OK - If you have selected more than one spectrum, the named spectrum is
processed and displayed. Then this dialog is redisplayed for the next spectrum.
OK All - If you have selected more than one spectrum, all the spectra are
processed and displayed without further interaction.
The expanded spectrum or spectra are displayed.
If you now zoom in on a peak, and label the peaks on the spectra, you may notice a
difference in the peak positions displayed on the original and processed spectra.
This difference is in the fourth or fifth decimal place.

Blank
W hat does Blank do to a spectrum ?
Blank marks regions of the spectrum that you do not want to use when processing the
data.

W hat can I use Blank for ?

It is useful for eliminating unwanted features from a spectrum, for example regions
affected by CO2, solvent or H20 bands.
When you save a spectrum that has blanked regions marked, a table is included in the
file listing these regions as unavailable.
The information on the blanked regions of spectrum is stored in a spectrum file. If you
save the spectrum as Data Manager file the blanked regions will be lost, that is the whole
spectrum will be displayed.

W hat do the param eters do ?

The parameters, Region Start and Region End define the region of your spectrum that
you want to blank.

104 . Spectrum

Using Blank
1. Display and select the spectrum or spectra that you want to mark blank regions in.
2. Display the Process menu and choose Blank.
The Blank dialog is displayed. It contains a shaded region, which you use to select
the blank regions.

Selecting a blank region

1. To move the shaded region, position the mouse pointer inside it; when you do this,
the mouse pointer changes to a four-headed arrow. Drag the shaded region to the
position you want.
The current start and end positions are shown in the Region Start and Region End
boxes.
If you want to remove a blanked region, select the region in the Blank Regions text
box and press DEL. The marker is removed.
2. To resize the shaded region, position the mouse pointer on one of its edges; when
you do this, the mouse pointer shape changes to a two-headed arrow. Drag the
edge to change the size of the shaded region.
NOTE: Alternatively, you can type values for the start and end of the blank region into
the Region Start and Region End text boxes.
3. When you are satisfied with the shaded region, choose Add Region.
The start and end of the region are displayed in the Blank Regions box, and the
blank region is marked on the spectrum with a horizontal range marker and that
region of the spectrum is not displayed..
4. To mark another blank region, choose New.
A new shaded region is displayed.
5. Repeat steps 1 through 3 to select more blank regions until you have marked all the
regions you want.
If you have selected other spectra to be processed, the next one is displayed.

Changing the Selected Blank R egion

1. You can also move or resize the regions already included in the table. Double-click
on the range marker of the blank region you want to adjust.
NOTE: If you want to remove a blanked region, double-click on that region in the Blank
Regions box. The marker is removed.
2. Choose OK to process the spectrum.
The spectrum is added to the graph window, with the blanked regions not
displayed. The data points in these regions have been marked as unavailable for
processing.
3. If you have selected other spectra to be processed, the next one is displayed.

Working with Spectra . 105

Status I nform ation

Every spectrum has information associated with it, which relates to the way that the data
were collected. This information is part of the file header of the spectrum, and is
displayed on the Status Information tabs.
These tabs enable you to view and in some cases update the status information that is
stored with the selected spectrum.
NOTE: Status information cannot be displayed if none was entered when the spectrum
was collected or saved to disk.
If more than one spectrum is selected, the Status Information tabs display the status
information for each spectrum in turn.

Displaying the Status I nform ation

From the File menu, choose Status.

The Status Information tabs are displayed.
Print- Prints the full status information.
To Report - Exports the full status information to Report Builder.
Copy - Copies the full status information to the Windows clipboard.

General Tab
The General tab reports the name of the spectrum, the date it was created, the name of
the analyst who created it, and displays any comments that were saved with the
spectrum. It also gives the start and end values for the abscissa scale (with the interval
between points), the maximum and minimum values for the ordinate, and the total
number of data points in the spectrum.
Filename - Displays the name of the spectrum.
Date Created - Displays the date that the spectral data were collected.
Analyst - The name of the analyst who collected the spectrum. If the GLP Lock is
off, you can edit the analyst name.
Description - Contains a description of the spectrum. If the GLP Lock is off, you
can edit the description.
Comments - Enables you to view and edit the comments saved with the spectral
file.
Abscissa - Displays the abscissa range and the data interval used on the abscissa.
Ordinate - Displays the maximum and minimum ordinate values for the spectrum.
Points - Displays the total number of data points used to create the spectrum.

106 . Spectrum

I nstrum ent Tab

The Instrument tab displays the information about the instrument that was used to
collect the spectral data. Any combination of the following may be displayed.
Accessory - The accessory (if any) used to collect the spectrum.
Accumulations - The number of scans collected.
Apodization - The apodization function applied.
Background Scans - The number of background scans against which the sample
spectra were ratioed.
Beamsplitter - The type of beamsplitter.
Beam Type - Type of spectrum collected, (single beam, background or ratio).
B-stop Size - The B-stop size, in mm.
Detector - The type of detector.
Dynamic Gain - The dynamic gain, if appropriate, including a list of the gain
parameters
Filterwheel Position - The filter that was in the beam when the spectrum was
collected (identified by its position in the filter wheel).
Gain - The detector gain.
Igram Type - The interferogram type used.
Instrument Model - The model of the instrument.
Instrument Number - The serial number of the instrument.
Instrument Software Version - The version number of the instrument software.
IR Laser Wavenumber - The infrared laser wavenumber, in cm-1.
IR Type - The infrared type: Fourier Transform or Dispersive
J-stop Size - The J-stop size, in mm.
Noise Filter - The noise filter used to collect the spectrum (applies to dispersive
instruments only).
OPD Velocity - The Optical Path Difference velocity (scan speed), in cm/sec.
Phase Correction - The phase correction mode and the number of points used, if
appropriate.
Polarizer Position - The polarizer position (if fitted) and angle.
Raman Laser Power - The Raman laser power, in mW.
Raman Laser Wavenumber - The Raman laser wavenumber, in cm-1.
Resolution - The resolution of the instrument.
Scan Direction - The interferogram scan direction.
Scan Mode - The scan mode used to collect the data (applies to dispersive
instruments only).
Scan Range - The maximum scan range, in cm-1.
Shuttle Cycle - The scan cycle of the sample shuttle (if one was used).
Source - The type of source.
Spectrum Type - The type of spectrum collected (interferogram or spectrum).

Accessories Tab
The Accessories tab is only displayed if the current spectrum was collected on a
Spectrum. The tab enables you to see the details for the sampling accessory that was
used to collect the spectrum.
This will include information such as part number and serial number of the accessory,
ATR top plate details, force applied by the pressure arm, what sampling type was used,
and so on.

Working with Spectra . 107

History Tab
The History tab enables you to see the processing history of the spectrum. If several
process commands have been used, each time a process command is performed it
creates its own record. You can view the records in the history using the Next and
Previous buttons.
Spectrum - The current name of the spectrum.
History Record - Shows which process commands have been used to create the
spectrum as it is now displayed, and the name of the original spectrum upon
which the process commands were performed.

Quality Checks Tab

The Quality Checks tab is only displayed if the current spectrum was collected on a PC
that had IR Expert software installed. The tab enables you to see the results of the
quality checks performed when the sample was collected. It also notes if any checks
were not performed.

108 . Spectrum

Process History
Abex History
You can view the History record generated by processing your spectrum with the Abex
command. To view the History record, display the Status Information of the spectrum
and select the History tab.

Date/time

The date and time at which the spectrum was processed.

Analyst Name

The Login Name of the analyst who processed the spectrum.

Transform Name

Normal (Abex performs the same transformation as Normalize).

Source Name

The name of the spectrum on which the transform was

performed.

Parameters

Abscissa value at which the maximum Ordinate value was found;

Absorbance to which this maximum Ordinate value was set;
Abscissa value at which the minimum Ordinate value was found,
which was then set to zero absorbance.

Absorbance History
You can view the History record generated by processing your spectrum with the
Absorbance command. To view the History record, display the Status Information of the
spectrum and select the History tab.

Date/time

The date and time at which the spectrum was processed.

Analyst Name

The Login Name of the analyst who processed the spectrum.

Transform Name

Absorbance.

Source Name

The name of the spectrum that was processed.

Working with Spectra . 109

ATR Correction History

You can view the History record generated by processing your spectrum with the ATR
Correction command. To view the History record, display the Status Information of the
spectrum and select the History tab.

Date/time

The date and time at which the spectrum was

processed.

Analyst Name

The Login Name of the analyst who processed the

spectrum.

Transform Name

ATR.

Source Name

The name of the spectrum that was processed.

Parameters

The contact correction factor used.

Baseline Correction History

You can view the History record generated by processing your spectrum with the
Baseline Correction command. To view the History record, display the Status Information
of the spectrum and select the History tab.

Date/time

The date and time at which the spectrum was processed.

Analyst Name

The Login Name of the analyst who processed the spectrum.

Transform Name

BaselineCorr.

Source Name

The name of the spectrum that was processed.

Parameters

Either auto (if the correction parameters were determined

automatically), or the abscissa values at which the correction
curve was fitted.

110 . Spectrum

Blank History
You can view the History record generated by processing your spectrum with the Blank
command. To view the History record, display the Status Information of the spectrum
and select the History tab.

Date/time

The date and time at which the spectrum was processed.

Analyst Name

The Login Name of the analyst who processed the spectrum.

Transform Name

Blank.

Source Name

The name of the spectrum that was processed.

Parameters

The start and end abscissa values for each of the regions marked
to be ignored in future processing.

Convert X History
You can view the History record generated by processing your spectrum with the Convert
X command. To view the History record, display the Status Information of the spectrum
and select the History tab.

Date/time

The date and time at which the spectrum was processed.

Analyst Name

The Login Name of the analyst who processed the spectrum.

Transform Name

cm_um: wavenumbers to microns um_nm: microns to

nanometers etc.

Source Name

The name of the spectrum that was processed.

Parameter

The data interval of the spectrum.

Working with Spectra . 111

Deconvolution History
You can view the History record generated by processing your spectrum with the
Deconvolution command. To view the History record, display the Status Information of
the spectrum and select the History tab.

Date/time

The date and time at which the spectrum was processed.

Analyst Name

The Login Name of the analyst who processed the spectrum.

Transform Name

Deconvolution.

Source Name

The name of the spectrum that was processed. The name of the
spectrum on which the transform was performed.

Parameters

1. The gamma value;

2. The smoothing length.

Derivative History
You can view the History record generated by processing your spectrum with the
Derivative command. To view the History record, display the Status Information of the
spectrum and select the History tab.

Date/time

The date and time at which the spectrum was processed.

Analyst Name

The Login Name of the analyst who processed the spectrum.

Transform Name

Deriv.

Source Name

The name of the spectrum that was processed

Parameters

1. The order of the derivative that was performed;

2. The number of points used.

112 . Spectrum

Difference History
You can view the History record generated by creating your spectrum with the Difference
command. To view the History record, display the Status Information of the spectrum
and select the History tab.

Date/time

The date and time at which the spectrum was processed.

Analyst Name

The Login Name of the analyst who processed the spectrum.

Transform
Name

Diff.

Source Name

The name of the spectra from which the difference spectrum was
created.

Parameters

The factor by which the second source spectrum was multiplied, before
it was subtracted from the first spectrum.

Working with Spectra . 113

I nterpolate History
You can view the History record generated by processing your spectrum with the
Interpolate command. To view the History record, display the Status Information of the
spectrum and select the History tab.

Date/time

The date and time at which the spectrum was processed.

Analyst Name

The Login Name of the analyst who processed the spectrum.

Transform Name

Interpol.

Source Name

The name of the spectrum that was processed.

Parameters

1. The abscissa start value;

2. The abscissa end value;
3. The data interval: note that this is negative if the end value
is lower than the start value, as it will be for a spectrum in
wavenumbers.

Kram ers-Kronig History

You can view the History record generated by processing your spectrum with the
Kramers-Kronig command. To view the History record, display the Status Information of
the spectrum and select the History tab.

Date/time

The date and time at which the spectrum was processed.

Analyst Name

The Login Name of the analyst who processed the spectrum.

Transform Name

KK.

Source Name

The name of the spectrum that was processed.

Parameters

1. The abscissa start value of the region processed.

2. The abscissa end value of the region processed.
3. a: absorbance spectrum;
k: absorption index spectrum;
n: refractive index spectrum.

114 . Spectrum

Kubelka-M unk History

You can view the History record generated by processing your spectrum with the
Kubelka-Munk command. To view the History record, display the Status Information of
the spectrum and select the History tab.

Date/time

The date and time at which the spectrum was processed.

Analyst Name

The Login Name of the analyst who processed the spectrum.

Transform Name

KM.

Source Name

The name of the spectrum on which the transform was

processed.

Norm alize History

You can view the History record generated by processing your spectrum with the
Normalize command. To view the History record, display the Status Information of the
spectrum and select the History tab.

Date/time

The date and time at which the spectrum was processed.

Analyst Name

The Login Name of the analyst who processed the spectrum.

Transform Name

Normal.

Source Name

The name of the spectrum that was processed.

Parameters

The abscissa value at which the ordinate maximum was set;

1. The absorbance value to which the ordinate maximum was
set;
2. The abscissa value at which the minimum value was set,
either:
min if the Zero Point selection was Auto Zero;
or
the Manual Zero value if one was set.

Working with Spectra . 115

Sm ooth History
You can view the History record generated by processing your spectrum with the Smooth
command. To view the History record, display the Status Information of the spectrum
and select the History tab.

Date/time

The date and time at which the spectrum was processed.

Analyst Name

The Login Name of the analyst who processed the spectrum.

Transform Name

Smooth.

Source Name

The name of the spectrum that was processed.

Parameters

1. The width of the smoothing window;

2. A number representing the type of weighting function
used:
0 is Block Average;
2 is Savitzky-Golay.

I nteractive Sm ooth History

You can view the History record generated by processing your spectrum with the
Interactive Smooth command. To view the History record, display the Status Information
of the spectrum and select the History tab.

Date/time

The date and time at which the spectrum was processed.

Analyst Name

The Login Name of the analyst who processed the spectrum.

Transform Name

Smooth.

Source Name

The name of the spectrum that was processed. The name of the
spectrum on which the transform was performed.

Parameters

1. The width of the smoothing window

2. A number representing the type of weighting function used:
1 is triangular, which is the only weighting function used for
Interactive Smooth.

116 . Spectrum

Spectral Calculator History

You can view the History record generated by processing your spectrum using the
Spectral Calculator. To view the History record, display the Status Information of the
spectrum and select the History tab.

Date/time

The date and time at which the spectrum was processed.

Analyst Name

The Login Name of the analyst who processed the spectrum.

Transform Name

The arithmetic operation that was performed.

Add (shows a negative value for subtraction);
Mult;
Div;
SqRoot for square root;
SLog for logarithm.

Source Name

The name of the spectrum that was processed.

Parameters

The name of the spectrum that was added.

Transm ittance History

You can view the History record generated by processing your spectrum using the
Transmittance command. To view the History record, display the Status Information of
the spectrum and select the History tab.

Date/time

The date and time at which the spectrum was processed.

Analyst Name

The Login Name of the analyst who processed the spectrum.

Transform Name

Transmittance

Source Name

The name of the spectrum that was processed.

Parameters

The name of the spectrum that was processed.

Controlling the I nstrum ent

118 . Spectrum

Controlling the Spectrom eter

The Scan and Instrument Setup dialog enables you to:
Collect spectra
Control accessories
Set up the instrument
Adjust the instrument
Perform validation routines
The choices available depend on your level of Instrument Access as defined on the
Instrument tab of the Options dialog from the Setup menu. The following help topics
assume Advanced access so if an item is mentioned that is not available on the dialog
you see, you probably have a lower access level. For details of the differences in the
other two access levels, see:
Routine Access Users
Standard Access Users

NOTE: If you use the

current setup.

tool to start a scan, the scan will immediately start using the

Controlling the Instrument . 119

Collecting Spectra
1. Open the Scan and Instrument Setup dialog by choosing Scan from the Instrument
Menu.
You may collect spectra using either the Sample tab (which may be familiar from
earlier versions of Spectrum), or the Multiple Sample tab (which can be far more
efficient).

2. Click Switch
to toggle between the Sample tab and the Multiple Sample tab.
On the Sample tab, specify the Name for your spectrum and add the Description
and Comments that will be saved with the spectrum.
On the Multiple sample tab, specify the Names for a series of spectra, and to add
the Description and Comments that will be saved with each spectrum. The
Multiple Sample tab is useful when working with accessories such as the Universal
ATR, the NIR Fiber Optic Probe, and the NIR Tablet Autosampler (where you also
specify the Position of each sample on a Carousel).
NOTE: If data collection is set up to automatically name your scans, each scan's Name
is completed automatically, and cannot be edited here.
3. The remaining tabs enable you to set up the instrument:
Set the Range, Scan Type, Units, and Duration on the Scan tab.
Set the Resolution on the Instrument tab.
Advanced Setting include Data Interval, Apodization, Phase Correction, Scan
Speed, CO2/H2O suppression, AVI settings, and Look Ahead. A button in
this section of the tab opens the Quality Checks dialog.
Check and change beampath items on the Beam tab.
Select the Configuration for the current accessory and check its details on the
Accessory tab.
NOTE: When Setting up the Instrument, the Instrument command in the Setup menu
also displays the Scan and Instrument Setup dialog, together with further File and
Setup options and the Adjustments Toolbox. Here, when changes are made to
the instrument settings, the Start button becomes the Apply button. Click Apply
to confirm the new instrument setup. The Apply button becomes the Start
button again.
4. To start the scan click Start.
The Scan Progress dialog is displayed.
If a valid background scan is not available, you are prompted to ensure that the
beam path is clear so that a background scan can be taken. When you are ready,
click Scan.

120 . Spectrum
5. If you are using the Sample tab, when data collection is complete, your scan is
transferred to the graph window. The Scan and Instrument Setup dialog and the
Scan Progress dialog are closed.
If you are using the Multiple Sample tab, when data collection is complete the Scan
Progress dialog closes. The Multiple Sample tab remains open so that you can
select, then view the spectra you have collected. If Quality Checks have been
selected, the Multiple Sample table enables you to view Quality Reports. To transfer
your scans to the graph window, Exit (or close) the Scan and instrument Setup
dialog.

NOTE: If you use the

current setup.

tool to start a scan, the scan will immediately start using the

Toolbar
The toolbar tools have the following functions:
Starts the instrument monitoring.
Enables you to open an instrument settings file.
Enables you to save the current setup in an instrument settings file.
Copies the current instrument settings to the clipboard.
Prints the current instrument settings.
Enables you to toggle between the Sample tab and the Multiple Sample tab.
Enables you to change the wavelength range on a dual-range instrument, for
example to change from MIR to NIR.
The icon on the far right of the toolbar shows which sampling accessory is currently
fitted. Many of the accessories also have special tools that appear on the toolbar when
the accessory is installed. For more information see the help topics for the individual
accessories.

Controlling the Instrument . 121

Sam ple tab

The Sample tab enables you to specify the Name for your spectrum and to add a
Description and Comments that will be saved with the spectrum.

Simply type in the text boxes as required.

Preview Scan
Select Preview Scan when you need a monitor mode to prepare a sample, or make
adjustments, and so optimize the scan conditions before initiating data collection. This is
useful with accessories such as the Universal ATR and the HATR, where the force applied
to the sample by the pressure arm can be important.

Toolbar
The toolbar you see depends on your Instrument Access Level and whether you opened
this dialog by choosing Scan on the Instrument menu or Instrument on the Setup
menu. The toolbar tools have the following functions:

Starts the instrument monitoring.

Enables you to open an instrument settings file.
Enables you to save the current setup in an instrument settings file.
Copies the current instrument settings to the clipboard.
Prints the current instrument settings.
Opens the Adjustments Toolbox to enable you to adjust your instrument.
Enables you to toggle between the Sample tab and the Multiple Sample tab.
Enables you to change the wavelength range on a dual-range instrument, for
example to change from MIR to NIR.
The icon on the far right of the toolbar shows which sampling accessory is currently
fitted. Many of the accessories also have special tools that appear on the toolbar when
the accessory is installed. For more information see the help topics for the individual
accessories.

122 . Spectrum

M ultiple Sam ple tab

The Multiple Sample tab enables you to specify the Name(s) for a series of spectra and
to add the Description and Comments that will be saved with each spectrum.

Num ber of Sam ples, Continuous and Preview Scan settings

Number of samples
Enter a Number of Samples, up to a maximum of 100, when you are working on a
specific number of similar samples. The sample table is populated with the correct
number of rows. This is useful with accessories such as the NIR Tablet AutoSampler,
when you can now enter the Carousel number (1 to 4) and Position number (1 to 29)
of each sample.
When the specified number of sample spectra have been collected the instrument stops.
Continuous
When data collection is set up to automatically name your spectra, the Continuous
checkbox is available. Select Continuous when you want to append a new sample row
each time you start a collecting a spectrum. This is useful with accessories such as the
NIR Fiber Optic Probe, where a scan can be started and stopped remotely from the
instrument.
Preview Scan
Select Preview Scan when you need a monitor mode to prepare a sample, or make
adjustments, and so optimize the scan conditions before initiating data collection. This is
useful with accessories such as the Universal ATR and the HATR, where the force applied
to the sample by the pressure arm can be important.

Am ending, or editing, fields in the sam ple table

If you have set up data collection to automatically name your spectra, each sample's
Name field is completed and updated automatically, and you cannot edit them here.
Otherwise simply select each Name field and enter the text required.

Select each Description field and enter the text required.

If Quality Checks have been set, the selected tests are performed as each spectrum
is collected, and a signal light (
,
or
) is placed in the QC column to
indicate its status.

For the NIR Tablet AutoSampler only:

If any of the default Position or Carousel numbers are incorrect, select the field
and enter the number required.

Controlling the Instrument . 123

M anipulating row s in the sam ple table

These buttons are available under the scan table to manipulate rows. Click the right
mouse button to display and select the corresponding command.
Add Row

Adds a new row to the bottom of the scan table. For the NIR
Tablet AutoSampler, the new row's tablet Position is the tablet
Position of the row above + 1.

Insert Row

Adds a new row under the selected row. For the NIR Tablet
AutoSampler the new row's tablet Position is the tablet Position
of the row above + 1.

Delete
Rows

Deletes the selected row, or rows. In Spectrum ES, you cannot

delete rows for which data has been collected.

Move Up

Moves the selected row up one place.

Move Down

Moves the selected row down one place.

NOTE: If you have set up data collection to automatically name your spectra, each
sample's Name field is completed and updated automatically.

Appending com m ents to Sam ples

Select a row, then click the

button to open the Append Comments dialog.

Click the right mouse button to display and select the corresponding Comments...
command.
You may add a new comment, or overwrite any existing comments. In Spectrum ES,
you cannot overwrite comments on rows for which data has been collected.

If you want to add a comment to a number of rows, use Shift+Click to blockhighlight the rows, then open the Append Comments dialog.

View ing one or m ore spectra

To view a spectrum, double-click on its row in the sample table.

To display several spectra, use Shift+Click to block-highlight the rows (or Ctrl+Click
to highlight each row), then click the

button.

Click the right mouse button to display and select the corresponding View
command.

View ing a Quality Report

If Quality Checks have been set, the selected tests are performed as each spectrum is
collected, and a signal light (
,
or
) is placed in the QC column to indicate
its status..

To examine quality check results in detail, select the appropriate scan then click the
button.
Click the right mouse button to display and select the corresponding Quality Report
command.

124 . Spectrum

Toolbar
The toolbar you see depends on your Instrument Access Level and whether you opened
this dialog by choosing Scan on the Instrument menu or Instrument on the Setup
menu. The toolbar tools have the following functions:

Starts the instrument monitoring.

Enables you to open an instrument settings file.
Enables you to save the current setup in an instrument settings file.
Copies the current instrument settings to the clipboard.
Prints the current instrument settings.
Opens the Adjustments Toolbox to enable you to adjust your instrument.
Enables you to toggle between the Sample tab and the Multiple Sample tab.
Enables you to change the wavelength range on a dual-range instrument, for
example to change from MIR to NIR.
The icon on the far right of the toolbar shows which sampling accessory is currently
fitted. Many of the accessories also have special tools that appear on the toolbar when
the accessory is installed. For more information see the help topics for the individual
accessories.

Controlling the Instrument . 125

Scan tab
The Scan tab enables you to specify the scan conditions for your spectrum or
interferogram:

R ange
The scan range you use depends on the area of the spectrum you are interested in.

To set the scan range simply type the Start and End limits.
The Start is the higher wavenumber.

The way the instrument is set up may change the scan range that your instrument can
collect. This will depend on:

the scan speed you have chosen;

the detector fitted to the instrument;

the beamsplitter fitted to the instrument;

any accessory you are using.

Options
You can select the Scan Type:
Type

Use

Background

To collect a background spectrum to be used when ratioing a sample

spectrum.

Interferogram

To display the raw interferogram.

Interleaved

Only available when a Sample Shuttle or NIRA are installed.

Sample

To collect a sample spectrum that is ratioed against the current

background spectrum.

Single beam

To collect a sample spectrum that is not ratioed against a background

spectrum.

126 . Spectrum
and the Units the result is to be displayed in:
Units

When Used

ArbY

Arbitrary ordinate units - a more literal unit single beam spectra than
Energy.

EGY

Energy is traditionally used for background spectra.

%T

% Transmittance is usually used for qualitative analysis because small

peaks are easier to see.

Absorbance is usually used for quantitative analysis because peak

height is proportional to concentration.

%R

% Reflectance is used for the collection of reflectance spectra; the

values generated are identical to %T.

K-M

Kubelka-Munk units are used when collecting diffuse reflectance

spectra.

log (1/R)

Log (1/Reflectance) units are used as an alternative to K-M when

collecting diffuse reflectance spectra.

PAS

PAS units are used when collecting spectra with a photo-acoustic

detector.

In both cases, simply click on

to select the required option.

NOTE: When a Tablet AutoSampler is fitted

Duration
You can select either the number of scans or the amount of time you want the
instrument to scan for.
If you collect too few scans your spectrum may be noisy (have a poor signal-to-noise
ratio) and you may not be able to distinguish peaks from the noise; however collecting
more scans takes extra time.
As a guide, we recommend that you collect 16 scans of your sample and then inspect the
spectrum to see if it is good enough for your purpose.
You may need to increase the number of scans you collect if you are looking for small
peaks, or if you are using an accessory that limits the amount of energy reaching the
detector.

Select either Scan number or Scan time and then type in the box.

NOTE: Scan time is in whole minutes, if you want to scan for less than a minute, select
a number of scans instead.

Controlling the Instrument . 127

Theory
The signal-to-noise ratio of a spectrum is dependant on the time scanned.
The longer the time taken to scan, the higher the signal-to-noise ratio:

therefore for a given scan speed:

this means that increasing the scan speed and correspondingly increasing the number of
scans will not improve the signal-to-noise ratio.
The signal-to-noise ratio improves as more scans are added to the spectrum because
noise occurs at random; the peaks in the noise are therefore not additive as the scans
are accumulated. Real peaks in the spectrum always occur at the same point on the
abscissa, they are therefore additive as the scans accumulate, making them larger than
the noise.

During Scanning
When the Spectrum is actually scanning, the scan tab is still available, however the only
item you can change is the Units text box which enables you to choose the ordinate
units of your spectrum.

Toolbar
The toolbar you see depends on your Instrument Access Level and whether you opened
this dialog by choosing Scan on the Instrument menu or Instrument on the Setup
menu. The toolbar tools have the following functions:

Starts the instrument monitoring.

Enables you to open an instrument settings file.
Enables you to save the current setup in an instrument settings file.
Copies the current instrument settings to the clipboard.
Prints the current instrument settings.
Opens the Adjustments Toolbox to enable you to adjust your instrument.
Enables you to toggle between the Sample tab and the Multiple Sample tab.
Enables you to change the wavelength range on a dual-range instrument, for
example to change from MIR to NIR.
The icon on the far right of the toolbar shows which sampling accessory is currently
fitted. Many of the accessories also have special tools that appear on the toolbar when
the accessory is installed. For more information see the help topics for the individual
accessories.

128 . Spectrum

I nstrum ent tab

The Instrument tab enables you to specify certain instrument settings for the scan. Only
the resolution of the scan is displayed when you enter the tab, but clicking on Advanced
gives access to other options as detailed below.
NOTE: Access to this tab and the Advanced button is determined by your Access Level.
For further information on these options see the individual topics:
Resolution
Data Interval
Apodization
Phase Correction
Scan Speed
Abscissa units (NIR)
2nd Derivative (NIR)

Other Options
The CO2/H2O control enables you to select whether the software will perform CO2/H2O
suppression on the spectrum when it is collected.
If the AVI methane cell has been installed in the filter wheel, switching on AVI will mean
that the software will perform AVI correction on the spectrum when it is collected.
The Advanced section of this tab also includes the ability to set up the Quality Checks you
want to perform on the spectrum as it is being collected.
NOTE: The CO2/H20 suppression, AVI, and Quality Checks functions are not
available in the FIR range
The Look Ahead control enables you to select whether the instrument will operate in
Look Ahead mode or not.

Toolbar
The toolbar you see depends on your Instrument Access Level and whether you opened
this dialog by choosing Scan on the Instrument menu or Instrument on the Setup
menu. The toolbar tools have the following functions:
Starts the instrument monitoring.
Enables you to open an instrument settings file.
Enables you to save the current setup in an instrument settings file.
Copies the current instrument settings to the clipboard.
Prints the current instrument settings.
Opens the Adjustments Toolbox to enable you to adjust your instrument.
Enables you to toggle between the Sample tab and the Multiple Sample tab.

Controlling the Instrument . 129

Enables you to change the wavelength range on a dual-range instrument, for
example to change from MIR to NIR.
The icon on the far right of the toolbar shows which sampling accessory is currently
fitted. Many of the accessories also have special tools that appear on the toolbar when
the accessory is installed. For more information see the help topics for the individual
accessories.

Resolution
Resolution can be set on the Instrument tab.

W hat is resolution?
Spectral resolution describes the ability of the instrument to distinguish between adjacent
features in the spectrum.
NOTE: The smaller the number, the greater the ability to distinguish peaks.

W hat resolution should I use?

The resolution you need to use depends on the physical nature of your sample and the
information you want to extract from the spectrum.
For collecting mid infrared spectra from solid and liquid samples we recommend that you
start by collecting at 8 or 4 cm-1 resolution and if your sample is a gas at 2 cm-1 resolution
or better. Samples of gasses containing very small molecules may need 0.5 cm-1
resolution. If you are going to use Spectrum Search Plus to identify your sample, the
resolution must be good enough for the application to distinguish the peaks in the
spectra.
Higher resolution spectra take longer to collect, when saved take up more disk space and
contains more noise.
If you are collecting ratio spectra, the background spectrum must be of a resolution
equal to or better than the resolution of the sample spectra.
For example, the effect of resolution on an HCl spectrum collected in a gas cell is shown:

130 . Spectrum

Apodization and resolution

Spectral resolution also depends on the apodization function used. In general, at worse
resolutions and low wavenumbers, the optical resolution depends only on interferometer
resolution and apodization.

How can I check that m y resolution is correct ?

1. Collect a spectrum at a low resolution, for example 8 cm-1.
2. Collect a spectrum of the same sample at a higher resolution, for example 4 cm-1.
3. Display the two spectra in overlay mode:
Display the View menu, choose Overlay/Split Display.
A sub-menu is displayed.
Select Overlay mode.
The spectra on the graph are displayed in Overlay mode.
4. Examine the two spectra:
if there is little or no difference between the two spectra, use the lower
resolution to collect your other spectra.
if there are additional peaks in the spectra, collect another spectrum at a higher
resolution, for example 2 cm-1 and repeat steps 3 and 4 again.

Controlling the Instrument . 131

Setting the Data I nterval

The data interval can be set in the Advanced section on the Instrument tab.

W hat is the data interval ?

Spectra and interferograms are stored digitally, that is as a series of data-points
The data interval, or digital resolution, is the abscissa spacing of data points in the
spectrum or interferogram. The unit for the data interval of a spectrum is the
wavenumber (cm-1) and for an interferogram it is the number of interferogram points
collected.

Auto Data Interval

If you select auto, the software automatically sets the data interval based on the
resolution that has been set:
Resolution

Data interval

0.5 - 0.99

0.125

1.0 - 1.99

0.25

2.0 - 3.99

0.5

4.0 - 7.99

1.0

8.0 - 64

2.0

132 . Spectrum

Apodization
Apodization can be set in the Advanced section on the Instrument tab.

W hat is apodization ?
Apodization is a mathematical function that is applied to your spectra as they are
collected.
The true interferogram of a light source is infinite in length. A spectrometer can only
measure a finite part of the interferogram; this means that unwanted oscillations or
sidelobes are produced on either side of narrow bands in the spectrum. Apodization
removes the sidelobes.

W hat does the apodization function do to the spectra ?

The unwanted sidelobes can be reduced by multiplying the interferogram by a function
that decreases steadily as it approaches the maximum path difference.
The apodization function causes some loss of resolution, which may produce line
broadening. However, the overall noise level in the spectrum is reduced (in a similar way
to smoothing).
Five apodization functions are provided. The various apodizing functions give different
compromises between line broadening and reduction of sidelobes on either side of
narrow bands in the spectrum.
None, or Boxcar, is included to enable the highest possible resolution to be obtained.
When it is used, all points in the interferogram are given equal weight. If the resolution is
not better than the smallest line width in the spectrum, sidelobes appear in the baseline
on either side of the peaks.
Three Norton Beer apodization functions are provided (Strong, Medium and Weak) to
give the best compromise between reduction of sidelobes and increase in spectral
bandwidth.
Filler apodization is a very strong apodization function - stronger than the Norton-Beer
Strong function. When Filler apodization is used, sidelobes are reduced more, but line
broadening is greater than when Strong apodization is used.

Controlling the Instrument . 133

The effect of changing the apodization on the spectrum is illustrated by:

No apodization

Weak apodization

Strong apodization

134 . Spectrum

P hase Correction
Phase correction can be set in the Advanced section on the Instrument tab.

W hat is phase correction ?

An ideal interferometer would produce an interferogram that was totally symmetrical
about its center. No interferometer produces an ideal interferogram. Phase correction is
applied to the interferogram to remove the asymmetry.

W hat are the default phase correction settings ?

At resolutions of 2 cm-1 and lower, magnitude phase correction is used by default. At
resolutions better than 2 cm-1 a combination of self and background phase correction is
used by default.

W hat phase correction should I use ?

Self

Suitable for most samples.

The sample spectrum is phase corrected from the sample interferogram
and the background spectrum is phase corrected from the background
interferogram.

Background

If you have a sample that strongly absorbs infrared, background phase

correction may improve the spectrum.
The phase correction routine for the sample spectrum is calculated from
the current background spectrum.

Magnitude

Magnitude phase correction is used, by default, at lower resolutions.

You cannot use magnitude phase correction at resolutions better than 2
cm-1.
The phase correction step in processing the interferogram can be
avoided by calculating the magnitude spectrum. Magnitude spectra are
not affected by phase errors but are subject to ordinate errors in regions
of low transmittance. Note that this method gives photometric errors for
highly absorbing bands. If you use magnitude phase correction, it must
be applied to both the background and sample spectra.

Previous

Enables you to ensure that the same phase correction is used on two
interferograms.

Controlling the Instrument . 135

Scan Speed
Scan speed can be set in the Advanced section on the Instrument tab.

W hat is Scan Speed?

Scan speed, for an interferogram is the rate at which the optical path difference (OPD) is
varied. The OPD is the difference in optical path between the two beams of the
interferometer.

W hat are the default scan speed settings ?

The default scan speeds depend on the type of detector you are using:
Detector Type

Default Scan Speed (cm/s)

TGS

0.2

FIR TGS

1.0

Lithium Tantalate (LiTaO3)

0.2

MCT

1.0

Photoacoustic (PAS)

0.2

INGAAS

1.0

INGAAS (NB)

0.2

These settings are the optimum scan speeds for the detectors to give the best signal-tonoise ratio in a reasonable collection time.

Setting the scan speed

If you are using a TGS or Lithium Tantalate detector, increasing the scan speed will result
in a lower signal-to-noise ratio. The decrease in signal-to-noise ratio is not offset by the
increased number of scans collected, to maintain collection time. A higher scan speed will
therefore result in a lower signal-to-noise ratio.
An MCT detector gives a better signal-to-noise ratio at higher scan speeds in a given
time.

136 . Spectrum

Abscissa units
NOTE: This feature is applicable to spectra collected in the Near Infrared.
Abscissa units can be set in the Advanced section on the Instrument tab.
Near Infrared spectra can be collected in nanometers (nm) or wavenumbers (cm-1).
NOTE: The default Abscissa units are cm-1.
The Start and End Range values on the Scan tab of the instrument Scan and Instrument
Setup dialog are displayed in the selected Abscissa units.

Selecting the Abscissa units.

NOTE: You must be an advanced user to have access to the Advanced section of the
Instrument tab.
1. Select Instrument from the Setup menu.
The Scan and Instrument Setup dialog is displayed.
2. Select the Instrument tab.
3. Click Advanced.
The Advanced section of the Instrument tab is displayed.
4. Select the required units from the Abscissa units drop-down list.
5. Click Apply.
The Apply button changes to Scan.
When spectra are collected in nanometers, one History page of the Status information for
the spectrum shows that the spectrum was collected in wavenumbers and then
converted into nanometers.

Controlling the Instrument . 137

2nd Derivative
NOTE: This feature is applicable to spectra collected in the Near Infrared.
2nd Derivative can be selected in the Advanced section on the Instrument tab.
A 2nd derivative spectrum of a sample can be obtained without the user having to
process the initial spectrum.

W hen should I use Derivative ?

Derivative spectra usually have sharper features than the original spectra. In quantitative
analysis, they are sometimes used to reduce the effects of overlapping bands. You can
use the amplitudes of features in derivative spectra in the same way as peak
absorbances. The elimination of some baseline effects in derivative spectra can be useful
in quantitative methods.
Second-derivative spectra have sharp minima where there are maxima in the original
spectrum and so can be used to identify band positions in complex regions.

How do I autom atically generate a 2nd Derivative spectrum ?

NOTE: You must be an Advanced User to have access to the Advanced section of the
Instrument tab.
1. Select Instrument from the Setup menu.
The Scan and Instrument Setup dialog is displayed.
2. Select the Instrument tab.
3. Click Advanced.
The Advanced section of the Instrument tab is displayed.
4. Select 2nd Derivative.
A tick appears in the check box to show that a 2nd Derivative spectrum is selected.
NOTE: 2nd Derivative is only available when selecting a Sample or Interleaved scan;
the Sample scan must be a ratio and the ordinate units of the Sample or
Interleaved scan must be A or log 1/R.
5. Select the number of points to be used to generate the 2nd Derivative spectrum
from the No. Points drop-down list.
6. Click Apply.
The Apply button changes to Scan.
NOTE: When 2nd Derivative is selected on the Instrument tab the processing of the
spectrum is automatic. It is NOT possible to view or save the spectrum before the
2nd Derivative is applied. If you wish to view and save the original spectrum and
a 2nd Derivative spectrum do not select 2nd Derivative on the Instrument tab.
Instead, collect a spectrum and then select Derivative from the Process menu.

138 . Spectrum

CO 2 / H 2 O Suppression
For the MIR and NIR ranges, CO2/H2O Suppression can be set in the Advanced section
on the Instrument tab. This function is not available for the FIR range.

If you want to suppress CO2/H2O effects by purging the instrument

sample compartment with clean, dry, oil-free nitrogen, refer to the
safety information included in the Getting Started Guide or the User's
Guide shipped with your instrument.
The Getting Started Guide is a printed manual; both the Getting
Started Guide and the User's Guide are included on the Spectrum
Manuals CD (L1050002) as .pdf files.

W hat is CO2/ H2O Suppression ?

All Spectrum software includes an atmospheric correction routine. This routine is more
powerful than simple subtraction, overcoming the following issues:

Non-linearity due to resolution

The measured spectrum is temperature dependent

Lineshape and calibration are affected by J-stop and sample or accessory

W hat does CO2/ H2O Suppression do ?

When CO2/H2O is switched on, the software uses a single reference spectrum derived
from high resolution data and our understanding of the FT instrument to model the
lineshape and then finds the current real instrument parameters by least squares fitting
to the measured spectrum.

AVI Correction
For the MIR and NIR ranges, AVI correction can be set in the Advanced section on the
Instrument tab. This function is not available for the FIR range.
NOTE: AVI correction uses a methane gas cell installed in the filterwheel, and AVI
correction is only available on the Instrument tab if this cell has been fitted.

W hat is AVI correction ?

The objectives of Absolute Virtual Instrument (AVI) correction are:

Consistent performance over time and between instruments

Traceability for all measurements

Although FT-IR spectrometers use a reference laser, the wavenumber calibration and
lineshape are affected by differences in beam divergence and uniformity. This is true for
all FT-IR spectrometers. Differences can occur between instruments, when using
different sampling accessories and when components are changed. AVI allows calibration
and lineshape to be maintained.

Controlling the Instrument . 139

The Absolute Virtual Instrument is an instrument with theoretical performance, such that
the result of measuring a known sample on such an instrument can be predicted. So, if
we measure with a real instrument and calculate the software transform to match the
theoretical result, we can apply this transform to future measurements.
The Absolute Instrument is defined by wavenumber calibration, instrument lineshape and
ordinate accuracy.

W hat does AVI correction do ?

When AVI is switched on, the software measures the current instrument performance
relative to an absolute standard (the methane cell in the filterwheel) and an ideal
lineshape function, and applies a correction. The use of an on-board methane cell means
that it also provides correction for any sampling configuration.
NOTE: AVI correction can only be performed if an AVI calibration has been set up for the
current sampling configuration.

This diagram shows spectra of methane at 4 cm-1 resolution as measured (top) and with
AVI (bottom).

Look Ahead
Look Ahead is a novel system where the spectrometer scans continuously and uses the
properties of the measured spectrum to identify changes corresponding to sample
removal, sample insertion, or sample change, automatically.
This information is then used to identify the scans that are being collected and to:

accumulate sample scans and so decrease scanning time for samples that require
accumulation.

update background scans automatically.

If Look Ahead has been enabled, when you request a sample scan the software checks
back to identify a relevant background spectrum and looks to see whether it has already
collected spectra belonging to the current sample. If it has, then not only is a background
not required, but the number of scans requested is decreased by the number of scans
already collected, so that the scanning time is decreased.

140 . Spectrum

Quality Checks
For the MIR and NIR ranges, Quality Checks can be set in the Advanced section on the
Instrument tab. Quality checks are not available in the FIR range.

W hat are Quality Checks ?

Quality Checking is a tool for less experienced IR users that identifies possible problems
in the spectrum being collected and suggests ways of improving the measurement.

W hat do Quality Checks do ?

Choosing Quality Checks displays a dialog that enables you to select the quality checks
you want to perform.
NOTE: For more information about each individual test, double click on the test in the
dialog.
Then when you collect your spectrum, the selected tests are performed as the data is
collected and the signal lights at the bottom of the Display tab,
current status.

, show the

There are two levels of alert from the Quality Checks:

Caution ( ) - IR Expert has identified a problem that you may want to investigate in
order to improve the quality of the spectra you are collecting.
Warning ( ) - IR Expert has identified a serious problem that you should attempt to
cure before collecting further spectra.
If a problem is identified a report can be displayed that not only alerts you to the
problem, but also explains what the problem means, how it may of occurred and gives
some suggestions on how to stop the problem occurring again.

Controlling the Instrument . 141

Beam tab
The Beam tab enables you view the components in your instrument, and to set up the
beam path through your system. When you hover the mouse over a beam path
component the current setting is displayed. When you click on the component a dialog is
displayed that enables you to change settings for that component. For example, if you
have a Spectrum 400 MIR/NIR instrument, you can change the source, beamsplitter, or
detector as individual elements (rather than by changing all the elements at the same
time as described in Changing Range). If an external accessory is fitted at the beam port
on the right of the instrument, or a Spotlight Imaging System is fitted, the Beam tab
includes addition elements that enable you to redirect the beampath to the accessory you
want to use.

Source

Clicking on either the internal source or the external source (if fitted)
selects that source and the beampath is redrawn. If you have a
dual-range instrument, the Select Source dialog is displayed which
enables you to choose between available sources.

Filter

The Filter dialog enables you to change the filter in the beampath.

Detector

Clicking on a detector selects the detector and changes the beampath.

Beamsplitter

The type of Beamsplitter and its range is displayed when you click on the
beamsplitter. If you have a dual-range instrument, the Select
Beamsplitter dialog is displayed which enables you to choose between
available beamsplitters.

J-stop

The J-stop dialog enables you to change the J-stop image size and the
J-stop wavenumber.

Setting up an item on the beam path

1. Click on the item you want to change.
A component dialog is displayed.
2. Change the setting.
3. Choose OK.
The change is made.
4. Choose Apply to apply the changes.
5. Choose Cancel to close the dialog, or Scan to start scanning.

142 . Spectrum

Toolbar
The toolbar you see depends on your Instrument Access Level and whether you opened
this dialog by choosing Scan on the Instrument menu or Instrument on the Setup
menu. The toolbar tools have the following functions:

Starts the instrument monitoring.

Enables you to open an instrument settings file.
Enables you to save the current setup in an instrument settings file.
Copies the current instrument settings to the clipboard.
Prints the current instrument settings.
Opens the Adjustments Toolbox to enable you to adjust your instrument.
Enables you to toggle between the Sample tab and the Multiple Sample tab.
Enables you to change the wavelength range on a dual-range instrument, for
example to change from MIR to NIR.
The icon on the far right of the toolbar shows which sampling accessory is currently
fitted. Many of the accessories also have special tools that appear on the toolbar when
the accessory is installed. For more information see the help topics for the individual
accessories.

Source
View ing the Current Source
1. From the Setup menu select Instrument.
The Scan and Instrument Setup dialog is displayed.
2. Choose the Beam tab.
The Beam tab is displayed.
3. Hover your mouse pointer over the current source on the Beam tab.
The type of source fitted is displayed.

Changing the Source (Dual Source instrum ents only)

1. From the Setup menu select Instrument.
The Scan and Instrument Setup dialog is displayed.
2. Choose the Beam tab.
The Beam tab is displayed.
3. To change the source, click on it.
The Select Source dialog is displayed.

Controlling the Instrument . 143

4. Select the required source.

5. Click OK.

Filterw heel
The introduction of a filter enables you to optimize the system for a particular
wavenumber range. For example, a filter can be used to enable the study of weakly
absorbing samples. Reducing the wavenumber range enables more energy in the region
of interest to reach the detector without saturating it. Thus, the signal-to-noise is
improved in the specified wavenumber range.
A filterwheel enables various filters and attenuators to be positioned in the beam. It
contains the polystyrene and Schott NG11 glass filters used for validation procedures. It
is also where the methane cell is installed if your instrument has the AVI correction
system.
The number and type of filters fitted in the filterwheel depends on the type and
configuration of your instrument.

Installing new filters

Instructions for fitting new or replacement filters can be found in your instrument's User's
Guide.
NOTE: You can fit new or replacement filters into the instrument filterwheel but not into
the Right Hand Side NIRA filterwheel.
After you manually install a new filter in the filterwheel update your Spectrum
configuration so that the software is aware of the new filter:
1. Start the program \Program Files\PerkinElmer\ServiceIR\[Link]
The Spectrum - Install Filter Utility dialog is displayed.
2. In the Install Filter Sets section, select APV or AVI to install the filters into their
default locations.
If you make a mistake, select None to clear the system.
OR
If you have installed the filters into different positions than those automatically
selected, you can individually select the filter in each position by using the drop
down lists in the Individual Filters section.
3. When you have set up the filters in their correct locations, choose Install to make
the changes to the configuration for your instrument.

144 . Spectrum
4. Click Close to exit this dialog.

Detectors
W hat detector should I use ?
The choice of detector depends upon the wavenumber range you want to study and the
sensitivity you require. The type of detector selected is displayed on the Beam tab of the
Scan and Instrument Setup dialog.

W hat detectors are available ?

LiTaO3 (Lithium Tantalate) and TGS (Deuterated TriGlycerine Sulfate) are pyroelectric
detectors, they do not have to be cooled. A TGS detector is more sensitive and hence has
a higher signal-to-noise ratio than a LiTaO3 detector. TGS detectors are the most
commonly used and are suitable for most routine applications.
MCT (Mercury Cadmium Telluride) detectors have to be cooled with liquid nitrogen. They
have faster response times and greater sensitivity than TGS detectors.
A wide band MCT detector is approximately ten times more sensitive than a TGS
detector, and a narrow band MCT detector is approximately three times more sensitive
than a wide band MCT detector.
PAS (photacoustic). This type of detector is fitted to the socket in the sample
compartment of the instrument.
The instrument has two positions for detectors. It can be fitted with an MCT detector in
the rear position and, at the same time, either a TGS or LiTaO3 detector in the front
position.
Detector

Wavenumber range (cm-1)

MIR TGS

15 000 370

NIR TGS

15 000 1250

FIR TGS

720 30

Mid infrared TGS with KBr window

10 000 370

Mid infrared TGS with CsI window

10 000 220

INGAAS

10 000 4000

Wide band MCT

10 000 450

Medium band MCT

10 000 580

Narrow band MCT

10 000 700

Photoacoustic (PAS)

4000 400

Lithium Tantalate

10 000 370

Controlling the Instrument . 145

View ing the Current Detector

1. From the Setup menu select Instrument.
The Scan and Instrument Setup dialog is displayed.
2. Choose the Beam tab.
The Beam tab is displayed.
3. Move your mouse pointer over the current detector on the Beam tab.
The type of detector fitted is displayed.
4. Choose Cancel to close the dialog or Scan to start scanning.

Changing the Detector

1. From the Setup menu select Instrument.
The Scan and Instrument Setup dialog is displayed.
2. Choose the Beam tab.
The Beam tab is displayed.
3. To select a detector, click on it.
The path from the beamsplitter to the detector is reset on the screen but the
detector is not selected until you choose Apply on the Scan and Instrument Setup
dialog.
4. Click Apply.

146 . Spectrum

Beam splitters
W hat is a beam splitter ?
The beamsplitter is part of the interferometer in your Spectrum. A beamsplitter is a plate
with approximately equal transmittance and reflectance; it is used to generate and
recombine the two beams of the interferometer.

W hat beam splitter should I use ?

The choice of beamsplitter material depends upon the wavenumber range you want to
study. Four different types of beamsplitter can be fitted to your instrument. Their
operating ranges are listed below:
Beamsplitter

Range (cm-1)

CaF2

15000 1250

Optimized KBr

7800 400

KBr

7000 400

CsI

5000 220

FIR Grid

700 - 30

View ing the beam splitter fitted to your instrum ent

1. From the Setup menu select Instrument.
The Scan and Instrument Setup dialog is displayed.
2. Choose the Beam tab.
The Beam tab is displayed.
3. Click on the beamsplitter.
The Beamsplitter dialog is displayed.

Changing the beam splitter (Spectrum One and Spectrum 100)

You can remove the beamsplitter and replace it with one of the same type very easily.
KBr and CsI beamsplitters are hygroscopic, and must be stored in desiccated boxes.
Instructions on how to change the beamsplitter are given in the User's Guide supplied
with your instrument.

Changing the beam splitter (Spectrum 400 only)

1. From the Setup menu select Instrument.
The Scan and Instrument Setup dialog is displayed.
2. Choose the Beam tab.
The Beam tab is displayed.
3. Click on the beamsplitter.
The Select Beamsplitter dialog is displayed.

Controlling the Instrument . 147

4. Select the required beamsplitter and then click OK.

J-Stop Dialog
W hat is a J-Stop?
The J-stop (Jacquinot-stop) is a software controlled iris in the beam path of the
spectrometer. The J-stop aperture defines the angle at which rays pass through the
interferometer and thus restricts the beam divergence to the maximum acceptable for
the required resolution.
Selecting the J-Stop Image Size and J-Stop Wavenumber
When you choose the interferometer resolution the size of the J-stop aperture (J-stop
image size) is updated to give the required interferometer resolution at all wavenumbers
up to the current J-stop wavenumber. You can override the automatic J-stop setting by
specifying the J-stop image size. A larger value increases the throughput of the
instrument, and improves the signal-to-noise ratio, at the expense of the highest
wavenumber at which the current interferometer resolution can be achieved. A smaller
value reduces the throughput. There is no improvement in interferometer resolution.
If the energy throughput is low, performance will be improved by setting the J-stop
wavenumber to the lowest value of interest, for example 2000 cm-1 rather than
4000 cm-1. This results in a larger J-stop image size without loss of interferometer
resolution up to 2000 cm-1.
1. Display the Setup menu and choose Instrument.
The Scan and Instrument Setup dialog is displayed.
2. Choose the Beam tab.
The Beam tab is displayed.

3. Click on the J-stop.

The J-Stop dialog is displayed.
4. Enter the required value in the Size or Wavenumber text box.
The limits for the image size are shown on the dialog.
When you change the J-stop Image size the J-stop wavenumber is changed
accordingly.
The default wavenumber is the upper limit of the beamsplitter. If the beamsplitter is
changed, the J-stop wavenumber is reset to the upper wavenumber limit of the new
beamsplitter.

148 . Spectrum
5. Choose OK.
The J-Stop dialog closes.
6. Choose Apply.
The change is applied.
7. Choose Cancel to close the dialog or Scan to start scanning.

Accessory tab
The accessory tab enables you to:

View the accessory description information that was automatically determined when
the accessory was installed;

Specify any accessory description information that could not be determined

automatically;

Manually load a sampling configuration that can specify the additional accessory
description information, as discussed above, and can specify new accessory scan
defaults.

Selecting a Configuration

If you have created your own configurations for the current accessory, you can use
the User defined drop down list to select the configuration you want to use.

Selecting additional description inform ation

The Details section of the dialog displays any information about the accessory that is
determined automatically when the accessory is installed, and for some accessories it
enables you to specify any further accessory description information that could not be
determined automatically but that you may want to record. For instance, the type of
sampling routine used for diffuse reflectance, that is whether you are using a micro cup,
macro cup, abrasive stick or abrasive pad.
The options available will depend on the accessory fitted, for more information see the
topic for the individual accessory.

Controlling the Instrument . 149

Toolbar
The toolbar you see depends on your Instrument Access Level and whether you opened
this dialog by choosing Scan on the Instrument menu or Instrument on the Setup
menu. The toolbar tools have the following functions:

Starts the instrument monitoring.

Enables you to open an instrument settings file.
Enables you to save the current setup in an instrument settings file.
Copies the current instrument settings to the clipboard.
Prints the current instrument settings.
Opens the Adjustments Toolbox to enable you to adjust your instrument.
Enables you to toggle between the Sample tab and the Multiple Sample tab.
Enables you to change the wavelength range on a dual-range instrument, for
example to change from MIR to NIR.
The icon on the far right of the toolbar shows which sampling accessory is currently
fitted. Many of the accessories also have special tools that appear on the toolbar when
the accessory is installed. For more information see the help topics for the individual
accessories.

Ranges tab
The Ranges tab enables you to view the wavenumber ranges over which the currently
selected source, beamsplitter and detector operate. The optimum scan range is
identified. This is the operating range common to the source, beamsplitter and detector
that is within the scan range limits you have set.
The wavenumber ranges shown for the currently selected source, beamsplitter and
detector are updated when you set a new beam path on the Beam tab.

Source Operating Ranges

Source

Range / cm-1

Near Infrared

15000 2000

Mid Infrared

8000 30

150 . Spectrum

Beam splitter Operating R anges

Beamsplitter

Range / cm-1

CaF2

15000 1250

Optimized KBr

7800 400

CsI

5000 220

FIR Grid

700 30

Detector Operating Ranges

Detector

Range / cm-1

MIR TGS

15000 370

NIR TGS

15000 1250

FIR TGS

720 30

Mid infrared TGS with KBr window

10000 370

Mid infrared TGS with CsI window

10000 220

INGAAS

10000 4000

Wide band MCT

10000 450

Medium band MCT

10000 580

Narrow band MCT

10000 700

Photoacoustic (PAS)

4000 400

Lithium Tantalate

10000 370

Controlling the Instrument . 151

Toolbar
The toolbar you see depends on your Instrument Access Level and whether you opened
this dialog by choosing Scan on the Instrument menu or Instrument on the Setup menu.
The toolbar tools have the following functions:

Starts the instrument monitoring.

Enables you to open an instrument settings file.
Enables you to save the current setup in an instrument settings file.
Copies the current instrument settings to the clipboard.
Prints the current instrument settings.
Opens the Adjustments Toolbox to enable you to adjust your instrument.
Enables you to toggle between the Sample tab and the Multiple Sample tab.
Enables you to change the wavelength range on a dual-range instrument, for
example to change from MIR to NIR.
The icon on the far right of the toolbar shows which sampling accessory is currently
fitted. Many of the accessories also have special tools that appear on the toolbar when
the accessory is installed. For more information see the help topics for the individual
accessories.

Changing Range (Spectrum 400 only)

You can change the instrument range from, for example MIR to NIR, using the Spectrum
software.
For an MIR/NIR instrument, changing ranges requires the instrument to change the
detector, beamsplitter and detector in concert.
For an MIR/FIR instrument, changing ranges requires the instrument to change the
beamsplitter and detector in concert, and requires you to change the windows in the
sample compartment.
NOTE: Depending on the beamsplitters and detectors fitted, the instrument requires
some time to equilibrate after changing ranges. Do not insert or remove
accessories while the instrument is changing range.
1. From the Setup menu select Instrument.
OR

Click

The Scan and Instrument Setup dialog is displayed.

The current range is displayed at the bottom left of the dialog.

152 . Spectrum

to change range immediately.

2. Click
OR

Click the small triangle next to the button to display a range selector
then select the range required (the current range is marked by a bullet).

, and

A confirmation dialog is displayed.

3. Click Yes.
The range change is monitored by messages and a progress bar at the bottom left
of the Scan and Instrument Setup dialog.
For example, changing to the NIR range displays NIR changing, then NIR initializing,
then NIR stabilizing, and finally NIR Ready.
If you are changing to, or from, the FIR range exchange the windows in the sample
compartment when prompted.
NOTE: You can also change the source, beamsplitter, and detector elements
independently in the Scan and Instrument Setup dialog using the Beam tab.
The Ranges tab displays a graphic that shows the Optimum Range for the currently
selected elements.

Changing w indow s
The Spectrum 400 MIR/FIR instrument is supplied with a set of KBr sample compartment
windows (for the MIR range) and a set of PE windows (for the FIR range). You can
exchange these windows, using the screwdriver provided, without opening the
instrument cover.

CAUTION

To avoid humidity damage, exchange windows quickly. NEVER leave

window apertures open to atmosphere.
KBr and CsI windows must be kept in a properly desiccated
compartment or box. For example, make sure that the humidity
indicator in the spare window compartment is completely blue and that
the compartment lid is fully closed. Do not open this compartment
except for periodic checks of the desiccant.

Controlling the Instrument . 153

Scan Progress
The Scan Progress dialog appears when the Spectrum starts scanning, and displays the
spectrum or interferogram you are collecting.
If you are using the Multiple Sample tab, you can select the Sample ID for the next scan
using the

buttons.

You can review your scan(s) within the Scan Progress dialog:

Change the scale by zooming in using a grow box

pan up and down and from side to side using the mouse to drag the x axis from left
to right, or the y axis from top to bottom.

Double-click on any point in the display to create an anchor. Use the drag the
anchor to pan graphs in any direction in the X-Y plane. Or, use the anchor as the
fixed point around which you can drag the abscissa (drag right to expand, drag left
to contract) or ordinate (drag up to expand, drag down to contract) scales.

Hover your mouse pointer over any point in a scan to display the scan Name, and
the abscissa and ordinate values for that point.

Change the scale and appearance of graphs displayed in Scan Progress dialog using
toolbar buttons:
Displays at full scale.
Autoranges the abscissa scale.
Autoranges the ordinate scale.
Displays the vertical cursor, and its position on the abscissa scale. The
information panel under the graph display shows the ordinate value for each
scan crossed by the vertical cursor.
Display at the previous range.
Format graphs. Displays the Graph Properties dialog, which includes General
(Title, Description), Axes, Appearance, and Advanced (Axis, Tool Tip, Data
Point and Interpolation options) tabs.
Add text labels. Displays the Label Properties dialog, which allows you to add
and format text and insert the Current Date and Time. To move a label,
select and drag it to the required position. Right click to remove a label, or
modify its properties.
Add peak labels. Displays the Peak Labels dialog. The Settings tab allows you
specify which peaks are to be labeled; the Format tab allows you to format
the label text. Use this button to toggle the labels on and off.
Toggle between Absorbance and Transmittance.
Toggle between Overlay and Split display.

154 . Spectrum

Stopping scanning

To stop scanning, click Halt.

Collecting a Background Spectrum

The Scan Progress dialog prompts you to collect a new background spectrum if none has
been collected; you have changed the sampling accessory; you have applied an
instrument setting that invalidates the background scan (higher resolution, apodization,
phase correction or scan speed); or the time or number of samples between backgrounds
(see Data Collection Setup) has been exceeded.

To manually collect a new background spectrum that will not be displayed, click
Background

Transferring your scans to the graph w indow

When you are ready to transfer your scans to the graph window, and close the Scan
Progress dialog, click Exit.

Scan Background
When collecting data to generate sample spectra, a first step is to collect a background
spectrum from the instrument with no sample present.
If no valid background spectrum is available, the Scan Progress dialog prompts Ensure
beampath is clear, press [Scan] to continue.

When the beampath is clear, click Scan.

A background spectrum is collected, but is not displayed.

NOTE: The Scan Progress dialog does not prompt for a new background spectrum unless
none has been collected; you have changed the sampling accessory; you have
applied an instrument setting that invalidates the background scan (higher
resolution, apodization, phase correction or scan speed); or the time or number
of samples between backgrounds (see Data Collection Setup) has been exceeded.

To collect a background spectrum that can be displayed and stored: On the Scan
tab, in the Options section, set the Scan type to Background. After you have
collected the background scan, reset the Scan type to Sample.

To manually collect a new background spectrum that will not be displayed, click
Scan Background

Halt
The Halt command on the instrument menu enables you to stop a scan.

Controlling the Instrument . 155

M onitoring
You can continuously monitor sample or single beam spectra, interferograms, or the total
throughput of infrared energy, while making adjustments to an accessory. When
monitoring is in progress, the data is displayed on the screen and continually updated.

Energy

Monitoring energy enables you to monitor the level of infrared energy

reaching the detector in your instrument. This is useful for optimizing
the alignment of accessories in the sample compartment. The horizontal
bars and corresponding values represent the current energy level and
the maximum level detected since monitoring began. If the bars reach
the edge of the screen, the scale is automatically reset so that the bars
are half the width of the screen.

Sample

When a sample spectrum is monitored, the sample spectrum is ratioed

against the current background spectrum in order to eliminate the
instrument response and features introduced into sample spectra by
atmospheric absorption, or possibly by using a cell or sampling
accessory.

Single Beam A single-beam spectrum is monitored without ratioing against a

background spectrum. This is useful when purging, as you can see the
water and C02 gradually being removed.
Interferogram The maximum data range for interferograms is determined by the
current resolution setting and interferogram sidedness.

156 . Spectrum

M onitor tab
The Monitor tab enables you to change the type, range and units of monitoring, set the
number of co-added scans before the spectrum is displayed and start monitoring.
Range

Enables you to set the range of monitoring:

For a spectrum, the start and end of the wavenumber range, by
choosing Full Range or typing the values.
For an interferogram, the portion of interferogram monitored.

Default and Full

If you choose Single Beam or Sample spectrum monitoring,

current range values are displayed in the From and To text boxes.
If you choose Default Range the range is set to the optimum
operating range for the detector, source and beamsplitter
combination and the scan speed chosen. If you choose Full Range
the range is set to the maximum range that can be scanned by the
instrument at the scan speed chosen.
When you monitor an Interferogram, if you choose Default Range
the range is set to a range around the centerburst of -500 to 500).
When you monitor an interferogram, if you choose Full Range the
range is set to the full width of the interferogram collected at the
resolution chosen.

Co-added Scans

Enables you to set the number of scans co-added before the

spectrum is updated.

Units

If you are monitoring a spectrum, enables you to set the type of

units.

If you change the details on this tab and then exit the dialog, the tab will return to
its default settings the next time you enter. If you want to keep a change, make the
change and then choose Save.

NOTE: The Monitor tab is not displayed if you are monitoring Energy.

Controlling the Instrument . 157

Display tab
While you are monitoring a spectrum or interferogram you can:

change the scale by zooming in using a grow box

pan up and down and from side to side using the mouse to drag the x axis from left
to right, or the y axis from top to bottom.

change the scale and appearance of graphs displayed using toolbar buttons:
Displays at full scale.
Autoranges the abscissa scale.
Autoranges the ordinate scale.
Displays the vertical cursor, and its position on the abscissa scale. The
information panel under the graph display shows the ordinate value for each
scan crossed by the vertical cursor.
Display at the previous range.
Format graphs. Displays the Graph Properties dialog, which includes General
(Title, Description), Axes, Appearance, and Advanced (Axis, Tool Tip, Data
Point and Interpolation options) tabs.
Add text labels. Displays the Label Properties dialog, which allows you to add
and format text and insert the Current Date and Time. To move a label,
select and drag it to the required position. Right click to remove a label, or
modify its properties.
Add peak labels. Displays the Peak Labels dialog. The Settings tab allows you
specify which peaks are to be labeled; the Format tab allows you to format
the label text. Use this button to toggle the labels on and off.
Toggle between Absorbance and Transmittance.
Toggle between Overlay and Split display.

Stopping m onitoring

Choose Stop or click on

, to display the Scan and Instrument Setup dialog.

158 . Spectrum

Force Gauge
If the currently installed accessory is an HATR or Universal ATR with the pressure arm
fitted, the dialog will include a Force Gauge readout, which will show the force being
applied by the arm. The green bar will flash red as a warning if too much force is being
applied.
CAUTION: Where an over-pressure clutch is fitted to the UATR pressure arm, it
significantly reduces the risk of crystal breakage, but should never slip in
day-to-day use.
In particular, DO NOT use the over-pressure clutch as a substitute for
Preview Scan function and the Instrument Monitoring Force Gauge. The
pressure applied by the force arm when the clutch slips is rather greater than
should be necessary to achieve optimum transmission of between 40% and
&0%, and sufficient for the Force Gauge to have generated a red
overpressure warning.

M onitoring toolbar

Stops monitoring and displays the Scan and Instrument Setup dialog.
Starts to monitor the energy reaching the detector.
Starts to monitor a sample spectrum (a valid background spectrum must have
been collected).
Starts to monitor a single-beam spectrum.
Starts to monitor an interferogram spectrum.
Displays the format view toolbar

Controlling the Instrument . 159

Controlling Accessories
Controlling Accessories
The icon in the top right hand corner of the Scan and Instrument Setup dialog shows
which accessory is installed.
As a different accessory is installed, this icon will change to that of the new accessory
and the toolbar may change to display new tools associated with that accessory.
The Accessory tab will also be updated to show the details and options for that
accessory.

Standard Sample Slide (useful in all wavelength ranges)

Sample Shuttle (useful in all wavelength ranges)
HATR
Universal ATR
Diffuse Reflectance (useful in all wavelength ranges)
NIRA (Near Infrared Reflectance Accessory)
NIR Tablet Autosampler (Near Infrared Tablet Autosampler)
NIR Fiber Optic Probe (Near Infrared Fiber Potic Probe)
Liquid Sipper

160 . Spectrum

Sam ple Shuttle

The sample shuttle provides a means of positioning either of two sample slides in the
optical beam of the spectrometer. The main function of the sample shuttle is to enable
interleaved operation, where the sample is moved smoothly in and out of the beam as
the instrument accumulates sample and background scans respectively. The use of an
interleaved scanning mode enables you to ratio the sample spectrum against a
background that is recorded almost simultaneously, this eliminates residual atmospheric
absorptions from the final spectrum. We recommend that the shuttle is used for
far infrared spectroscopy.
An alternative use of the shuttle is to enable an accessory to be switched in and out of
the beam without disturbing the alignment of the accessory. The sample shuttle
accommodates most PerkinElmer sampling accessories.

M odes of Operation of the Sam ple Shuttle

When a sample shuttle is installed in the Spectrum, the Scan and Instrument Setup
dialog enables two modes of operation:

Manual - you change the position of the shuttle by clicking on the

toolbar.

tool on the

Automatic - the shuttle moves between the sample and background positions as sample
and background spectra respectively are collected. The series of cycles of background
and sample spectra is enabled when you select Interleaved as the Scan Type on the
Scan tab.
There is also a drop down list that enables you to identify the Sampling accessory being
used so that this information can be stored with the spectrum.

Controlling the Instrument . 161

HATR
When a Horizontal ATR accessory is installed in the Spectrum, the Accessory tab of the
Scan and Instrument Setup dialog reports:

The type of crystal

The type of plate (flat or trough)

The angle of the crystal

tool that enables you to perform a contamination check to ensure

There is also a
that the crystal is clean before you collect a spectrum.
NOTE: The first time you install the accessory, you will have the option of performing the
Shipping Checks.

Preview Scan
Both the Sample tab and the Multiple sample tab include the Preview Scan option. When
this option is selected, after you click Start, the Scan Progress dialog opens in a monitor
mode that can help you optimize the scan conditions.

Tutorial
A tutorial about using the HATR accessory is on the Spectrum Multimedia CD.

162 . Spectrum

Universal ATR
Accessory tab
When a Universal ATR accessory is installed in the Spectrum, the Accessory tab of the
Scan and Instrument Setup dialog reports:

The type of crystal

The number of bounces

There is a drop down list that enables you to identify any UATR Option being used so
that this information can be stored with the spectrum.

tool that enables you to perform a contamination check to ensure

There is also a
that the crystal is clean before you collect a spectrum.
NOTE: The first time you install the accessory, you will have the option of performing the
Shipping Checks.

NOTE: A standard calibration film may be damaged by the UATR pressure arm.

Preview Scan
Both the Sample tab and the Multiple sample tab include the Preview Scan option. When
this option is selected, after you click Start, the Scan Progress dialog opens in a monitor
mode that can help you optimize the scan conditions.
For example, you could use Preview Scan (in conjunction with the Force Gauge
displayed in the Scan Progress dialog), while adjusting the pressure arm to achieve
transmission of between 30% and 70% (without applying a force that could damage the
crystal).
CAUTION: Where an over-pressure clutch is fitted to the UATR pressure arm, it
significantly reduces the risk of crystal breakage, but should never slip in
day-to-day use.
In particular, DO NOT use the over-pressure clutch as a substitute for
Preview Scan function and the Instrument Monitoring Force Gauge. The
pressure applied by the force arm when the clutch slips is rather greater than
should be necessary to achieve optimum transmission of between 40% and
&0%, and sufficient for the Force Gauge to have generated a red
overpressure warning.

Tutorial and Further Inform ation

A tutorial about using the Universal ATR accessory is on the Spectrum Multimedia CD. For
further information, see the Universal ATR User's Guide provided with the accessory.

Controlling the Instrument . 163

Diffuse Reflectance
When a Diffuse Reflectance accessory is installed in the Spectrum, the Accessory tab of
the Scan and Instrument Setup provides a drop down list that enables you to identify the
Sampling type being used so that this information can be stored with the spectrum.
The toolbar also provides the following tools:
Tool

Function
Nudges the sample holder upwards - used for manually focusing the beam.
Nudges the sample holder downwards - used for manually focusing the beam.
Automatically focuses the beam on the sample holder.

NOTE: For more information about using the Diffuse Reflectance Accessory, see the
tutorial on the Spectrum Multimedia CD.

NOTE: The first time you install the accessory, you will have the option of performing the
Shipping Checks.

164 . Spectrum

NI RA
The NIRA (Near Infrared Reflectance Accessory) is used for collecting diffuse reflectance
spectra of solids, liquids and powders. The sample is placed on a sapphire window
located on the top of the accessory. The infrared beam from the spectrometer enters the
NIRA through the port on the left-hand side of the accessory and is focused and directed
onto the sample. The beam diffusely reflected from the sample is then imaged onto the
detector.
For many types of sample, no preparation is required. For example, a piece of textile or a
glass sample vial containing a powder to be analyzed, can be placed directly on the
sapphire window to obtain a spectrum.
The NIRA has two modes of operation: manual and interleaved.
In manual mode you collect sample and background spectra separately. There are two
options available for collecting sample and background scans:

Upper the scan is taken in the upper position. A background scan in the upper
position is useful if, for example, you want to take a background of a vial containing
a background reference material to ratio against a vial containing your sample.

Lower the scan is taken in the lower position.

The default position for sample and background scans is set in the Accessory
Configuration dialog, which can be accessed by Advanced users.
In interleaved mode the spectrometer determines when to collect background scans.
Interleaved mode enables sample and background scans to be collected together. If you
specify a relatively small number of sample scans, the spectrometer collects that number
of background scans, followed by sample scans. For a larger number of scans, groups of
background scans alternate with groups of sample scans.

NIR A Sam ple Spinner

The NIRA Sample Spinner is an optional accessory that is designed to provide faster and
more representative sampling of non-homogeneous samples such as wheat and blended
feeds. Using the NIRA Sample Spinner allows faster, easier analysis and reduces effects
such as sample orientation, inhomogeneity and re-pack.
The NIRA Sample Spinner locates on top of the NIRA and receives power via a connector
which is plugged into a socket on the NIRA. A sampling dish placed on the carrier ring of
the Sample Spinner is located directly above the sample window.
To scan using the Sample Spinner, select the Spinner check box on the Scan tab of the
Scan and Instrument Setup dialog. The Sample Spinner will start to rotate when scanning
commences.
NOTE: To exploit the improved reproducibility offered by using the spinner, it is
recommended to scan for at least one minute.
For more information on using the NIRA Sample Spinner see the Near Infrared

Reflectance Accessory User's Guide.

Controlling the Instrument . 165

NIR A Liquids Sam pling Accessory

The optional Liquids Sampling Accessory facilitates the sampling of liquids and gels. The
Liquids Sampling Accessory comprises a flat, clear glass sample dish into which the
sample is placed, and a machined aluminium diffuse reflector which is pressed into the
sample.
For more information on using the NIRA Liquids Sampling Accessory see the Near

Infrared Reflectance Accessory User's Guide.

R ight Hand Side NIR A

The right hand side NIRA is an optional accessory that can be used with the
Spectrum 400 MIR/NIR instrument.

166 . Spectrum

NI R Tablet Autosam pler

The NIR Tablet Autosampler is used to collect spectra from a batch of up to 30 tablets.
The technique is fast, automated and non-destructive. Custom tablet holders that are
unique to a particular tablet shape and size ensure that measurements are reproducible.
For further information on making the tablet holders see the NIR Tablet Autosampler
User's Guide provided with the accessory.
By default, the Tablet Autosampler collects diffuse reflectance spectra in the same
manner as a NIRA. However, the external detector allows the accessory to be used in
transmission mode.
Set up the Tablet Autosampler in the Scan and Instrument Setup dialog:

Scan tab settings

If you are using the Sample tab, select the Position of the sample from the drop-down
list and position the sample at the correspondingly numbered position on the sample
carousel. This setting is not available if you use the Multiple sample tab, where you set
the tablet Position and Carousel number for each scan in the sample table.
Select the appropriate orientation for the accessory mirror. In the upper orientation, light
is directed to the sample position. In the lower orientation, light is diverted so that a
background spectrum can be collected for diffuse reflectance spectra.

M ultiple sam ple tab settings

The Multiple sample tab allows you to collect a series of spectra from a number of
samples. When the Tablet Autosampler is installed, the Position field on the Scan tab is
not available; set the tablet Position and Carousel number for each scan in the sample
table.
1. Enter the total number of scans needed.
The required number of rows is displayed.
NOTE: The alternative Continuous setting is used with the NIR Fiber Optic Probe; the
Preview Scan setting is used with the Universal ATR.
2. If you have set up data collection to automatically name your scans, each row's
name field is completed and updated automatically, and you cannot edit them here.
Otherwise, for each row, complete the Name field.
3. For each row, enter a description of the scan.
This description is optional.
4. Enter the Position of each sample (the number of the corresponding position on
the sample carousel), and the number of the Carousel used.
NOTE: You can also append comments to scans, and reorder, insert and delete scans:
see Multiple sample tab.
5. When you have set up your samples, click Start.

Controlling the Instrument . 167

If Quality Checks have been set, the selected tests are performed as each spectrum is
collected, and a signal light (
,
or
) is placed in the QC column to indicate
its status..

To examine quality check results in detail, select the appropriate scan then click the
button.
Click the right mouse button to display and select the corresponding Quality Report
command.

Accessory Page settings

When the NIR Tablet Autosampler is installed, the Transmission and Gain must also be
set on the Accessory page of the Scan and Instrument Setup dialog.
Transmission

Select Transmission mode On or Off. By default Transmission is set

to Off.

Gain

Gain is only available when Transmission is set to On. Select High,

Low or Auto from the drop-down list.

Gain
The detector signal is amplified before being digitized. The gain of the amplifier can be
changed to make sure that the analog to digital converter is not overloaded by highly
transmitting samples, and that it is used efficiently for strongly absorbing samples.
NOTE: If the Transmission and Gain are set within the AssureID software, this overrides
the settings made on the Scan and Instrument Setup dialog.

168 . Spectrum

NI R Fiber Optic Probe

The NIR Fiber Optic Probe allows you to collect Near Infrared reflectance spectra from
bulk powders. It includes a trigger and display that allows a scan to be started (and
stopped, if necessary) remotely.
NOTE: If the probe does not have a display or trigger, each scan must be controlled
from the instrument.

Using the Fiber Optic Probe to collect spectra from m ultiple sam ples
1. Open the Scan and Instrument Setup dialog, and click the Switch
display the Multiple Sample tab.

button to

2. Select Continuous.
NOTE: The alternative Number of Scans setting is used with the NIR Tablet
Autosampler; the Preview Scan setting is used with the Universal ATR.
Each time a new scan is started, either from this dialog or by using the Fiber Optic
Probe trigger, a new row is added.
3. If you have set up data collection to automatically name your scans, each row's
name field is completed and updated automatically, and you cannot edit them here.
Otherwise, for each row, complete the Name field.
4. For each row, enter a description of the scan.
This description is optional.
NOTE: You can also append comments to scans, and reorder, insert and delete scans:
see Multiple Sample tab.
If Quality Checks have been set, the selected tests are performed as each spectrum is
collected, and a signal light (
,
or
) is placed in the QC column to indicate
its status..

To examine quality check results in detail, select the appropriate scan then click the
button.
Click the right mouse button to display and select the corresponding Quality Report
command.

Controlling the Instrument . 169

Accessory tab settings

When a NIR Fiber Optic Probe is installed, the Details section of this tab reports whether
the Fiber Probe includes a display, whether or not it is triggered, and - for the NIR Fiber
Optic Probe - its serial number. The NIR Fiber Optic Probe is serialized for ATEX
compliance.
When you install an NIR Fiber Optic Probe, the default Detector Channel is 2, and Gain
setting is High.

Detector Channel 1 is present for compatibility with earlier fiber optic probe designs.
When an NIR Fiber Optic Probe is installed, Detector Channel 1 is not used.

The Low Gain Setting, which is only available for Detector Channel 2, is a lower
energy setting suitable for transmission probes. Previously, this lower energy setting
was obtained by changing a resistor in the optical interface module.

Changing the length of the fiber optic cable

The fiber optic cable, which is available in a number of lengths, is factory fitted and
calibrated. You cannot either shorten or lengthen this cable, or make repairs if it is
damaged. Contact your PerkinElmer Service Representative for advice.

Tutorial and Further Inform ation

A tutorial about using the NIR Fiber Optic Probe accessory is provided on the Spectrum
Multimedia CD. For further information, see the NIR Fiber Optic Probe User's Guide
provided with the accessory.
See Also: Fiber Probe Display

170 . Spectrum

Liquid Sipper
When a Liquid Sipper accessory is installed in the Spectrum, the Accessory tab of the
Scan and Instrument Setup provides drop down lists that enable you to identify the
Material and Pathlength of the flow cell being used so that this information can be
stored with the spectrum.
The toolbar also provides the following tools:
Tool

Function
Starts the sample procedure set up in the sampling configuration.
Starts the flush procedure set up in the sampling configuration.
Moves the flow cell from its current position (as shown on the icon) to the
alternative position. When the cell moves the icon changes to show its new
position.
Enables you to simply start or stop the pump, the icon changes as
appropriate. These tools are also available on the monitoring dialog, to
enable you to start and stop the pump while monitoring.

NOTE: For more information about using the Liquid Sipper Accessory, see the tutorial on
the Spectrum Multimedia CD (version 2 or later).

NOTE: The first time you install the accessory, you will have the option of performing the
Shipping Checks.

Controlling the Instrument . 171

Setting Up the I nstrum ent

1. Open the Scan and Instrument Setup dialog by choosing Instrument from the Setup
Menu.

2. Click Switch

to toggle between the Sample tab and the Multiple Sample tab.

On the Sample tab, specify the Name for your spectrum and to add the
Description and Comments that will be saved with the spectrum.
On the Multiple sample tab, specify the Names for a series of spectra, and to add
the Description and Comments that will be saved with each spectrum. The
Multiple Sample tab is useful when working with accessories such as the
Universal ATR, the NIR Fiber Optic Probe, and the NIR Tablet Autosampler
(where you also specify the Position of each sample on a Carousel).
3. The remaining tabs enable you to:
Set the Range, Scan Type, Units, Duration and whether to Scan minimized on
the Scan tab.
Set instrument options of Resolution, Data Type, Apodization, Phase
Correction, Scan Speed, CO2/H2O suppression, AVI and Quality Checks on
the Instrument tab.
Check and change beampath items on the Beam tab.
Select the Configuration for the current accessory and check its details on the
Accessory tab.
4. If you change any of the settings the Start button changes to Apply, choose Apply
to set the changes.
The Apply button changes back to a Start button.
5. To start the scan choose Start.
The Scan Progress dialog is displayed.

172 . Spectrum

M enus
There are three menus displayed at the top of the dialog:

File M enu:
Use these commands, or their equivalents in the toolbar, to work with Instrument
Settings Files.
Open

Enables you to open an instrument settings file.

Save

Enables you to save changes to the current setup in the

instrument settings file.

Save As

Enables you to save the current setup as an instrument settings

file.

Print

Enables you to print the current instrument settings.

Summary Info

Displays the current instrument settings.

Copy to
Clipboard

Copies the current instrument settings to the Windows

clipboard.

Exit

Exits the Scan and Instrument Setup dialog.

Setup M enu:
Accessory
Configuration

Enables you to set up the Sampling Configuration for the current

accessory.

Data Collection

Enables you to change the Data Collection Setup.

Help M enu:
Contents

Displays this help file.

About

Displays a dialog stating the version information for ths instrument

control software and the Instrument ID, Serial number and
IP address of the Spectrum currently being controlled.

Controlling the Instrument . 173

Toolbar
The toolbar tools have the following functions:
Starts the instrument monitoring.

Enables you to open an instrument settings file.

Enables you to save the current setup in an instrument settings file.

Copies the current instrument settings to the clipboard.

Prints the current instrument settings.

Opens the Adjustments Toolbox to enable you to adjust your instrument.

Enables you to toggle between the Sample tab and the Multiple Sample tab.
Enables you to change the wavelength range on a dual-range instrument, for
example to change from MIR to NIR.
The icon on the far right of the toolbar shows which sampling accessory is currently
fitted. Many of the accessories also have special tools that appear on the toolbar when
the accessory is installed. For more information see the help topics for the individual
accessories.

174 . Spectrum

I nstrum ent Settings Files

Instrument settings (.set) files contain all the information on the beam path, scan mode
parameters, and instrument details. They enable you to save the current customized
instrument settings for future use. You can also create new instrument setup files without
changing the current instrument setup.
The name of the current setup file and a description, that was entered when the setup
was saved, are displayed below the toolbar on the Scan and Instrument Setup dialog.

View ing the current instrum ent settings

Display the File menu and choose Summary Info.

The current instrument settings are displayed.

Opening an Instrum ent Settings File

1. Display the File menu and choose Open.
The Open Setup File dialog is displayed.
2. Choose the settings (.set) file you want to open.
3. Choose OK.
The dialog closes and the instrument settings file opens. The new setup is displayed
on the Scan and Instrument Setup dialog.
If the new file contains settings that are not the same as the settings recorded on
the Instrument Configuration dialog the settings on the dialog are not changed.
4. To change the current instrument settings to those in the file, choose Apply.
If the instrument settings file is not compatible with the instrument, for example if a
sample shuttle is not fitted, a warning message is displayed.
OR
To leave the instrument settings as they are, choose Cancel.

Saving the Instrum ent Settings File

Spectrum enables you to save your instrument settings in instrument settings files. This
enables you to store a number of instrument setups for different tasks.
1. Set the sample, scan, instrument, beam and accessory details as required.
2. Display the File menu and choose Save or Save As.
The Save Setup File dialog is displayed.
3. Type a name, and a description if required, for the settings (.set) file.
4. Choose OK.
The dialog closes and the file is saved.

Controlling the Instrument . 175

Printing the Instrum ent Settings File

1. Display the File menu and choose Print
The Print dialog is displayed showing the default printer, but you can select a
different printer, and change settings on the printer if required.
2. Choose OK.
The current instrument settings are printed.

Copying the Instrum ent Settings File to the Clipboard

Display the File menu and choose Copy To Clipboard

The current instrument settings are copied to the Windows clipboard.
You can now open a different Windows application and paste the information in.

Sam pling Configuration

The Sampling Configuration dialog enables you to create or edit a configuration file for an
accessory which you will then be able to select from the drop down list on the Accessory
tab in the Scan and Instrument Setup dialog. The dialog also enables you to edit the
default settings.
There are two ways to use this dialog:

If you select a configuration file before entering this dialog, or open a configuration
file using Open, this dialog enables you to edit that file.
You save the file after editing and when you want to use the file, you select it from
the Configuration section of the Accessory tab by choosing User Defined and then
selecting the configuration you require.

If you enter the dialog without selecting a configuration file, the dialog will enable
you to edit the default settings for the current accessory.
This then means that when you install the accessory the default conditions that
appear are the ones you set here, not the ones set at the factory.

Description tab
The Description tab shows the currently installed accessory and enables you to select
defaults for any of the options that are not determined by auto-detection (you cannot
change attributes of an accessory that are determined automatically when the accessory
is installed), these will then be defaulted on the Accessory tab in the Scan and
Instrument Setup dialog.

Scan Conditions tab

The Scan Conditions tab enables you to define some of the default settings that will be
used when collecting data. When you change the default scan conditions, you will still be
able to modify them further on the Scan and Instrument Setup dialog, before you collect
the scan. However, the System Suitability check will also use the default conditions you
set here.

176 . Spectrum

Quality Checks tab

This tab will only be available if you have installed the IR Expert software, and it enables
you to define which checks should be performed when that accessory is being used.
Some quality checks are not appropriate for some accessories, so these will not be
available to be set.

Sipper Setup tab

The Sipper Setup tab is only displayed when you have a Liquid Sipper Accessory installed.
It consists of two sub-tabs that enable you to set up the behavior of the sample and flush
controls on the Scan and Instrument Setup dialog and the buttons on the Liquid Sipper
itself.
There are two ways of setting up your liquid sipper for collecting sample spectra. The
simplest method is by setting the pump time and pause time. The other method is autodetection where the software checks for the presence of a sample. This is carried out by
checking for peaks above a nominated threshold in a given part of the spectrum.
The flush tab enables you to set up the software to flush out the sample and then
automatically check for any residual samples.

Controls
Command

What it does

OK

If you are working with the default file, this will save any changes to the
defaults. If you are working with a user defined configuration it will save the
changes to that file.

Cancel

Exits the dialog without implementing any changes.

Restore

If you have edited the defaults for an accessory, this will restore the defaults
to those set at the factory.
NOTE: You cannot Cancel once you have chosen Restore.

Open

Enables you to open a configuration file so you can edit it.

Save As

Enables you to save the current configuration, and any changes you have
made, with a new name.

Controlling the Instrument . 177

Data Collection Setup

The Data Collection Setup dialog enables you to set certain options that apply to all
scans.
1. From the Setup menu, choose Instrument.
The Scan and Instrument Setup dialog is displayed.
2. From the Setup menu, choose Data Collection.
The Data Collection Setup dialog is displayed.

Save tab
The Save tab enables you to automatically name and save spectra as they are collected.
NOTE: If the system administrator has defined data collection options for your group in
the Administration Options Utility, the Save tab will not be available.
When you choose Auto-increment the spectra are named with a common Prefix,
followed by a number that is automatically incremented from the Start number you
select. The filename for each spectrum will be automatically displayed in the Name text
box on the Sample tab of the Scan and Instrument Setup dialog. Choosing User
specified, switches off this function and means that the user must enter a name for
each spectrum collected.
NOTE: When Auto-increment is selected, the Multiple Sample tab includes a checkbox
for the Continuous option.
When you choose Enable auto-save the spectra you collect are automatically saved, in
the Format specified from the drop down list, as they are collected.

Background tab
When collecting ratioed sample spectra, the Background tab enables you to set the
following options:
Confirmation panel:
Perform background
confirmation

A dialog will be displayed reminding you collect a new background

after the selected minutes and/or samples have passed. This
dialog gives you the opportunity to have a background
automatically collected.
NOTE: If a System Suitability setup has been created for the
current sampling configurations and if that setup has
contamination check enabled, then the background scan
performed will have a contamination check performed on it.

Advanced tab
The Advanced tab enables you to choose to delay collecting your spectrum by the
selected number of seconds.
NOTE: Delay scan does not apply when you are using the instrument monitor function,
or when you have selected the Preview Scan option on the Sample tab or the
Multiple Sample tab. In these cases the scan begins immediately.

178 . Spectrum

Adjustm ents Toolbox

The Adjustments Toolbox enables access to the adjustment commands.
To access the Adjustments Toolbox you must have Advanced Instrument Access (as set
on the Instrument tab of the Options dialog from the Setup menu).

Maintenance
WCal
Align
Centre Burst
AVI Calib
Instrument Display

Change the contrast on your instrument

display.

Calibrate LCD

Calibrate the touchscreen on the LCD display of

your instrument.

Fiber Probe Display

Change the settings on your NIR Fiber Optic

Probe display.

The Instrument Display tool is only available when connected to a Spectrum 100
series or Spectrum 400 spectrometer.

The Calibrate LCD tool is only available when connected to a Spectrum One (or
Spectrum One NTS) fitted with the optional LCD screen.

The Fiber Probe Display tool is only available when an NIR Fiber Optic Probe
sampling accessory is fitted.

Controlling the Instrument . 179

Using the Adjustm ents Toolbox

1. Select Instrument on the Setup menu.
The Scan and Instrument Setup dialog is displayed.

2. Click on

The Adjustments Toolbox is displayed.

3. Click on the tool for the adjustment you want to make.
A dialog will appear or the adjustment will be implemented, depending on the tool
selected.
4. When you have finished making adjustments, click Close.
The Adjustments Toolbox closes and the Scan and Instrument Setup dialog is
displayed.

180 . Spectrum

M aintenance
The Maintenance dialog enables you to set and record desiccant change dates and
routine service periods.
The dialog enables you to:

View the date of the last desiccant change or routine service.

Set the interval for the desiccant and service warning messages to appear.

Acknowledge that the desiccant has been changed or that a routine service has
been performed.

To use this dialog

1. Select Instrument on the Setup menu.
The Scan and Instrument Setup dialog is displayed.

2. Click on

The Adjustments Toolbox is displayed.

3. Click on

The Maintenance dialog is displayed.

4. Make the changes required.
, to set that the desiccant has been Changed or that the
Click in the box,
instrument has been Serviced.
5. Click OK.
The changes are applied and the Maintenance dialog closes.

Controlling the Instrument . 181

W avenum ber Calibration

A wavenumber shift may be observed as a result of sample effects. When the
wavenumber calibration is re-defined, care should be taken when comparing spectra with
previously-collected spectra, library spectra or performing instrument validation.
Calibration of the wavenumber axis can be validated relative to a NIST (National Institute
for Standards Technology) standard (SRM 1921) using the Instrument Performance
Validation Kit (L136 5335).
Wavenumber calibration is controlled by the value of the stored HeNe laser wavenumber.
You can adjust the calibration by up to 1% (158 cm-1) of the nominal HeNe value by
entering expected and observed wavenumber positions for a reference peak.
Changing the HeNe laser wavenumber only affects the interpolation of data collected
subsequently. You cannot make the laser wavenumber different for sample and
background spectra.
Wavenumber Calibration enables you to define the position of a reference band that is
then used to calculate a correction to the current value of the HeNe wavenumber,
according to the relationship:

W hen should I re-calibrate m y instrum ent?

If you have an Instrument Performance Validation Kit you can check whether your
instrument needs recalibration (for more information see the IPV Users Guide).
NOTE: For a Spectrum 400 MIR/NIR instrument, wavenumber calibration in one range
does not affect the wavenumber calibration in the alternate range.
However, for the Spectrum 400 MIR/FIR instrument, wavenumber calibration in
the MIR range (using the Instrument Performance Validation Kit) also applies to
the FIR range.

Changing the Laser W avenum ber Using a Reference Band

Wavenumber Calibration enables you to define the position of a reference band that is
used to calculate a correction to the current value of the HeNe wavenumber according to
the relationship:
Corrected HeNe Wavenumber =
Current Wavenumber x (Expected Wavenumber/Observed Wavenumber)
NOTE: You cannot use Wavenumber Calibration if the AVI correction on the Instrument
tab is selected.
1. Select Instrument on the Setup menu.
The Scan and Instrument Setup dialog is displayed.

2. Click on

The Adjustments Toolbox is displayed.

182 . Spectrum
3. Click on

The Wavenumber Calibration dialog is displayed.

4. Choose Calibrate from known band.
5. Enter the expected position of a band in cm-1 in the Expected position text box.
We recommend the reference band at 3060.02 cm-1 in the polystyrene spectrum.
6. Enter the observed position of that band in cm-1 in the Observed position text box.
That is, the position of the same band in a spectrum just run on the instrument. For
example, if you were using a polystyrene reference as suggested above, you would
now enter the observed position of the 3060.02cm-1 band in a spectrum recently
run.
7. In the Apply calibration to configuration section, select the appropriate wavelength
range and accessory from the Configuration drop-down list.
For example, if you were using a polystyrene reference as suggested above, you
would select MIR - All accessories. You can also calibrate your system for when you
are using the instrument with a number of specific NIR accessories. The available
options include NIR - Reflectance (NIRA), NIR - Reflectance (NIRA) external, NIR
Fiber probe (triggered), NIR Fiber probe (passive), and NIR - Other accessories. The
current configuration is indicated by a *.
8. Click OK.
If the correction to the HeNe wavenumber is greater than 1.0% (this is very
unlikely) the following error message will be displayed:
Laser Wavenumber > 1% from nominal value
In this case we recommend that you make sure that the positions of the bands
entered in the Observed position and Expected position text boxes are correct.
If a correction to the HeNe wavenumber greater than 1% is required, we recommend
that you:
1. Reset the laser by choosing Set laser wavenumber, entering the new number,
then choosing OK.
2. Repeat the calibration using your standard.
If a correction greater than 1% is still required, we recommend that you contact
your local PerkinElmer Service Department.
3. Click OK.
The value of the Laser Wavenumber in the instrument is reset.

Controlling the Instrument . 183

Aligning the I nstrum ent

Alignment is the adjustment of the interferometer mirror angles to optimize the
amplitude of the interferogram centerburst. This is achieved by maximizing the energy of
the region of the interferogram around the centerburst.
The Align command aligns one mirror in the interferometer in order to achieve this.
1. Allow the temperature in the optical module to stabilize.
This takes approximately 30 minutes.
2. Make sure that the sample compartment is empty.
3. Select Instrument on the Setup menu.
The Scan and Instrument Setup dialog is displayed.

4. Click on

The Adjustments Toolbox is displayed.

5. Click on

The Align dialog is displayed.

6. Click OK.
Alignment of the instrument begins.
When alignment is complete, the improvement factor is displayed.
NOTE: If significant absorption occurs in the sample area, the beam energy reaching the
detector may not be sufficient to enable alignment. During alignment, do not
disturb the instrument by, for example, obstructing the infrared beam in the
sample compartment.

Relocating the Centerburst

The Relocate Centerburst command is used to find the position of the scanning mirrors
in the interferometer such that there is zero path difference between the two beams
when they recombine. In this position the infrared radiation interferes constructively at all
wavelengths, so the amplitude of the interferogram is at its maximum.
To relocate the centerburst:
1. Select Instrument on the Setup menu.
The Scan and Instrument Setup dialog is displayed.

2. Click on

The Adjustments Toolbox is displayed.

3. Click on

The centerburst is relocated.

To stop the process before completion, choose Halt.

184 . Spectrum

AVI Calibration
This is the routine that takes a spectrum of the methane in the cell in the filterwheel and
calculates the correction needed for the current sampling configuration.
To perform AVI calibration:
1. Select Instrument on the Setup menu.
The Scan and Instrument Setup dialog is displayed.

2. Click on

The Adjustments Toolbox is displayed.

3. Click on

The AVI calibration routine begins.

4. Make sure that the sample area is clear and nothing is blocking the beam, and then
click OK.
At the end of the calibration a confirmation message is displayed.
5. Click OK.
You can now use AVI correction for this instrument configuration.

Controlling the Instrument . 185

I nstrum ent Display

The Instrument Display tool is only available when connected to a Spectrum 100 series or
Spectrum 400 spectrometer.
It enables you to adjust the contrast of the instrument display.

To use the Instrum ent Display tool

1. Select Instrument on the Setup menu.
The Scan and Instrument Setup dialog is displayed.

2. Click on

The Adjustments Toolbox is displayed.

3. Click the Instrument Display button

The Display Settings dialog is displayed.

4. Adjust the Contrast to suit your working environment, then click OK.
The Scan and Instrument Setup dialog is displayed.
5. Click Exit.

186 . Spectrum

Calibrate LCD
The Calibrate LCD tool is only available when connected to a Spectrum One (or Spectrum
One NTS) fitted with the optional LCD screen.
Where the LCD screen is fitted, the calibrate LCD dialog enables you to adjust the
instrument display.

To invoke the Calibrate LCD tool:

1. Select Instrument on the Setup menu.
The Scan and Instrument Setup dialog is displayed.

2. Click on

The Adjustments Toolbox is displayed.

3. Click the Calibrate LCD button

You are referred to the calibration instructions on your LCD screen.

4. When you have completed the screen calibration, click OK.
The Scan and Instrument Setup dialog is displayed.
5. Click Exit.

Controlling the Instrument . 187

Fiber P robe Display

The Fiber Probe Display tool is only available when an NIR Fiber Optic Probe is connected
to the spectrometer.
It enables you to adjust the Fiber Probes display.

To use the Fiber Probe Display tool

1. Select Instrument on the Setup menu.
The Scan and Instrument Setup dialog is displayed.

2. Click on

The Adjustments Toolbox is displayed.

3. Click the Fiber Probe Display button

The Display Settings dialog is displayed.

4. Adjust the display to suit your working environment, then click OK.
The Scan and Instrument Setup dialog is displayed.
5. Click Exit.

188 . Spectrum

I nstrum ent Validation

A number of Validation tests are available for the MIR and NIR ranges. These tests are
not applicable in the FIR range, and cannot be selected.

System Suitability
System Suitability is a fit-for-purpose test on the complete system, including an
installed accessory, whereas Instrument Validation is a fit for purpose test on the
instrument alone.

Instrument Validation
Instrument Validation is the procedure of demonstrating that your instrument is
functioning correctly.

ASTM 0
ASTM 0 is a specific test following ASTM Designation E1421-99, titled "Standard
Practice for Describing and Measuring Performance of Fourier Transform Infrared
(FT-IR) Spectrometers: Level Zero and Level One Tests".

USP
USP is a near-infrared reflectance test which applies when the instrument is fitted
with the Near Infrared Reflectance Accessory (NIRA).

Click on the relevant link above for more details on what the test are about and how to
set them up.

To perform a test:

On the Instrument menu, choose Validate and then select the type of validation
required.
The validation is performed using the current validation setup.

Controlling the Instrument . 189

System Suitability
NOTE: These tests are not applicable in the FIR range, and cannot be selected.
System Suitability is the procedure of demonstrating that your complete system,
including accessory, is performing fit-for-purpose; a common requirement for regulatory
compliance.
The System Suitability provided with Spectrum is used to provide a test of wavenumber
precision and a check on noise, throughput and contamination. You can set up a routine
validation procedure for Ready-for-Work checks using the Automatic Precision Validator
(APV) that is built into the instrument. You can also use a reference sample placed in the
accessory manually, to validate a particular method. This external reference standard can
be either the polystyrene sample from an Instrument Performance Validation kit or your
own standard.
A polystyrene standard sample is used in the checks.

Polystyrene film
The polystyrene film in the APV is primarily intended for testing that the instrument is
performing consistently, rather than for calibrating the wavenumber (abscissa) scale.

Setting up System Suitability Tests

When you create a system suitability test, it is specific to the current instrument
configuration displayed in the System Details panel at the top of the System Suitability
Setup dialog. This configuration includes the instrument name, the instrument serial
number, the current source, the current beamsplitter, the current detector, and the
accessory name and part number. However, if you have manually loaded a sampling
configuration from the Accessory tab, the setup being created will now be specific to that
sampling configuration, and the System Details panel will indicate the sampling
configuration name rather than the accessory description.
To set up for tests:
1. On the Setup menu, choose Validation and then System Suitability.
The System Suitability Setup dialog is displayed.
If you choose Auto Setup, default settings for the current accessory will be set,
including collection of Throughput and Contamination spectra, and Noise settings
will be calculated.

190 . Spectrum
2. On the Checks tab, select the following options as required:
Option

Action

Abscissa

Selects whether to validate the wavenumber precision.

Noise

Selects whether to measure peak-to-peak and r.m.s. noise over a

range and report the baseline trend.

Throughput

Selects whether to check for unexpected reduction of the

transmittance.

Contamination

Selects whether to check for the presence of peaks that signal a

contamination problem.

Screen Report

Selects whether the report of the results of the test is displayed on

the screen at the end of the test. If there are errors reported by the
test, the report will be displayed on the screen whether this option
was selected or not.

Print Report

Selects whether the report of the results of the test is sent to the
default printer at the end of the test.

3. On the Options tab, select the sampling type:

Option

Action

Internal APV

When selected, the ASTM test will be performed by automatically

placing the internal APV filter, in the filterwheel, into the beampath.

Sample Area

When selected, the ASTM test is performed using a sample placed by

the user in the sample area. Choose Prompts to edit the messages
that are displayed on the screen as the tests proceed.

4. On the Options tab, if Internal APV sampling has been selected, decide whether to
use Auto Check.

When selected, the ASTM test will automatically be performed at a set Time at the
set Interval.
NOTE: If you use Auto Check, we recommend that you do not exit from Spectrum. If
you switch Spectrum off the auto check will not be run. If you switch Spectrum
on again at a later date, the auto check will run at the correct interval. For
instance if you set the interval at 2 days and then switch Spectrum off until the
third day, the checks will still run on the fourth day.

Controlling the Instrument . 191

5. On the Archive tab, set up:
Option

Meaning

Log Filename

The filename and path for the log of the test results.
NOTE: A comma separated variable (csv) file will also be created with
the same filename.

Archive Prefix

The prefix for each test which will then be followed by an incremental
number each time the test is performed.

Directory

The directory where you want the spectra collected during the test to
be archived.

Spectra are automatically named as follows:

the first three characters are specified by the Archive Prefix;

the next four characters are an automatically incremented number;

the final character is:

B

for background spectra,

for abscissa check,

for noise check,

for throughput check,

for contamination check.

6. On the Abscissa tab, set up the reference data for the test.
This enables you to set the Nominal abscissa value and Lower and Upper limits for
the positions of up to three peaks measured in the abscissa test. During the
abscissa test, a spectrum is collected, and the wavenumber is measured at the
specified peaks. If the measured wavenumber at each peak is within the upper and
lower limits for that peak, the test passes.
7. On the Noise tab, set up the reference data for the test.
This enables you to set the Range within which the noise is measured, and to set
the Nominal value and upper Limit for the RMS noise, Peak to Peak noise, and
noise Trend.
NOTE: When you set the upper limit for the noise trend, enter a positive number. This
limit is applied independent of the direction of the slope.
8. On the Throughput tab, set up the reference data for the test.
This enables you to set the Nominal ordinate value and the Lower limit at up to
three abscissa Positions. During the throughput test, the ordinate value is
measured at the specified abscissa positions. If the measured ordinate value is
above the lower limit, the test passes.
You need to specify the filename and path of a reference Background spectrum for
the current accessory.

192 . Spectrum
9. On the Contamination tab, set up the reference data for the test.
This enables you to set the Nominal absorbance and the Upper limit at up to three
abscissa ranges, denoted by a Start and End position. During the contamination
test, the absorbance is measured over the specified ranges. If the measured value is
below the upper limit, the test passes.
You need to specify the filename and path of a reference Background spectrum for
the current accessory.
10. Click OK.
NOTE: If you later perform an Auto Setup, new noise data will be calculated and all
other data will be reset to the default settings for the current accessory.

Suggested R eference Data

When deciding what tolerances to set in the Instrument Validation Setup, consideration
should be given to the definition of fit-for-purpose for the individual application.
NOTE: It is important to take into account any sampling accessory when setting the
validation protocol.
Abscissa Test
If you intend to perform routine validation using internal reference materials, choose
three peaks from the third column of the Certificate of Performance Validation (supplied
with the optional IPV kit) as nominal reference values. We recommend that you use the
three peaks at nominally 3060.02, 1601.34 and 1028.34 cm-1. As a guide for analytical
applications involving the use of liquids and solids, 0.5 cm-1 might be an appropriate
tolerance.
Differences in temperature and beam geometry at the internal and sample compartment
positions may give different peak positions. It is therefore important that routine
validation tests are always performed using the sample position used for this calibration.
Spectra collected using the APV give peaks 10 cm-1 or more wide; the peak positions can
be consistently measured to 0.1 cm-1, provided that the noise level is low enough.
NOTE: Peaks in the spectrum of polystyrene above 1800 cm-1 are broader than most of
the peaks below 1800 cm-1, and may therefore show more variation for a given
noise level. The peaks at 1943 and 1802 cm-1 are subject to interference by water
vapor and should not be used.
Noise, Throughput and Contamination tests
Noise limits can be automatically set by performing an Auto Setup. For throughput and
contamination tests, the values entered in the nominal and limit columns must be
determined experimentally by you, using the accessory/sampling configuration defaults.
We recommend that you perform a series of tests several times over several days, to
take into account variation in ambient temperature, time that the instrument has been
switched on, humidity and other variables. Use these values to calculate the limits and
nominal values for the tests.
Tolerance limits are dependent upon the definition of fit for purpose for the individual
application. Upper Limit for Trend is entered as a positive number, but is applied
independent of the direction of the slope.

Controlling the Instrument . 193

Perform ing System Suitability Tests

To perform a test:

On the Instrument menu, choose Validate and then select System Suitability.
The validation is performed using the current System Suitability setup.

Validate I nstrum ent

NOTE: These tests are not applicable in the FIR range, and cannot be selected.
Instrument validation is the procedure of demonstrating that your instrument is
functioning correctly.
The Instrument Validation provided with Spectrum is used to provide a test of
wavenumber precision, ordinate repeatability and noise. You can set up a routine
validation procedure for Ready-for-Work checks using the Automatic Precision Validator
(APV) that is built into the instrument. You can also use a reference sample placed in the
sample area manually, to validate a particular method. This external reference standard
can be either a calibrated polystyrene sample or your own standard.
Two standard samples - polystyrene and Schott glass - are used in the checks.

Polystyrene film
The polystyrene film in the APV is primarily intended for testing that the instrument is
performing consistently, rather than for calibrating the wavenumber (abscissa) scale.

Schott NG11 glass

The sample provided for testing the ordinate performance is a piece of Schott NG11 glass
with a nominal thickness of 1 mm. This is a very stable material, and has a series of
broad spectral features with transmission between 70% and 0%. It can be used for
checking that the instrument is performing consistently, but not for testing the accuracy
of the transmittance scale, because accurate values for the transmittance of the glass
sample are not available.

194 . Spectrum

Setting up Instrum ent Validation Tests

When you create an instrument validation test, it is specific to the current instrument
configuration displayed in the System Details panel at the top of the Instrument
Validation Setup dialog. This configuration includes the instrument name, the instrument
serial number, the current source, the current beamsplitter, and the current detector.
To set up for tests:
1. On the Setup menu, choose Validation and then Instrument.
The Instrument Validation Setup dialog is displayed.
2. On the Tests tab, select the following options as required:
Option

Action

Abscissa

Selects whether to validate the wavenumber precision.

Ordinate

Selects whether to validate %T repeatability.

Noise

Selects whether to measure peak-to-peak and r.m.s. noise over a range

and report the baseline trend.

Screen Report Selects whether the report of the results of the test is displayed on the
screen at the end of the test. If there are errors reported by the test, the
report will be displayed on the screen whether this option was selected
or not.
Print Report

Selects whether the report of the results of the test is sent to the default
printer at the end of the test.

3. On the Options tab, select the sampling type:

Option

Action

Internal APV

When selected, the ASTM test will be performed by automatically placing

the internal APV filter, in the filterwheel, into the beampath.

Sample Area

When selected, the ASTM test is performed using a sample placed by the
user in the sample area. Choose Prompts to edit the messages that are
displayed on the screen as the tests proceed.

4. On the Options tab, if Internal APV sampling has been selected, decide whether to
use Auto Check.

When selected, the ASTM test will automatically be performed at a set Time at the
set Interval.
NOTE: If you use Auto Check, we recommend that you do not exit from Spectrum. If
you switch Spectrum off the auto check will not be run. If you switch Spectrum
on again at a later date, the auto check will run at the correct interval. For
instance if you set the interval at 2 days and then switch Spectrum off until the
third day, the checks will still run on the fourth day.

Controlling the Instrument . 195

5. On the Archive tab, set up:
Option

Meaning

Log Filename The filename and path for the log of the test results.
NOTE: A comma separated variable (csv) file will also be created with
the same filename.
Archive Prefix The prefix for each test which will then be followed by an incremental
number each time the test is performed.
Directory

The directory where you want the spectra collected during the test to be
archived.

Spectra are automatically named as follows:

the first three characters are specified by the Archive Prefix;

the next four characters are an automatically incremented number;

the final character is:

B

for background spectra,

for abscissa check,

for ordinate check,

for noise check.

6. On the Abscissa tab, set up the reference data for the test.
This enables you to set the Nominal abscissa value and Lower and Upper limits for
the positions of up to three peaks measured in the abscissa test. During the
abscissa test, a spectrum is collected, and the wavenumber is measured at the
specified peaks. If the measured wavenumber at each peak is within the upper and
lower limits for that peak, the test passes.
7. On the Ordinate tab, set up the reference data for the test.
This enables you to set the Nominal ordinate value and Lower and Upper limits for
the ordinate value at up to three abscissa Positions. During the ordinate test, the
ordinate value is measured at the specified abscissa positions. If the measured
ordinate value is within the upper and lower limits, the test passes.
8. On the Noise tab, set up the reference data for the test.
This enables you to set the Range within which the noise is measured, and to set
the Nominal value and upper Limit for the RMS noise, Peak to Peak noise, and
noise Trend.
NOTE: When you set the upper limit for the noise trend, enter a positive number. This
limit is applied independent of the direction of the slope.
9. Click OK.

196 . Spectrum

Suggested R eference Data

When deciding what tolerances to set in the Instrument Validation Setup, consideration
should be given to the definition of fit-for-purpose for the individual application.
Abscissa Test
If you intend to perform routine validation using internal reference materials, choose
three peaks from the third column of the Certificate of Performance Validation (supplied
with the optional IPV kit) as nominal reference values. We recommend that you use the
three peaks at nominally 3060.02, 1601.34 and 1028.34 cm-1. As a guide for analytical
applications involving the use of liquids and solids, 0.5 cm-1 might be an appropriate
tolerance.
Differences in temperature and beam geometry at the internal and sample compartment
positions may give different peak positions. It is therefore important that routine
validation tests are always performed using the sample position used for this calibration.
Spectra collected using the APV give peaks 10cm-1 or more wide; the peak positions can
be consistently measured to 0.1 cm-1, provided that the noise level is low enough.
NOTE: Peaks in the spectrum of polystyrene above 1800 cm-1 are broader than most of
the peaks below 1800 cm-1, and may therefore show more variation for a given
noise level. The peaks at 1943 and 1802 cm-1 are subject to interference by water
vapor and should not be used.
Ordinate test and noise test
The values entered in the Nominal column must be determined experimentally by you,
using the chosen instrument validation setup.
We recommend that you perform a series of tests several times over several days, to
take into account variation in ambient temperature, time that the instrument has been
switched on, humidity and other variables. Use these values to calculate the limits and
nominal values for the tests.
Tolerance limits are dependent upon the definition of fit-for-purpose for the individual
application. Upper Limit for Trend is entered as a positive number, but is applied
independent of the direction of the slope.

Perform ing Instrum ent Validation Tests

To perform a test:

On the Instrument menu, choose Validate and then select Validate Instrument.
The validation is performed using the current Instrument Validation setup.

Controlling the Instrument . 197

ASTM 0
NOTE: These tests are not applicable in the FIR range, and cannot be selected.
ASTM Level Zero tests - follow ASTM Designation E1421-99, titled "Standard Practice for
Describing and Measuring Performance of Fourier Transform Infrared (FT-IR)
Spectrometers: Level Zero and Level One Tests", which is available from ASTM at:
American Society for Testing and Materials
100 Barr Harbor Drive
West Conshohocken
PA 19428
USA.
Web site = [Link]

R eference Spectra
During the ASTM Level Zero tests, spectra will be recorded and compared to two
reference spectra that you must previously store on disk. Reference spectra should be
collected under the instrument conditions that will be used for each sampling
configuration. The ASTM method recommends scanning for 30 seconds, which with the
TGS detector at the default scan speed of 0.2, is about 5 scans. If you are using a
different detector, or different instrument conditions, you will need to specify the number
of scans to be performed.
To perform an ASTM 0 test you will need to:
1. Collect a single-beam energy spectrum (background).
Which we suggest you name Reference [Link].
2. Collect a transmittance spectrum of a polystyrene sample.
Which we suggest you name Reference [Link].
NOTE: ASTM tests are performed with CO2/H2O suppression switched off, so the
reference spectra must be collected the same way.
Save both of these spectra to disk.
The names and directory paths of these reference spectra will need to be entered in
to the ASTM Tests Setup dialog before performing an ASTM Level Zero test.
NOTE: The same polystyrene sample that is used to collect this polystyrene reference
spectrum must be used when performing ASTM Level Zero tests. The sample
must also be used in the same sample position and orientation, while we
recommend that the test is performed using the internal APV filter, the
polystyrene sample card (part number 0186-2082) is suitable for this purpose.

NOTE: If the Spectrometer's laser wavenumber is adjusted, an AVI calibration is

performed or if the source, detector, beamsplitter or power supply is changed in
your instrument, you must collect new reference spectra for subsequent ASTM
Level Zero tests.

198 . Spectrum

Setting up ASTM 0 Tests

When you create an ASTM test, it is specific to the current instrument configuration
displayed in the System Details panel at the top of the ASTM Tests Setup dialog. This
configuration includes the instrument name, the instrument serial number, the current
source, the current beamsplitter, and the current detector.
To set up for ASTM 0 tests:
1. On the Setup menu, choose Validation and then ASTM.
The ASTM Tests Setup dialog is displayed.
2. On the Tests tab, select the following options as required:
Option

Action

ASTM Level 0

Selects whether ASTM 0 test is performed.

Screen Report

Selects whether the report of the results of the test is displayed on the
screen at the end of the test. If there are errors reported by the test,
the report will be displayed on the screen whether this option was
selected or not.

Print Report

Selects whether the report of the results of the test is sent to the
default printer at the end of the test.

3. On the Options tab, select the sampling type:

Option

Action

Internal APV

When selected, the ASTM test will be performed by automatically

placing the internal APV filter, in the filterwheel, into the beampath.

Sample Area

When selected, the ASTM test is performed using a sample placed by

the user in the sample area. Choose Prompts to edit the messages
that are displayed on the screen as the tests proceed.

4. On the Options tab, if Internal APV sampling has been selected, decide whether to
use Auto Check.

When selected, the ASTM test will automatically be performed at a set Time at the
set Interval.
NOTE: If you use Auto Check, we recommend that you do not exit from Spectrum. If
you switch Spectrum off the auto check will not be run. If you switch Spectrum
on again at a later date, the auto check will run at the correct interval. For
instance if you set the interval at 2 days and then switch Spectrum off until the
third day, the checks will still run on the fourth day.

Controlling the Instrument . 199

5. On the Archive tab, set up:

Option

Meaning

Log Filename

The filename and path for the log of the ASTM test results.
NOTE: A comma separated variable (csv) file will also be created with
the same filename.

Archive Prefix

The prefix for each test which will then be followed by an incremental
number each time the test is performed.

Directory

The directory where you want the spectra collected during the test to
be archived.

Spectra are automatically named as follows:

the first three characters are specified by the Archive Prefix;

the next four characters are an automatically incremented number;

the final character is:

B

for background spectra.

for a ratio spectrum that is calculated in an ASTM test by ratioing the

background spectrum collected against the stored background
reference spectrum.

for a difference spectrum that is calculated in an ASTM test by

subtracting the stored polystyrene reference spectrum from the
collected polystyrene spectrum.

for abscissa check.

for noise check.

NOTE: ASTM log files always store graphs (5 per test report), so the file size will
accumulate quite quickly, approximately 150K per ASTM test. Hence 100 tests is
a 15 MByte file. To enable viewing of larger file sizes sufficient memory must be
available in the PC. We have tried this on a Log file size of 16 MBytes on a PC
with 64 MBytes of memory without any apparent problems, however, if the PC
memory is limited then it is recommended that a new "Log Filename" be created
on a regular basis. The regularity depending on the capability of your PC.
6. On the ASTM 0 tab, set up the filename and path to the two reference spectra you
collected.
You are now ready to perform ASTM 0 validation checks.
7. Click OK.

200 . Spectrum

Perform ing ASTM 0 Tests

To perform a test:

On the Instrument menu, choose Validate and then select ASTM 0.

The validation is performed using the current ASTM 0 setup.

USP
W hat is USP ?
The test follows USP <1119> (United States Pharmacopoeia, Chapter 1119),
Near-Infrared Spectrophotometry.
USP is a near-infrared reflectance test which applies to the instrument fitted with a Near
Infrared Reflectance Accessory (NIRA).

Setting up USP Validation Tests

NOTE: These tests are not applicable in the FIR range, and cannot be selected.
When you create a USP validation test, it is specific to the current instrument
configuration displayed in the System Details panel at the top of the USP Validation Setup
dialog. This configuration includes the instrument name, the instrument serial number,
the current source, the current beamsplitter, and the current detector.
The instrument settings that are used for the test are the NIRA defaults of Resolution
16 cm-1 and 5 scans. However, if you have manually loaded a sampling configuration
from the Accessory tab of the Scan and Instrument Setup dialog, the setup created will
be specific to that sampling configuration and the top panel will be specific to that
sampling configuration name rather than the accessory description.
To set up for tests:
1. On the Setup menu, choose Validation and then USP.
The USP Validation Setup dialog is displayed.
2. On the Checks tab, select the following options as required:
Option

Action

Abscissa

Selects whether to validate the wavenumber precision.

Noise

Selects whether to measure r.m.s. noise over a range of segments.

Linearity

Selects whether to validate the reflectance of standards of known

reflectance.

Screen Report

Selects whether the report of the results of the test is displayed on the
screen at the end of the test. If there are errors reported by the test,
the report will be displayed on the screen whether this option was
selected or not.

Print Report

Selects whether the report of the results of the test is sent to the
default printer at the end of the test.

Controlling the Instrument . 201

3. On the Archive tab, set up:

Option

Meaning

Log Filename

The filename and path for the log of the test results.
NOTE: A comma separated variable (*.csv) file will also be created
with the same filename.

Archive Prefix

The prefix for each test which will then be followed by an incremental
number each time the test is performed.

Directory

The directory where you want the spectra collected during the test to
be archived.

Spectra are automatically named as follows:

the first three characters are specified by the Archive Prefix;

the next four characters are an automatically incremented number;

the final character(s):

AB
A

for abscissa background spectrum

for abscissa check

NB01

for noise check background (high flux)

N01

for noise check (high flux)

NB02

for noise check background (low flux)

N02

for noise check (low flux)

LB

for linearity background

Lxx

for linearity check (where xx depends on the number of reference

spectra. A minimum of 4 are required, i.e. L01 to L04 will be generated.
A maximum of 10 reference spectra can be specified.

4. On the Abscissa tab, set up the reference data for the test.
This enables you to set the Nominal abscissa value and Lower and Upper limits for
the positions of up to three peaks measured in the abscissa test. Three peaks are
set as a default. During the abscissa test, a spectrum is collected, and the
wavenumber is measured at the specified peaks. If the measured wavenumber at
each peak is within the upper and lower limits for that peak, the test passes.
5. On the Noise tab, set up the reference data for the test.
This enables you to set the Range within which the noise is measured, the segment
size over the range, and to set the Nominal value and upper Limit for the average
RMS noise and maximum individual RMS noise for the High flux and Low flux noise
tests.

202 . Spectrum
6. On the Linearity tab, define up to three abscissa positions at which to validate the
reflectance or the reflectance standards. Specify the limits for the slope and
intercept.
The values entered in the position slope and intercept must be determined
experimentally using your chosen instrument setup. Click Setup Ref Spectra on the
Linearity tab to display the Linearity Reference Spectra dialog. The reference spectra
to be used for the Linearity test must be specified here; the ordinate units must be
Absorbance. A minimum of 4 reflectance standards are required; a maximum of 10
spectra can be specified. Details of suitable reflectance standards are provided in
USP <1119>.
7. Click OK.

Suggested R eference Data

When deciding what tolerances to set, consideration should be given to the definition of
fit-for-purpose for the individual application.
Abscissa Test
Insert the nominal values for the peaks to be detected from your reference reflectance
material. The limits should be adjusted to suit your instrument conditions for routine
validation. The default values are the wavenumber equivalents of the bands listed on the
certificate for NIST SRM 1920a for a spectral band width of 10 nm. The bands are
1261.8 nm, 1681.4 nm and 1935.5 nm (7925.2, 5947.4 and 5166.6 cm-1 respectively).
NOTE: 10 nm at 2500 nm is equivalent to 16 cm-1 at 4000 cm-1.
Noise Test
The values entered in the Nominal column for High Flux and Low Flux must be
determined experimentally by you, using the chosen instrument setup, although the
default limits are compliant with USP<1119>. The test is performed in absorbance.
High Flux is measured using a highly reflective reference material whilst Low Flux is
measured using a lower reflectivity reference material. The reflectance standard is used
as the sample and background reference. At reduced light flux, significant contributions
are made to the noise from the optics, source, electronics and the detector. Low light flux
occurs when a low reflectance or highly absorbing sample is measured.
We recommend that you perform a series of tests several times over several days, to
take into account variation in ambient temperature, time that the instrument has been
switched on, humidity and other variables. Use these values to calculate the limits and
nominal values for the tests.
Tolerance limits are dependent upon the definition of fit-for-purpose for the individual
application.
Select the Range over which to calculate the Noise. The default range is 8350 to
4450 cm-1.
Select the Segment size over which to calculate the Noise. The default size is 300 cm-1.
The Noise is then calculated for successive segments of the defined size, over the
specified Range. There are 13 segments over the range 8350 to 4450 cm-1. We have
allowed a maximum of 20 segments to be used.

Controlling the Instrument . 203

Linearity Test
The test is to be performed using at least four reference standards in the range 10% to
90% for analytes with absorbances below 1.0. Where analytes have absorbances which
exceed 1.0 then a 2% or a 5% standard (or both) should be included.
NOTE: These reference spectra must be collected in Absorbance.
Reflectance spectra collected are compared with stored reference reflectance spectra of
the same samples. A plot of Aobs vs Aref for each reflectance standard at the specified
wavelength is performed. The slope and intercept values are calculated at the specified
wavenumbers. The difference of the slope from 1 and the difference of the intercept
from zero are reported. USP<1119> requires a slope of 1.0 +/- 0.05, and an intercept of
0.0 +/- 0.05.

Perform ing USP Validation Tests

To perform a test:

On the Instrument menu, choose Validate and then select USP.

The validation is performed using the current USP Validation setup.

NOTE: You must not set the auto check to perform more than one type of validation (for
example USP and Instrument Validation) at a particular time. If you wish to set
the auto check for more than one validation, ensure that there is sufficient time
for one validation to be completed before the next validation commences.

204 . Spectrum

Validation Errors
This topic describes some of the errors that may occur during validation. The errors
described are errors that may be expected, caused, and potentially remedied by the user.
Other errors are system problems and the user should contact PerkinElmer.

Abscissa Test (Instrum ent Validation and System Suitability):

Nominal position not within the abscissa range of the abscissa reference spectrum
- This means that an abscissa position specified for the test was outside the range of the
generated spectrum. This can occur in a System Suitability check if the default scan
range for the sampling configuration has been modified since the System Suitability for
that sampling configuration was setup.
Peak not found - This means that no peak (or at least no peak greater than the abscissa
test threshold) was found near to the nominal position specified. To correct this, either
check that the material used produces the peak expected at the required threshold,
re-specify the position, or switch off that element of the test.

Noise test (Instrum ent Validation and System Suitability):

Specified abscissa range is not encompassed by the noise spectrum - This means
that the abscissa range over which the noise is to be measured is not covered by the
scan range of the collected spectrum. This can occur in a System Suitability check if the
scan range for the sampling configuration has been modified since the System Suitability
for that sampling configuration was setup. This should not occur for Instrument
Validation runs.

Throughput (System Suitability):

Position not within the abscissa range of the contamination reference spectrum This means that an abscissa position set for the throughput was outside of the range of
the generated spectrum. This will be due to either the background reference spectrum
specified for the test not covering the required range, or the scan range for the sampling
configuration has been modified since the System Suitability for that sampling
configuration was setup.

Contam ination (System Suitability):

Check range not within the abscissa range of the contamination reference
spectrum - This means that the specified abscissa range over which to find the
maximum absorbance is not covered by the collected spectrum. This will be due to either
the background reference spectrum specified for the test not covering the required
range, or the scan range for the sampling configuration has been modified since the
System Suitability for that sampling configuration was setup.

ASTM 0:
ASTM0 Energy Reference spectrum does not extend over the required abscissa
range; 4050-150 cm-1 - This means that the reference spectrum specified on the ASTM
Tests Setup dialog has not been collected over the required range. You will need to
collect a new spectrum or make sure that the dialog is specifying the correct spectrum.

Controlling the Instrument . 205

Validation Reports
This document describes the contents of the reports generated in the Instrument
Validation, System Suitability, and ASTM 0 instrument performance checks.
Validation report files have .vrf file extensions. To view a validation report, you need to
use the Report Viewer. You can start this program from the Edit menu.
Every run will result in the appending of a series of fields to the report log indicated in
the performance check setup. The field assignments for all variations in setup of each
performance check will remain the same, no matter what the setup. For example, two
instrument validation runs, one with the ordinate and abscissa tests enabled, one with
only the ordinate test enabled, will result in two rows of entries in the log, with the
results for the ordinate tests aligned in the same columns (the results fields for the
abscissa test blank in the report row of the test with the abscissa test disabled).

R eport Header:
The report header is the same for all three instrument performance checks types. The
new report row will begin with these fields:

Title (for example, Instrument Validation Report)

Report reference ID

Analyst (blank if no Login selected in Spectrum)

Date

Time

Auto-check ("Yes" or "No")

Text report log filename

Spectrum software revision (for example, Spectrum 4.00)

Instrument Alias

Instrument Serial Number

Instrument configuration (essentially the details that appear in the System Details
panel of the setup dialog)

"Internal APV" or "Sample Area" Sampling (may be blank if no sampling was

required i.e. if the test did not contain an Abscissa or Ordinate check and was not
an ASTM0 test)

Resolution

Number of scans

Overview errors (errors that occurred that could not be associated with any
particular part of the performance check)

206 . Spectrum

Instrum ent Validations, report carries on from header:

Path and name with which the Background spectrum was saved

Background spectrum collection errors

Path and name with which the collected abscissa reference spectrum was saved

Abs ref spectrum collection errors

Then three lots of:

Nominal abs position

Observed abs position

Upper limit

Lower limit

Result - will include error string associated with measuring the peak position if result
is 'ERROR'

Path and name with which the collected ordinate reference spectrum was saved

ord ref spectrum collection errors

Then three lots of:

Position of ord reference point

Nominal ordinate value

Observed ordinate value

Upper limit

Lower limit

Result - will include error string associated with measuring ordinate value if result is
'ERROR'

Path and name with which the collected noise reference spectrum was saved

Abscissa start position of range over which noise is measured

Abscissa end position of range over which noise is measured

Then the following for each of RMS, Peak-to-Peak, and Trend

Nominal value

Observed value

Upper limit

Result - will include error string associated with measuring the noise if result is
ERROR

Controlling the Instrument . 207

System Suitability Checks, report carries on from header:

Path and name with which the Background spectrum was saved

Background spectrum collection errors

Abscissa test and Noise test entries as in Instrument Validations above

Path and name with which the collected Throughput reference spectrum was saved

Throughput spectrum collection errors

Path and name of the background reference spectrum

Then three lots of:

Abscissa position at which the throughput was measured

Nominal ordinate value (%T) at this position

Observed ordinate value (%T) at this position

Result - will include error string associated with reading the ordinate value if result
is ERROR

Path and name with which the collected Contamination reference spectrum was
saved

Contamination spectrum collection errors

Path and name of the background reference spectrum

Then three lots of:

Abscissa start position of the range over which the contamination was measured
(for this element)

Abscissa end position of the range over which the contamination was measured (for
this element)

Nominal max ordinate value (%A) over this range

Observed ordinate value (%A) at this position

Result - will include error string associated with reading the max ordinate value in
the range if result is ERROR

208 . Spectrum

ASTM 0 Tests, report carries on from header:

Energy reference spectrum path and name

Path and name with which the newly collected background spectrum was collected

Errors generated in collected background spectrum

Path and name with which the energy ratio spectrum was saved

Errors generated calculating the energy ratio spectrum (ratio of new background to
energy ref spectrum)

Path and name with which the newly collected noise spectrum was saved

Errors generated in collecting noise spectrum

Polystyrene reference spectrum path and name

Path and name with which the newly collected Polystyrene ref spectrum was saved

Errors generated in abs ref spectrum

Path and name with which calculated polystyrene difference spectrum was saved

Polystyrene difference spectrum calculation errors

Three lots of energy ratio results: E4000/E2000, E2000/E1000, and E150/EMax

Ratio for energy reference spectrum - or error in calculation

E4000/E2000 for newly collected energy spectrum (background) - or error in calc

Difference between reference ratio and new ratio

Four lots of noise results: for range 4050-3950, 2050-1950, 1050-950, and 550 to
450 cm-1

RMS or Error string if error in calculating values

Peak-to-peak - or blank if error

Trend - or blank if error

Controlling the Instrument . 209

R outine Access and Standard Access Users

Routine Access Users
Routine Access users have very limited access to the instrument:

Access to only the Sample and Accessory tabs on the Scan and Instrument Setup
dialog;

Ability to monitor only Energy or Sample;

No access to the instrument setup functions.

Standard Access Users

Standard Access users do not have access to the following instrument controls:

The Advanced functions on the Instrument tab of the Scan and Instrument Setup
dialog, and the Beam tab is only available if you enter the dialog from Instrument
on the Setup menu, not from Scan on the Instrument menu.

The ability to monitor interferograms;

The Sampling Configuration, Data Collection and Adjustments Toolbox dialogs.

210 . Spectrum

W orking w ith Files and

W indow s

212 . Spectrum

W orking w ith Files and W indow s

This section of the help includes topics on general manipulation of windows within the
main application window, including the use of templates and how to save or print in
Spectrum:
Opening or Closing Files - This topic tells you about opening and closing files.
Printing - This topic tells you about printing from Spectrum.
Working with Graphs - This topic tells you about opening and saving graphs and graph
templates.
Saving and Renaming Spectra - This topic tells you about the Save and Rename
commands.
Arranging Windows and Icons - This topic tells you about cascading and tiling windows,
and about lining up icons.
Exiting Spectrum - This topic notes some important points about exiting Spectrum.
Finally, this section includes a topic on how you can view small images of spectra and
information about them from within Windows Explorer. See Viewing Spectrum
Information in Windows Explorer.

Working with Files and Windows . 213

Opening or Closing Files

Opening a File
The Open command on the File menu enables you to open any file that can be used with
Spectrum. You can open a spectrum file, a graph or a template.
To use the Open command:
1. Display the File menu, and choose Open, or press CTRL+O
The Open dialog opens.
2. Choose a file.
You can choose a spectrum file, a graph file or a template file. The type of file you
choose is shown by the extension you choose from the List Files of Type: box.
3. Choose OK.
The file that you chose is opened.

Selecting Files in the File Selector

It is often useful to be able to open more than one spectrum at a time. To do this, all the
files that you want to open must be selected:

To select one file, click on the filename you want to select.

The file is selected and the other files are deselected.

To select more than one file, hold down CTRL while you click on the filenames.
The files you click on are selected.

To select a block of files, hold down SHIFT and click on the first and last filenames
in the block.

To deselect some files, leaving the others selected, hold down CTRL and click on the
filenames you want to deselect.
The files you clicked on are deselected, leaving the others selected.

To close a file:

Display the File menu and choose Close.

If any of the spectra on the active graph are selected, these are closed.
If there are no spectra selected on the active graph, the active graph is closed.
If there are no graphs displayed, the template file is closed.
If Confirm Deletes has been enabled, a warning dialog is displayed before the
graph is deleted. Choose OK to confirm the deletion.

To close all the open w indow s

Display the Window menu and choose Close All.

Any windows that are currently open within the main Spectrum application window,
are closed.

214 . Spectrum

Printing
The Print command on the File menu enables you to print or plot graphs or text
windows. The term print denotes print or plot and printer denotes printer or plotter.

P rinting a tex t w indow

Display the File menu and choose Print.

P rinting a graph w indow

1. Display the File menu and choose Print.
The Print Graph dialog is displayed.
2. Make sure that Current Window is selected.
3. Choose OK.
The current window is printed.

Changing the P age Layout

To change the page layout for the printer, make a graph window the current window
then:
1. Display the File menu and choose Print.
The Print Graph dialog is displayed.
2. Choose Current Window.
The Layout button is activated.
3. Choose Layout.
The Layout dialog is displayed.
4. Change the Page Orientation by selecting Portrait or Landscape.
Default layout uses the page orientation set on the Print Setup dialog.
5. Change the margins by typing the widths in the fields for Left, Right, Top, and
Bottom.
You can also choose the units of measurement for the margins.
6. Choose OK to return to the Print Graph dialog.

Working with Files and Windows . 215

P rinting a Graph using a Report Tem plate

It is possible to print a graph, while linking it up to a template from Report Builder. This
will produce a print out that has more information on it than just the graph. Exactly what
information is included depends on the report template.
1. Display the File menu and choose Print.
The Print Graph dialog is displayed.
2. Choose With Report Template.
The Template button is activated.
3. Choose Template.
The Open dialog opens.
4. Choose the drive, path and report template file that you want.
The default directory for templates is indicated by the Options command, File tab.
5. Choose OK to return to the Print Graph dialog.

Changing the P rint Setup

The Print Setup command on the File menu enables you to choose the default printer
settings, including the printer in use, and the paper size and orientation. To use the Print
Setup command:
1. Display the File menu and choose Print Setup.
2. Select a printer from the list of Installed Printers.
The name of the chosen printer is displayed in the Default Printer field.
3. Choose Setup from the Select Default Printer dialog.
The Setup dialog for the currently-selected printer is displayed. The dialog that is
displayed enables you to make basic changes to the settings of the current printer.
4. Choose OK from the printer Setup dialog.
The printer Setup dialog closes.
5. Choose OK.
The Select Default Printer dialog closes.

216 . Spectrum

P rint Spectra Colors

When you print graphs in color, you can choose to print a different color from that which
is displayed on the screen.
The colors that are used to print the spectra on the graph are defined by the Print Setup
command from the File menu.
1. Display the File menu and choose Print Setup.
The Select Default Printer dialog is displayed.
2. Choose the Colors.
The Spectrum Print Colors dialog is displayed. This enables you to choose the colors
in which the spectra on your graph are printed.
3. Click on the color in the Palette that you want to print.
The color is selected.
4. Click in the Printer column for the spectrum you want displayed in the chosen color.
The color in the Printer column changes to the palette color. The display colors are
shown only for your information.
5. Choose OK.
The Spectrum Print Colors dialog closes.
6. Choose OK.
The Select Default Printer dialog closes and the new print colors are available for
use.

Black and W hite P rinting

If you do not have a color printer, spectra on graphs can still be identified, because the
spectra are printed with different line-styles. However, you must have a printer that
supports line-styles. There is a maximum of five different line-styles, which are:

Line-styles are allocated to colors in the same order as the spectrum colors and are reused if there are more than five colors on the graph. Black and gray are always printed
as solid lines.

Working with Files and Windows . 217

W orking w ith Graphs

Creating a New Graph
The New command on the File menu enables you to open a template file. You can then
use the template as a basis to create a new graph by adding spectral files to it.
1. Display the File menu and choose New, or press CTRL+N.
The Open dialog opens.
2. Choose a graph template from the file selector.
The default directory for graph templates is defined in the File Options.
3. Choose OK.
The template opens. The format of the template can now be used as a basis for a
new graph.
New graphs are numbered, in the order that you create them: Graph-1, Graph-2,
etc.

Saving Graphs
Using the Save and Save As commands on a graph window enables you to save
spectra, graphs and graph templates.
1. Make sure that none of the spectra are selected.
A spectrum is selected if its name is underlined.
2. Display the File menu and choose Save or Save As.
Save keeps the current name of the graph, Save As enables you to specify new
names or a different format.
3. If the Save As dialog is displayed, type or choose a filename.
Choose the .gph extension from the List Files of Type filter. If you type the
filename, you do not need to type an extension because the extension that is
displayed in the file selector filter is added automatically when you choose OK. The
default directory for graphs is defined in the File Options.
4. Choose OK.
If you want to save the graph format as a template, use the file selector to choose a
.gfm extension. The file that is saved does not include any spectra that are
displayed on the graph at the time you saved the template, only the axes and the
formatting information.

218 . Spectrum

Creating a New Graph Tem plate

You create a new graph template by saving the format of a graph to a new file. A graph
template file does not include any spectra that were displayed on the graph at the time
you saved the template, only the axes and the formatting information.
To save the graph format as a template:
1. Make sure that the graph has the appearance you require.
2. Display the File menu and choose Save As.
The Save As dialog opens.
3. In the List Files of Type box, choose Graph Templates (*.GFM).
4. Type or choose a filename.
5. Choose OK.
The file is saved.

Working with Files and Windows . 219

Saving and R enam ing Spectra

Saving Spectra
Using the Save and Save As commands on a graph window enables you to save
spectra, graphs and graph templates.
1. Select the spectra you want to save.
When spectra are selected, their names are underlined.
2. Display the File menu and choose Save or Save As.
Save keeps the current names of the spectra, Save As enables you to specify new
names or a different format.
3. If the Save As dialog is displayed, type or choose a filename.
Choose the .sp extension from the List Files of Type filter. If you type the filename,
you do not need to type an extension because the extension that is displayed in the
file selector filter is added automatically when you choose OK. The default directory
for spectra is defined in the File Options.
4. Choose OK.

Renam ing Spectra

The Rename command on the File menu enables you to change the name of a spectrum
in memory
1. Select the spectrum or spectra that you want to rename.
When a spectrum is selected, its filename is underlined.
2. Display the File menu and choose Rename.
The Rename dialog is displayed, with the name of the spectrum displayed in the
Current Name field.
3. Type a new name in the New Name field.
4. Choose OK.
The spectrum is saved with the new name.
If more than one spectrum is selected, the Rename dialog enables you to change
the name of each of the selected spectra in turn.
NOTE: It is important to realize that in Spectrum ES spectra cannot be overwritten or
deleted.

220 . Spectrum

Arranging W indow s and I cons

Changing the W ay W indow s are Displayed
The Cascade, Tile Vertical and Tile Horizontal commands on the Window menu,
arrange how the current windows are displayed.
Display the Window menu and choose the required command.
The windows that are currently open within the Spectrum window are arranged as
selected.

The windows that are currently open within the Spectrum window are arranged in a
cascading style.

Tiled horizontally

Tiled vertically

When windows are tiled horizontally, they are displayed full width across the window, but
the height of the window depends on how many windows are open in Spectrum. All the
open windows are displayed one on top of the other.
When windows are tiled vertically, they are displayed full height but the width of the
window depends on how many windows are open in Spectrum. All the open windows are
displayed side by side.

Arranging I cons
Arranges the icons that represent graphs that have been iconized.
The Arrange Icons command in the Window menu arranges the icons that represent
graphs that have been iconized.

Display the Window menu and choose Arrange Icons.

The icons that are currently displayed within Spectrum are arranged in a row along
the bottom of the Spectrum window.

Working with Files and Windows . 221

Ex iting Spectrum
Ex iting from Spectrum

Display the File menu and choose Exit.

The Spectrum application closes.
If Confirm Deletes has been enabled, a warning dialog is displayed before the
graph is deleted. Choose OK to confirm the deletion.

Unsaved data
On exiting Spectrum any spectra obtained are automatically saved using the file naming
convention (prefix etc) as set by the administrator within the admin utility. This only
applies to raw spectra obtained from the instrument. Spectra that have processing
applied (such as smooth) will not be automatically saved in this manner and an Exit
dialog will be displayed requesting whether you want to save the processed spectra or
not. Within the Exit dialog you may choose to save your spectra, before clicking Exit or
to close the dialog and return to Spectrum, by clicking on Cancel.

Closing the Data Server

You may have noticed that when you are using Spectrum, the Data Server icon is
displayed at the bottom of the screen.
You do not usually need to close the Data Server, because it closes automatically when
you exit the final instance of any of the PerkinElmer applications. If it remains after all
the PerkinElmer applications have closed, restart Windows.

222 . Spectrum

View ing Spectrum I nform ation in W indow s

Ex plorer
If you select a Thumbnail view of a Windows folder that contains spectral files, for
example C:\pel_data\spectra, the display shows a small image of each spectrum.

For a Detail view, the following additional data items are available for optional display:

Analyst

Spectrum Description

Ordinate

Abcissa

Scan Start

Scan End

Scan Interval

Working with Files and Windows . 223

For further information on how to configure the Detail view for your Windows folders,
consult the documentation or Help files supplied with your operating system.

224 . Spectrum

Custom izing Spectrum

226 . Spectrum

Custom izing Spectrum

This section of the help includes topics on different ways to adapt Spectrum for the way
you want it:
IR Assistant - The IR Assistant is a wizard interface to Spectrum, that enables new or
sporadic users to quickly perform the tasks they want without being faced by the
complexity of the standard Spectrum interface. This topic gives you an overview of the IR
Assistant and its use.
The Toolbar and Toolbox Tools - This section tells you what all the tools do and tells you
how you can change the way the toolbar and toolbox are displayed.
Logging on as a Different User - This section tells you about logging on to Spectrum.
Using the Options Dialog - This section tells you about using the Options dialog to set up
defaults for the way Spectrum behaves.
Learn Mode - Learn Mode is a system for teaching Spectrum standard tasks so that you
can re-run them as required. This section tells you how to use Learn Mode.

Customizing Spectrum . 227

I R Assistant
An alternative way to use Spectrum is the IR Assistant. This is a wizard system that
provides access to the full power of Spectrum, but uses default options where possible to
avoid the complexity of the full Spectrum interface.
The IR Assistant has a unique help system, which displays information just when you
need it. When you hold the mouse pointer over a control on the software, help for that
control appears, to guide you in its function.

When you have built your task you can save it so that it can be used again. This then is a
simple way to automate tasks that are routinely performed.

Starting the I R Assistant

To start the IR Assistant at any time, choose IR Assistant on the Help menu.
The Spectrum window is minimized and the IR Assistant starts.

Alternatively, you can start IR Assistant using Windows Start > All Programs >
PerkinElmer Applications > Spectrum > IR Assistant.
If Spectrum is running, its window is not minimized. If Spectrum is not running, IR
Assistant will call it when required.

It is possible to setup Spectrum so that the IR Assistant starts when Spectrum is started:

For Spectrum, on the login dialog, choose Yes for Activate IR Assistant.
When Spectrum starts, the IR Assistant will be displayed.

For both Spectrum and spectrum ES, on the first IR Assistant dialog, select Always
show Assistant when Spectrum starts.
From now on, when you start Spectrum, the IR Assistant will be displayed.

228 . Spectrum

Using the I R Assistant

When you start the IR Assistant, you have four options:
- This option enables you to create a task that will collect a spectrum
from your instrument. You can also include in the task processing options to be
performed on the spectrum as soon as it has been collected.
- This option enables you to create a task that will perform
processing functions on spectra. You can design the task to either put up a file selector
so you can process spectra as required from disk, or to automatically process the
currently selected spectra on the graph in Spectrum.

to disk.

- This option enables you to run a task previously created and saved

- option enables you to re-run the last task. The name of the last
used task will be displayed on the dialog, and the description of the task will be displayed
in the information window:

Customizing Spectrum . 229

P erform ing a Task

When you run an IR Assistant task, the main Spectrum window is displayed and the task
is performed as designed, with dialogs opening automatically and only waiting for you to
interact with them if that is the way you designed the task.
At the end of the task, a dialog is displayed that enables you to choose what to do next:
Return to
IR Assistant

The Spectrum window is minimized and the IR Assistant is redisplayed.

Repeat Task

The task you have just finished runs again.

NOTE: If the task has been designed to be performed on the currently
selected spectra in Spectrum, this will include any spectra created by
running the task the first time.

Remain within
Spectrum

The IR Assistant closes and you can continue to work with the data in
Spectrum.

230 . Spectrum

Tools
Below are all the icons or tools that can be displayed in the Toolbar or Toolbox.

The following tools have a second function which you can start by clicking on them with
the right mouse button:

There are also tools that appear on interactive dialogs that have special functions:

Customizing Spectrum . 231

Using the Toolbox

The toolbox is a group of icons that can be positioned anywhere on the desktop. The
tools in the Toolbox provide a quick way of executing some of the commands that you
may want to use most often. When you move the mouse pointer over a Toolbox button,
the function of the button is displayed as a tooltip and in the status bar at the bottom of
the Spectrum window. To use a tool, click on the button.
NOTE: The system administrator can configure the toolbox to include the required
buttons.

Displaying and Hiding the Toolbox

Display the Setup menu and choose Toolbox followed by Show Toolbox.
When the Toolbox is displayed, a check mark appears next to the Show Toolbox
command.

Displaying the Toolbox captions

Each tool has a caption that describes the tool's function. You can choose whether or not
to have the captions displayed on the icons when the Toolbox is displayed.

Display the Setup menu and choose Toolbox followed by Show Toolbox Captions.
When the captions are displayed, a check mark is displayed next to the Show
Toolbox Captions command.

232 . Spectrum

The Options Dialog

Options
The Options dialog enables you to set some of the default behaviors of Spectrum.
NOTE: The system administrator may have defined some of these settings globally for
the group of users of which you are a member. In this case, some tabs will not
be available, and some individual settings will be disabled.
The options that can be changed are:
File - Sets the default directories for certain types of files. This means that when you
open a file selector to find that type of file, this is the directory that will be displayed.
View - Sets the defaults for display options, the font for text, the cursor / peak display,
graph template and the GLP lock.
Process - Sets the defaults for the way processed spectra are saved, the changes made
by Data Tune-up and the noise threshold.
Instrument - Sets the access level and the default instrument for Spectrum to connect to
at start-up.
Peak - Sets whether peak tables work with peaks or bases and which label is displayed.
Also sets peak thresholds.
Others - Configures which text editor is called from the Edit menu and what items appear
on the Procedures menu.

Customizing Spectrum . 233

File Options
The File tab on the Options dialog enables you to choose default directories for the files
used in Spectrum. You can also set the default template used when viewing graphs.
NOTE: If the system administrator has configured default directories for you (Spectrum),
or your group (Spectrum ES), the File tab will not be available.
1. Display the Setup menu and choose Options.
The Options tabs are displayed.
2. On the File tab, position the cursor in the text box you want to change.
3. Type the paths of the default directory or template.
OR
Choose Browse, then use the file selector to select the path.
4. Choose OK.

234 . Spectrum

View Options
The View Options enable you to set the following defaults:
1. Display the Setup menu and choose Options.
The Options tabs are displayed.
2. Select the View tab.
The View tab is displayed.
3. Select the options you require:
Default Mode Enables you to choose the default display mode for spectra on a
graph. You can choose from overlay or split.
Windowed
Mode

When Windowed Mode is on

separate window. When it is off
Window.

each graph is displayed in a

each graph fills the Spectrum

Autorange
New View

all spectra added to the graph have Autorange

When selected
X and Autorange Y performed on them.

Confirm
Deletes

, a warning dialog is displayed

When Confirm Deletes is on
when deleting spectra from the graph or deleting graphs.

Default Text
Font

Displays the default Font, Size, and Color.

Fonts

Enables you to change the default font.

Cursor / Peak Enables you to choose the number of decimal places or significant
Display
figures to be displayed for the horizontal and vertical cursors and
the peak display. Any spectra that are currently displayed will
retain the previous settings. Switch Label Peaks off and on again
to use the new setting. The value of the cursor position will change
to the new setting as soon as you move the cursor.
Default View
Template

The name and path of the graph template that is used when you
create a new graph by choosing New from the File menu. Choose
Browse to choose a new template.

GLP lock

Enables you to prevent the users from changing the Analyst and
Description information in the status information dialog.
NOTE: If the system administrator has set the GLP Lock option for
you (Spectrum Standard), or your group (Spectrum ES), the GLP
lock setting will not be available.

4. Choose OK.

Customizing Spectrum . 235

P rocess Options
Many of the Process commands generate new spectra. You can choose the way that
these spectra are named.
NOTE: If the system administrator has defined a process configuration for you
(Spectrum), or your group (Spectrum ES), the Process tab will not be available.
1. Display the Setup menu and choose Options.
The Options tabs are displayed.
2. Select the Process tab.
The Process tab is displayed.
3. Select the naming Mode option you want:
Overwrite
Original

The spectrum to be processed will be replaced by the spectrum

that has been processed. No warning will be given. However,
you will be able to undo the action of the previous Process
command using the Undo command on the Process menu.

Auto Name

Spectrum will name the new spectrum with a unique name. It

consists of the original spectrum name with a new extension.

User Name

A dialog will be displayed, prompting you to enter a name for

the processed spectrum. If you enter a spectrum name that
already exists, you will be warned and given the option to
overwrite or choose a different name.

4. Select the Data Tune-up functions you want:

Smooth

The spectrum will be automatically smoothed.

Flat

The spectrum will have the baseline automatically flattened.

Blank

Blank regions will automatically be set where the noise is greater

than the Noise Threshold.

5. Choose OK.

236 . Spectrum

I nstrum ent Options

The Instrument options enable you to select the level of instrument access.
NOTE: If the system administrator has defined the instrument access level for you
(Spectrum), or your group (Spectrum ES), the Instrument tab will not be
available.
1. Display the Setup menu and choose Options.
The Options tabs are displayed.
2. Choose the Instrument tab.
3. Choose the instrument access you want: Routine, Standard or Advanced.
Advanced access is full access to all instrument controls.
4. Choose OK.

Customizing Spectrum . 237

P eak Options
The Peak Table and the Peak Cursor commands both use the Peak Options to
determine their behavior.
1. Display the Setup menu and choose Options
The Options tabs are displayed.
2. Choose the Peak tab.
The Peak tab is displayed.
3. Choose the settings you require.
Find

When using the Interpolated Peak algorithm, enables you to find

Peaks or Bases or both in your spectrum.
When using the Center of Gravity algorithm, Peaks are always
found. If you choose to find Bases as well, the bases found will be
real data points, rather than interpolated values.

Label

Enables you to choose whether the Abscissa value, Ordinate

value, or both are used when labelling peaks.

Algorithm

By default, the peak positions are calculated using the

Interpolated Peak algorithm, which derives peak position from
maximum intensities. Alternatively, you can select the Center of
Gravity algorithm, as used by NIST, which derives peak position
from the shape of the peak.

Thresholds

Enables you to choose the thresholds used when detecting peaks

or bases.
The threshold used for the Interpolated Peak algorithm is
%T (or %R); Abs (or Log 1/R); and Units (for any other units)
- depending on the type of spectrum examined.
The Pk Ht threshold defines how much of a peak is used when
calculating its center of gravity. Where peaks are well defined a
Pk Ht threshold of 0.8 could be appropriate. However, where two
poorly-defined peaks overlap to produce a shoulder, and Pk Ht is
set to include the overlap, the Center of Gravity algorithm will
calculate a peak position shifted towards the shoulder.
For example: This effect will cause an NIR Abscissa check using the
Center of Gravity algorithm (refer to Instrument Validation) at the
5669 cm-1 peak to fail unless the Pk Ht threshold is set to 0.2 or
less.

Reset

Click Reset to return to the default threshold values: 2.00%T,

0.0088 Abs, 10.00 Units, 0.20 Pk Ht.

4. Choose OK.
NOTE: Any peak tables in memory are recalculated with the new settings.

238 . Spectrum

Other Options
The Options command, Others tab is used to setup the Procedures menu.
NOTE: If the system administrator has configured these options for you (Spectrum), or
your group in (Spectrum ES), the Others tab will not be available.
1. Display the Setup menu and choose Options.
The Options tabs are displayed.
2. Choose the Others tab.
The Others tab is displayed.
The Procedures menu is set up in the lower half of the tab.
The box shows the menu items that are currently configured.
3. To add a new procedure, choose Insert.
You can modify an entry by using the scroll bar to scroll through the defined
procedures, and then choose the item on the list that is to be modified. To delete a
procedure, select the procedure and choose Delete.
4. Type the text to be displayed in the Procedures menu into the Menu Text text box.
The character that you choose to be underlined, and therefore activated by the
ALT + underlined letter keyboard shortcut, must be preceded by an ampersand (&).
5. Type the command line path of the procedure or application in the Command Line
text box.
OR
Click in the procedures Command Line text box, then choose Browse to find the
required drive path and file.
6. Choose OK.
The settings using Options are saved. They do not return to default settings the
next time that you start Spectrum.

Procedures Created using Spectrum Procedures

You can set up the Procedures menu to run procedures that have been created using
Spectrum Procedures.

In the Command Line text box, type the path and filename of the procedure,
followed by <spectra>.
When you run the procedure from the Procedures menu, the selected spectra are
input into the procedure, in the same order as they are on the graph.

Customizing Spectrum . 239

Learn M ode
Learn M ode
Learn mode enables you to record, in a script file, a sequence of steps that you use
regularly in Spectrum . The script file can then be saved, opened or replayed. The
Procedures menu enables you to run a script directly from a menu item.
Learn mode is controlled by three buttons:

- LrnCtrl - Enables you to open, edit or save a Learn Mode script.

- Create - Enables you to Record a New Learn Mode Script.

- Play - Enables you to Play a Learn Mode Script.

To enable you to use Learn mode you must ask the system administrator to add these
buttons to your toolbar or toolbox.

The Learn M ode Dialog

Learn Mode is controlled from a window that appears at the bottom of the main
Spectrum window.

1. Click on
, or double-click on the panel in the status bar that is next to the
Login Name panel.
The Learn Mode dialog is displayed, this dialog enables you to record, play, open
and save learn mode scripts:
New

Enables you to start recording a new learn mode script.

NOTE: The current learn mode script is deleted.

Learn

Starts recording a learn mode script. To add steps to the current

script, highlight the step before the point where you want to add the
new steps.

Play

Plays the current learn mode script.

Repeat Play Replays the learn mode script until it is interrupted by choosing
Cancel on a dialog, the play button
Mode dialog.

, or Stop on the Learn

Open

Enables you to open a saved learn mode script file.

Save

Enables you to save the current learn mode script file.

Help

Starts the help system at this page.

240 . Spectrum

Opening a Learn M ode Script

You can open a saved learn mode script file and then edit it.
NOTE: Any unsaved learn mode script will be lost when you open a learn mode script
file.

1. Click on
, or double-click on the panel in the status bar that is next to the
Login Name panel, then choose New on the Learn Mode dialog.
The Learn Mode dialog is displayed.
2. In the Learn Mode dialog choose Open.
The Open dialog is displayed.
3. Choose the script file you want to open.
4. Choose OK.
The learn mode script file is opened and you can edit it.

Saving a Learn M ode Script File

When you have recorded your learn mode script, you can save it as a learn mode script
(.lrn) file. This enables you to add the script to the Procedures menu or to open and edit
it.
1. In the Learn Mode dialog, choose Save.
The Save As dialog is displayed.
2. Type or choose a filename.
If you type the filename, you do not need to type an extension because it is added
automatically when you choose OK.
3. Choose OK.
The learn mode script file is saved.

Customizing Spectrum . 241

Recording a New Learn M ode Script

Preparing to Record a Learn M ode Script
Before you start recording a script, we recommend that you plan the sequence of steps
you want to perform.
We also recommend that you note any parameters that you want to set, for example
when setting up an instrument. You cannot change the values of the parameters
recorded after you have recorded the script.
To make sure that the commands entered operate on the correct window, we
recommend that the first command in a new learn mode script is Close All.

R ecording a Script
1. To start recording, choose
, or double-click on the panel in the status bar that
is next to the Login Name panel, then choose New on the Learn Mode dialog.
OR
Click on

The Create button and a red box in the status bar flash.
2. Perform the steps you want to record.
The steps are added to the Learn Mode dialog.
3. When you have finished the steps you want to record, choose Stop on the Learn
Mode dialog.
OR
Click on

Recording stops.

242 . Spectrum

P laying a Learn M ode Script

You can replay a learn mode script after it has been recorded by adding it to the
Procedures menu, or from a button in the toolbar or toolbox.
NOTE: The system administrator can modify the toolbar and the toolbox using the
Administration Options Utility.
While you are developing your learn mode script, we recommend that you test the script
frequently:
1. Choose Play in the Learn Mode dialog.
OR
Click on

The learn mode script starts, when it reaches the end of the script it stops.
To stop the script, choose Stop or choose Cancel on a dialog.
2. To play the script without stopping at the end, choose Repeat Play.
The learn mode script starts, when it reaches the end of the script it re-starts at the
beginning.
To stop the script, choose Stop or choose Cancel on a dialog.

Customizing Spectrum . 243

Editing a Learn M ode script

To edit a Learn Mode script, double-click on the name of the learn mode script in
the Learn Mode dialog.
The Learn Mode - Edit and Setup dialog is displayed, this dialog enables you to edit
a learn mode script and to choose whether the dialog is floating or fixed.
Current Command Displays the steps in the learn mode script. The current step
is highlighted.
Interactive and
Non-Interactive

Becomes active when a process command that can be either

interactive or non-interactive is highlighted. Enables you to
choose whether the command is interactive or non-interactive
when the learn mode script is played.

Delete

Deletes the step highlighted in the Current Command

window.

User Comment

Enables you to add a comment to the learn mode script.

Add Comment

Adds the comments you have typed in the User Comment

text box to the learn mode script.

Pause Control

Enables you to choose between Timed, User Prompt, and

Until Continue pauses.
When you choose Timed, text boxes are displayed that
enable you to choose the length of the pause.
When you choose User Prompt, a text box is displayed that
enables you to add your own prompt to the message box.

Add Pause

Adds the type of pause you have chosen in Pause Control,

to the learn mode script.

Play Options Always play from

start

Enables you to choose whether the learn mode script is

always played from the start or plays from where it was last
interrupted.

Play Options Enables you to choose whether the learn mode script is
Always repeat this repeated until it is interrupted by the user choosing Cancel or
script
an error occurring.
Learn Mode Dialog Enables you to choose between a Floating and Fixed Learn
Mode dialog.
Open

Enables you to open a saved learn mode script file.

Save

Enables you to save the current learn mode script file.

244 . Spectrum

Adding Steps to a Learn M ode Script

You can add steps to the learn mode script at any point in the script.
1. In the Learn Mode dialog, highlight the step before the point where you want to add
the steps.
2. To start recording, choose Learn.
The Create button and a red box in the status bar flash.
3. Perform the steps you want to add.
The steps are added to the Learn Mode dialog.
4. When you have finished the steps you want to add, choose Stop.
OR
Click on

Recording stops.

Deleting Steps from a Learn M ode Script

You can delete steps from a learn mode script.
1. Double-click on the name of the learn mode script in the Learn Mode dialog.
The Learn Mode - Edit and Setup dialog is displayed.
2. In the Current Command window, highlight the step you want to delete from the
script.
3. Choose Delete.
The step is removed from the script.

Adding Com m ents to a Learn M ode Script

You can add comments to a learn mode script, these may be useful later when the script
is edited. The comments will not be displayed when the script is run but are saved in the
learn mode script file.
1. Double-click on the name of the learn mode script in the Learn Mode dialog.
The Learn Mode - Edit and Setup dialog is displayed.
2. In the Current Command window, highlight the step before the point where you
want to add the comment.
3. Type your comment in the User Comment text box.
Add Comment.
Rem: followed by your comment is added to the learn mode script.

Customizing Spectrum . 245

Adding Pauses to a Learn M ode Script

You can add pauses to a learn mode script, for example to prompt the script user to put
a sample in the sample compartment. When the learn mode script is paused, a box in the
status bar flashes yellow.
1. Double-click on the name of the learn mode script in the Learn Mode dialog.
The Learn Mode - Edit and Setup dialog is displayed.
2. In the Current Command window, highlight the step before the point where you
want the script to pause.
3. Choose Timed, User Prompt or Until Continue.
If you have chosen Timed, text boxes enabling you to enter the pause time are
displayed.
Timed pauses the script for the time set on the Learn Mode - Edit and Setup
dialog.
If you have chosen User Prompt, the User Prompt text box is displayed.
User Prompt displays a message box on the screen, the script pauses until the
user chooses OK on the message box.

Until Continue pauses the script until the user clicks on the play button
Continue button or the yellow flashing box in the status bar.
4. Enter the pause time or User Prompt as required.
5. Choose Add Pause.
The pause is added to the learn mode script.

, the

246 . Spectrum

Play Options
The Always repeat this script option enables you repeat the script until the user
chooses Cancel on a dialog or an error occurs.
1. Double-click on the name of the learn mode script in the Learn Mode dialog.
The Learn Mode - Edit and Setup dialog is displayed.
2. Choose Always repeat this script.
In the Current Command window, LEARN SCRIPT changes to REPEAT LEARN
SCRIPT.
When the script is replayed, it is repeated until the script user chooses Cancel on a
dialog or an error occurs.
The Always play from start option enables you to choose whether, when the script is
played, it always starts at the beginning or from the point where it was interrupted.
1. Double-click on the name of the learn mode script in the Learn Mode dialog.
The Learn Mode - Edit and Setup dialog is displayed.
2. Choose Always play from start.
When you play the script it always begins at the start of the script. If Always play
from start is not chosen, the script starts playing from the point where it was
interrupted or from the step highlighted in the Current Command window.

Opening and Saving Files in a Learn M ode Script

If you use the Open, Save, or Save As commands in your script, the files you use in the
recording will not be opened or saved when the script is played back. Instead a dialog
will be displayed that enables the script user to open or save any file they choose.

Customizing Spectrum . 247

Com m ands that Cannot be Added to a Learn M ode

Script
Some of the commands available in Spectrum cannot be recorded in a learn mode script
file. This restriction includes all the Administration commands, and:
Menu

Menu item

Edit menu

Paste

Sub-menu item

Text Editor
Process menu

Undo

Instrument menu

Halt

Setup menu

Login

Define Login

Report Template
Options
Toolbar

Show Toolbar
Show Toolbar Captions
Define Toolbar

Toolbox

Show Toolbox
Show Toolbox Captions
Define Toolbox

Window menu

Arrange Icons

Help

Contents
Search for Help On
Learning Spectrum
IR Tutor
About

248 . Spectrum

Using I nteractive Com m ands in a Learn M ode Script

Some Process menu commands are interactive - they enable the user to set parameters.
After you have recorded the script you can change it to enable the user of the script to
change the parameters, or leave them at set values.
The Instrument menu command Scan Sample can be interactive or non-interactive. When
recording the script, use the menu item for interactive commands and the toolbar button
to record a non-interactive command.
Only some of the commands can be non-interactive as shown in interactive commands.

Choosing w hether a com m and is interactive or non-interactive

1. Double-click on the name of the learn mode script in the Learn Mode dialog.
The Learn Mode - Edit and Setup dialog is displayed.
2. In the Current Command window, highlight the interactive command you want to
change.
Interactive and Non-Interactive are enabled.
3. Choose Interactive or Non-Interactive.
When interactive is enabled, i- is added to the command.
When the script is replayed, the script user is able to change parameters on a
dialog.

Customizing Spectrum . 249

Interactive Com m ands

Some interactive commands cannot be made non-interactive. The table below indicates
which commands are interactive, which are non-interactive, and which can be either.
Command

Interactive

Non-interactive

Data Tune-up

Absorbance

Transmittance

Kubelka-Munk

Convert X

Difference

Baseline Correction

Smooth

Deconvolution

Spectral Calculator

Normalize

Abex

Derivative

Interpolate

Blank

Kramers-Kronig

ATR Correction

Compare

IR Search

Interactive Interpretation

Quant Prediction
Peak Area/Height
Peak Table

X
X

X
X

250 . Spectrum

Spectrum Adm inistration

252 . Spectrum

Adm inistration M enu

This chapter includes topics on the administration tasks associated with Spectrum and
Spectrum ES (Enhanced Security).
NOTE: Only users that have permission to perform administration tasks in Spectrum
have access to the Administration menu. For other users, this menu is not
displayed.
Spectrum ES implements the very high levels of data integrity and security mandated for
21 CFR Part 11 technical compliance, so has an enhanced Administration command set
compared to Spectrum.
In Spectrum ES, each user must have a password. You configure the level of access
required by groups of users, then grant users appropriate group membership. Spectrum
ES also includes audit trails for both user administration and software configuration, and
controls access to legacy files and methods.
In Spectrum, user password control is much less strict, and you configure the level of
access required by each user.

Adm inistration for Spectrum

These are the commands available in the Administration menu for Spectrum. To learn
more about a command, click on its name.
Setup Users...
User Configuration...
Instrument and Accessory Configuration

>

Adm inistration for Spectrum ES

These are the commands available in the Administration menu for Spectrum ES. To learn
more about a command, click on its name.
Setup Users and Groups...
Group Configuration...
View Admin Audit Trail...
View Spectrum Audit Trail...
Instrument and Accessory Configuration
Legacy File Converter...
Quant Import...

>

Spectrum Administration . 253

Setting up Users, Groups and Passw ords

Each person using the Spectrum software must be set up as a user by a person who has
permission to perform administration tasks.
To set up users, select the Administration menu, then choose the Setup Users And
Groups command in Spectrum ES, or the Setup Users command in Spectrum. These
commands access the Users, Groups, and Password Control dialog in Spectrum ES, and
access the Users and Password Control dialog in Spectrum.
In Spectrum ES, the Supervisors and Analysts groups are predefined. The access rights
applied to these groups can be customized, and additional groups with particular access
rights created. A user's access rights depend entirely on group memberships.
In Spectrum, the Users group is predefined. The access rights applied to the Users group
cannot be amended, or additional groups created. However, particular access rights can
be granted to each user.
The Administrators group is predefined for a range of PerkinElmer software, including
Spectrum and Spectrum ES. The access rights applied to the Administrators group cannot
be customized. For this reason, the default Spectrum user named Administrator has
membership of both the Administrators group and another group (the Supervisors group
for Spectrum ES; the Users group for Spectrum).
++++++
If a group defined for another ES application also exists in Spectrum ES, its members will
appear in the Users list for Spectrum ES. However, these users will have no group
memberships in Spectrum ES. Any group memberships must be applied by a Spectrum
ES administrator.
The Users group exists for the standard versions of a range of PerkinElmer software, but
not the ES versions. A user defined for another standard PerkinElmer application will
appear in the Users list for Spectrum, but that user must be enabled by a Spectrum
administrator.
NOTE: When making any changes in the Users, Groups, and Password Control dialog
(Spectrum ES), or the Users and Password Control dialog (Spectrum), click Apply
to accept the changes and keep the dialog open. Click OK to apply the changes
and close the dialog.
See Also
Default Users
Default Groups
Assigning a User to a Group; Removing a User from a Group
Creating a Group; Deleting a Group
Assigning instruments to a Group
Adding a New User
Disabling a User; Deleting a User
Passwords; Changing a Password

254 . Spectrum
Maximum and Minimum Password Age
Password Length
Re-using Passwords
Limiting failed Login attempts
Reinstating Locked Out Users
Windows Login
Logging in to Spectrum using a Windows Login
Removing a User from the PKIUsers Windows Group

Default Users
The following users are pre-defined in Spectrum ES: Administrator, Supervisor and
Analyst.
The following users are pre-defined in Spectrum: Administrator and User.
The table below lists the passwords for the default users, and the default group that each
user belongs to:

Spectrum ES
User

Password

Group Membership

Administrator

administrator

Administrators, Supervisors

Supervisor

supervisor

Supervisors

Analyst

analyst

Analysts

Spectrum
User

Password

Group Membership

Administrator

administrator

Administrators, Users

Analyst

analyst

Users

NOTE: Another default user for both Spectrum and Spectrum ES is PEService. This
account exists for use by Perkin Elmer service engineers.

Spectrum Administration . 255

Default Groups
The Administrators group applies across a range of PerkinElmer software including both
Spectrum and Spectrum ES. Members of the Administrators group can log in to Spectrum
or Spectrum ES and Work Offline.

Default Groups for Spectrum ES

Group
Analysts

The Analysts group does not have access to the Administration

menu.

Supervisors

The Supervisors group does not have access to the Administration

menu.

Administrators

Only members of the Administrators group have access to the

Administration menu. The predefined user named Administrator is,
by default, a member of the Administrators group and a member
of the Supervisors group.

These predefined groups have no default access to instruments. Instruments and

accessories are setup by administrators using the Instrument and Accessory
Configuration command, then access permissions set from the Users, Groups and
Password control dialog Groups tab.

In Spectrum ES instrument access can be granted to all groups except the

Administrators group. An administrator who is not also a member of another
Spectrum ES group cannot access instruments. For this reason, the predefined user
named Administrator is, by default, also a member of the Supervisors group, and
can access whichever instruments are associated with that group.

In principle, a Spectrum ES administrator could be an member of the Analysts

group, or a member of another customer-defined group, rather than a member of
the Supervisors group. Any subsequent change to this more restricted access would
be logged.

Default Groups for Spectrum

Group
Users

The Users group does not have access to the Administration menu.

Administrators

Only members of the Administrators group have access to the

Administration menu. The predefined user named Administrator is a
member of the Administrators group and a member of the Spectrum
Users group.

In Spectrum, it is members of the Users group that can access instruments. An

administrator who is not also a member of the Users group cannot access instruments.

256 . Spectrum

Adding a New User

To add a new user to Spectrum or Spectrum ES:
1. From the Administration menu, select the Setup Users and Groups command
(Spectrum ES), or the Setup Users command (Spectrum).
The Users, Groups and Passwords Control dialog (Spectrum ES), or the Users and
Passwords Control dialog (Spectrum), is displayed.
2. Select the Passwords tab.
If Windows Login has been selected as the Login Type new users should be added
using Windows User Management.
Otherwise:
3. Select the Users tab and click New
The New User dialog is displayed.
4. Enter the User name, Full name and Password, then enter the Password again in
the Confirm password entry field.
NOTE: The password length is defined on the Password Control tab. Passwords are casesensitive, and can consist of letters, numbers and single spaces only.
5. By default the Status of the user is Enabled, which allows the user to login
straightaway. Select Disabled if you wish to enable the login later.
NOTE: When you enable a previously disabled user, you must enter a new password and
confirm it.
6. In Spectrum ES, if Enabled is selected, the User must change password at next
login setting is selected and grayed out, forcing the user to change password at
first log in.
In Spectrum, if Enabled is selected, the User must change password at next
login setting is optional.
7. Click OK.
The User name drop-down list is updated with the new user.

Spectrum Administration . 257

Creating or Deleting a Group

NOTE: These procedures apply to Spectrum ES only.

To Create a Group:
1. From the Administration menu, select the Setup Users and Groups command.
The Users, Groups, and Password Control dialog is displayed.
2. Select the Groups tab and click New.
A New Group dialog is displayed.
3. Enter a Group name and click OK.
The drop-down list is updated to include the new group.
4. Select the Instruments that the group members should be able to access.
By default, none of the options in the Instruments list are selected.
5. Click OK.
The New Group dialog is displayed
6. Select the existing group that the new group should be based on, then click OK.
The new group is created.

To Delete a Group
1. From the Administration menu, select the Setup Users and Groups command.
The Users, Groups, and Password Control dialog is displayed.
2. Select the Groups tab, select the Group Name that you want to delete from the
drop-down list, then click Delete.
A Group Administration dialog asks whether you are sure you want to delete the
group.
3. Click Yes.
The group is deleted.

258 . Spectrum

Assigning Users to, and Rem oving Users from , a Group

NOTE: In Spectrum ES, the Administration Audit Trail records all changes to security
settings in compliance with 21 CFR Part 11. All changes to users, groups, and
password settings are recorded.

Assigning a User to a Group

Users can be assigned to one or more groups.
1. From the Administration menu, select the Setup Users and Groups command
(Spectrum ES), or the Setup Users command (Spectrum).
The Users, Groups and Passwords Control dialog (Spectrum ES), or the Users and
Passwords Control dialog (Spectrum), is displayed.
2. Select the User tab, then the user Name from the drop-down list.
3. Select the Group from the list of Available groups for user and then click Add.
The Group is added to the User is a member of list, and removed from the
Available groups for user list.

To rem ove a User from a Group:

1. From the Administration menu, select the Setup Users and Groups command
(Spectrum ES), or the Setup Users command (Spectrum).
The Users, Groups and Passwords Control dialog (Spectrum ES), or the Users and
Passwords Control dialog (Spectrum), is displayed.
2. Select the User tab, then the user Name from the drop-down list.
3. Select the Group from the User is a member of list and then click Remove.
The Group is removed from the User is a member of list, and added to the
Available groups for user list.

Assigning I nstrum ents to a Group

NOTE: This procedure applies to Spectrum ES only.
Select the instruments available to each group on the Users, Groups and Password
Control dialog Groups tab.
1. From the Administration menu, select the Setup Users and Groups command.
The Users, Groups, and Password Control dialog is displayed.
2. Select the Groups tab, then the Group Name from the drop-down list.
NOTE: The Administrators group is not present. Spectrum administrators who are also
members of another Spectrum group have the instrument access granted to that
group.
3. Select the Instruments that the group members should be able to access.
4. Click Apply.

Spectrum Administration . 259

Disabling, or Deleting, a User

NOTE: These procedures are not applicable when the Login Type is set as Windows
Login on the Password Control tab of the Users, Groups and Passwords Control
dialog (Spectrum ES), or the Users and Password Control dialog (Spectrum). In
this case, add or delete users using Windows User Management.

To Disable an ex isting User:

1. From the Administration menu, select the Setup Users and Groups command
(Spectrum ES), or the Setup Users command (Spectrum).
The Users, Groups and Passwords Control dialog (Spectrum ES), or the Users and
Passwords Control dialog (Spectrum), is displayed.
2. Select the Users tab, select the user's Name from the drop-down list, then click
Edit.
The Edit User dialog is displayed.
3. To disable the user, select Disabled, then click OK.
When this user attempts to login the error message 'Your user name has been
locked or disabled. Please contact your system administrator' will be displayed.
NOTE: To enable a previously disabled user, select Enabled on this dialog, then enter a
new password and confirm it. The User must change password at next login
selection is recommended.

To Delete a User:
1. From the Administration menu, select the Setup Users and Groups... command
(Spectrum ES), or the Setup Users... command (Spectrum Standard).
The Users, Groups and Passwords Control dialog (Spectrum ES), or the Users and
Passwords Control dialog (Spectrum), is displayed.
2. Select the user from the User name drop-down list on the Users tab and then click
Delete.
A User Administration message will be displayed asking you to confirm that you wish
to delete the user.
3. Click Yes.
The user is deleted.
NOTE: It is not possible to reuse a User name that has been deleted.
NOTE: It is not possible to delete the Administrator from the Administrators group.

260 . Spectrum

P assw ords
For Spectrum ES, a password is mandatory. However, for Spectrum, users can either be
asked for just their User Name, or for their User Name and Password.
1. From the Administration menu, select the Setup Users and Groups command
(Spectrum ES), or the Setup Users command (Spectrum).
The Users, Groups and Passwords Control dialog (Spectrum ES), or the Users and
Passwords Control dialog (Spectrum), is displayed.
2. Select the Password Control tab.
3. In the Login and Type section, select:
PerkinElmer Login, which requires the user to enter a User Name and
Password.
Windows Login, which requires that the PKIUsers group created during the
installation of Spectrum has been populated by an IT Administrator. See
Windows Login
No Passwords Login (Spectrum only), which requires the user to enter just a
User Name.
NOTE: The No Passwords Login setting alters the behaviour of the Spectrum Login
dialog. When selected, the user can select their user name from a drop-down list.
When de-selected, the user must enter their user name manually because, for
security reasons, a drop-down list is not available.

Changing a P assw ord

NOTE: This procedure is only applicable when the Login Type is set as PerkinElmer Login
on the Password Control tab of the Users, Groups and Passwords Control dialog
(Spectrum ES), or the Users and Password Control dialog (Spectrum). When the
Login Type is set as Windows Login, change passwords using Windows User
Management.

Passw ord changes initiated by a user

A user must change their password when prompted during login. This prompt occurs
when an administrator mandates User must change password at next login, or when
the password has expired.
A user is also free to change their password during login, subject only to the Minimum
password age set for all users by an administrator.
1. At login, enter a valid User name and Password, then click Change Password
The Change Password dialog opens.
2. Enter a New password, enter in again in the Confirm password field, then click
OK.

Spectrum Administration . 261

3. To complete the login, click OK.
NOTE: A user can always change their password when prompted during login. However,
a user cannot then change their password more often than the Minimum
password age set by an administrator for all users.
In Spectrum, the Minimum password age: Allow changes after (days) is set to
1, so if the user attempts to change their password, the following message is
displayed: 'You have changed your password less than 1 days ago. You
cannot change your password again'.
To change passwords within the first day, an administrator must set Minimum
password age: Allow Changes Immediately.

Passw ord changes initiated by an adm inistrator

The following procedure enables an administrator to set a new password for a user
unable to login because their password is lost or forgotten:
1. From the Administration menu, select the Setup Users and Groups command
(Spectrum ES), or the Setup Users command (Spectrum).
The Users, Groups and Passwords Control dialog (Spectrum ES), or the Users and
Passwords Control dialog (Spectrum), is displayed.
2. On the Users tab, select the user from the Name drop-down list, then click Edit.
The Edit User dialog is displayed.
3. Enter a new Password and then enter the password again in the Confirm
password entry field.
NOTE: Passwords are case sensitive, and can consist of letters, numbers and single
spaces only.
4. Select Enabled if you wish the user to be able to login straightaway, or Disabled if
you wish to enable the login later.
5. In Spectrum, if Enabled is selected, the User must change password at next
login setting is optional.
NOTE: When creating a new user in Spectrum ES, User must change password at
next login is selected and grayed out, forcing a password change at first log in.
6. Click OK.
The new password is implemented.

262 . Spectrum

M ax im um and M inim um P assw ord Age

NOTE: These topics are only applicable when the Login Type is set as PerkinElmer Login
on the Password Control tab of the Users, Groups and Passwords Control dialog
(Spectrum ES), or the Users and Password Control dialog (Spectrum Standard).
When the Login Type is set as Windows Login, administer passwords using
Windows User Management.
NOTE: The settings on the Password Control tab apply to all users. It is not possible to
define individual Password Controls for each user.

M ax im um Passw ord Age

On the Password Control tab, Maximum password age defines the maximum number of
days that users can retain the same password before they must change it. By default the
password expires after 42 days. The minimum is 1 day and the maximum is 999 days.
The Maximum password age cannot be set less than or equal to the Minimum
password age.
NOTE: If you want to set the Maximum password age to 1 day the Minimum
password age must be set to Allow changes immediately.
If it is not necessary for users to change their password, select Password never
expires.
In Spectrum ES, users are forced to change their password the very first time they login.

M inim um Passw ord Age

On the Password Control tab, Minimum password age defines the number of days that
users must retain the same password before being allowed to change it. The default
setting for Allow changes after (days) is 1. Setting Allow changes after (days)
prevents users from changing their password several times in a short space of time in
order to return to a previous password.
To allow users to change their password immediately, select Allow changes
immediately.
The Minimum password age cannot be set greater than or equal to the Maximum
password age. The minimum is 1 day and the maximum is 999 days.
NOTE: If you want to set the Maximum password age to 1 day the Minimum
password age must be set to Allow changes immediately.
In Spectrum ES, users will be forced to change their password the first time they login.
In Spectrum, select Change Password at First Login to force users to change their
password the first time they login.

Spectrum Administration . 263

P assw ord Length

NOTE: This topic is only applicable when the Login Type is set as PerkinElmer Login on
the Password Control tab of the Users, Groups and Passwords Control dialog
(Spectrum ES), or the Users and Password Control dialog (Spectrum). When the
Login Type is set as Windows Login, all password processing is performed by
Windows.
Minimum password length on the Password Control tab defines the minimum number
of characters that must be used in the password. By default, the At least (characters)
setting is 6. The minimum setting is 1 character, and the maximum is 16 characters.
Allow blank password is an alternative option for Spectrum, but NOT for Spectrum ES.
This means that users are not required to enter a password at login, providing the user
has previously opted not to enter a password when they last changed their password, or
they have never logged in before.
NOTE: For Spectrum, if a blank password expires (the Maximum password age setting
is not Password never expires), a second blank password cannot be used
immediately unless the Password uniqueness setting is Do not keep a password
History.

Re-using P assw ords

NOTE: This topic is only applicable when the Login Type is set as PerkinElmer Login on
the Password Control tab of the Users, Groups and Passwords Control dialog
(Spectrum ES), or the Users and Password Control dialog (Spectrum). When the
Login Type is set as Windows Login, all password processing is performed by
Windows.
Password uniqueness on the Password Control tab defines the number of new
passwords that must be used before a previous password can be reused. For example, if
the first password is spectrumid, and Number of passwords to remember is set to 24
(the default setting), a user must use 24 other passwords (in addition to their current
password) before being able to use spectrumid as their password again.
For Spectrum ES, the minimum Number of passwords to remember is 1 and the
maximum is 24.
For Spectrum, an additional Password uniqueness setting is Do not keep a password
history, where no record of previous passwords is kept.

Passw ord R ecords

In Spectrum ES, a record of previous passwords is automatically made and there is no
way of turning this off.
Changes to passwords are recorded in the Admin Audit Trail. However the actual
passwords are not visible; the word Hidden is displayed instead.
NOTE: The Administration Audit Trail records all changes to security settings in
compliance with 21 CFR Part 11. All changes to users, groups and password
settings are recorded.
In Spectrum, select Do not keep password history if you do not wish to retain a record
of the number of previous passwords.

264 . Spectrum

Lim iting failed Login attem pts using Lockout

NOTE: This procedure is only applicable when the Login Type is set as PerkinElmer Login
on the Password Control tab of the Users, Groups and Passwords Control dialog
(Spectrum ES), or the Users and Password Control dialog (Spectrum). When the
Login Type is set as Windows Login, all password processing is performed by
Windows.
This procedures enables you to lock out a user that persistently fails to login correctly.
1. From the Administration menu, select the Setup Users and Groups command
(Spectrum ES), or the Setup Users command (Spectrum).
The Users, Groups and Passwords Control dialog (Spectrum ES), or the Users and
Passwords Control dialog (Spectrum), is displayed.
2. Select the Password Control tab.
3. Click Account Lockout.
The Account Lockout dialog is displayed.
4. Enter the Number of failed logins allowed before lockout.
For example, if Number of failed logins allowed before lockout is set to 5 (the
default value), the user is locked out on their 5th failed attempt until an
administrator allows them access again (Permanent) or for a specified period of
time (Duration).
The minimum number of failed login attempts before a user is locked out is 1. The
maximum number of allowed failed login attempts before a user is locked out is 10.
NOTE: If Number of failed logins allowed before lockout is 1 the user is locked out
after their first incorrect login attempt. That is, an incorrect login attempt is not
allowed; the user must login successfully at their first attempt or be locked out.
5. Select the Lockout Duration as Permanent, until Administrator unlocks, or
Duration. If you select Duration, enter the time (in minutes) for the lockout.
Permanent means that the user will be unable to login again until an administrator
has assigned a new password. Duration is grayed if Permanent is selected.
Duration prevents the user being able to login again until the time specified has
elapsed. If Duration is selected, the default is 60 minutes. The minimum Duration
is 1 minute and the maximum Duration is 32767 minutes (22.75 days).
NOTE: Details of failed login attempts are recorded in the Login History.

Spectrum Administration . 265

Reinstating Locked Out Users

NOTE: This topic is only applicable when the Login Type is set as PerkinElmer Login on
the Password Control tab of the Users, Groups and Passwords Control dialog
(Spectrum ES), or the Users and Password Control dialog (Spectrum). When the
Login Type is set as Windows Login, all password processing is performed by
Windows.
If Account Lockout is set to Permanent until Administrator unlocks and the user has
failed to login correctly within the allowed number of attempts, an administrator must
assign a new password before the user is able to login again.
If one or more users a has been locked out, when an administrator next logs in a list of
Locked Out Users is displayed.
1. Highlight the name of the user that you wish to reinstate and then click Edit.
The New/Edit User dialog is displayed.
NOTE: If you click OK rather than Edit when the list of Locked Out Users is displayed,
the list is closed. Any locked out users will remain locked out. The list will be redisplayed each time you login until all locked out users have been assigned a new
password.
2. Enter a new Password and repeat it in the Confirm password field.
3. Click OK.
The user is removed from the list of Locked Out Users.
4. Click OK to close the Locked Out Users dialog.
The previously locked out user will now be able to login using the new password,
which they will be forced to change if you are using the Enhanced Security version
of Spectrum. If you are using the Standard version, the user will only be forced to
change the password if User must change password at next login was selected.
NOTE: Users locked out for a specified duration can be unlocked by the administrator in
the same manner.

266 . Spectrum

W indow s Login
It is possible for users to log in to Spectrum using their Windows User Name and
Password (instead of having a separate Spectrum User Name and Password).
It is not possible to have some users that log in using their Windows User Name and
Password while others use a separate Spectrum login.
To facilitate the use of Windows User Names and Passwords, the PKIUsers group is
created on the local PC during the installation of Spectrum. When Spectrum is installed
and run on a local PC, the Windows administrator should add all the users who will
access Spectrum to the PKIUsers group. When Spectrum is used across a network, the
Windows Administrator should create a network group on an accessible domain and then
add users to that group.

To Add W indow s users to the PK IUsers group on a local PC:

1. Install Spectrum.
2. From the Windows Start menu, select Control Panel then select the User
Accounts category.
3. Select the Control Panel icon named User Accounts
The User Accounts dialog opens.
4. Select the Advanced tab, then click the Advanced user management: Advanced
button.
5. Select Local Users and Groups.
6. Select the Groups folder to see the list of available Groups on the PC.
7. Double-click on PKIUsers.
The PKIUsers Properties dialog is displayed. The Members list already contains
Everyone. This group has been created for folder access only, not as a Windows
user group as it contains no user members.
8. To add a user member to the Group, click Add.
The Select Users, Computers, or Groups dialog is displayed.
9. To select a user from a different location (domain), click Locations and then select
the required location for the user you wish to add.
10. To add a user to the group, enter the name of the user in the Enter the object
name to select field and then click Check Names.
Clicking Check Names will validate the name on the specified domain.
NOTE: If you are not logged onto this domain already, a login dialog will be displayed.
11. Click OK.
The Select Users, Computers, or Groups dialog is closed and the user is added as a
member to the PKIUsers Properties dialog.

Spectrum Administration . 267

12. To add more users, repeat steps 8 to 11.
NOTE: It is possible to add a user more than once if they are on more than one domain
as each Location together with the User name and Password will be unique.
All users added to the PKIUsers Group on the local PC, or added to a network users
group, will be able to log in to Spectrum once a Spectrum administrator has defined the
Login Type as Windows Login.
NOTE: Any users added to the PKIUsers Group before logging into Spectrum for the first
time will appear in the Name drop-down list on the Users tab of the Users,
Groups and Passwords Control dialog (Spectrum ES), or the Users and Passwords
Control dialog (Spectrum). If users are subsequently added, click Update users
on the Users tab to refresh the Name drop-down list.

To define the Spectrum Login Type as W indow s Login:

NOTE: The Login Type (Windows Login, PerkinElmer Login or No Passwords Login
(Spectrum Standard only)) applies to all users. It is not possible to have some
users that log in using their Windows Login while others use a separate Spectrum
login.
1. Start Spectrum.
[Select Start, All Programs, PerkinElmer Applications, Spectrum (ES), then
Spectrum (ES)].
2. Log in as a Spectrum administrator.
The default User Name is Administrator and the Password is administrator.
3. From the Administration menu, select the Setup Users and Groups command
(Spectrum ES), or the Setup Users command (Spectrum).
The Users, Groups and Passwords Control dialog (Spectrum ES), or the Users and
Passwords Control dialog (Spectrum), is displayed.
4. Select the Password Control tab.
5. From the Login Type drop-down list select Windows Login.
All the other information previously displayed on the tab is removed as the
password controls are now from Windows rather than Spectrum.
The Load Windows Users dialog is displayed.
6. Select the domain and specify the group of Windows users that you wish to add to
the list of Spectrum users.
The default selection is the PKIUsers group on the local PC.

268 . Spectrum
7. Click OK.
The Windows users will be loaded and you may be prompted to select a new
Spectrum administrator.
NOTE: If users are subsequently added to the PKIUsers group, to add these new
Windows users to the list of Spectrum users a Spectrum administrator must click
Update users on the User tab of the Users, Groups, Password Control and
Summary dialog (Spectrum ES), or the Users and Passwords Control dialog
(Spectrum).

To assign users Spectrum group m em berships:

NOTE: If a user is not added to at least one group, an error message will be displayed
when they try to log in informing them that they do not have access to the
application.
1. Select the user from the Name drop-down list on the User tab.
2. Select the Group from the list of Available groups for user and then click Add.
The Group is added to the User is a member of list.
3. Click OK to close the dialog and apply the changes.
NOTE: During the installation of Spectrum, PE21CFR server, 21CFR_Admin group and
21cfr user are installed. PE21CFR server needs to run under Windows admin
authority. By default it uses the 21cfr admin user for this. You can change which
user is used to run PE21CFR using the PE21CFR configuration program
([Link]) which can be found under C:\Program
Files\PerkinElmer\PE21CFR. Running [Link] displays the Enhanced
Security Configuration dialog. Select the Security Server tab and change the
Account Name. Click Save and Close for the new Account Name to be activated.

Spectrum Administration . 269

Logging in to Spectrum using a W indow s Login

If you have been set up to log in to Spectrum using your Windows login:
1. Start the Spectrum application.
[Select Start, All Programs, PerkinElmer Applications, Spectrum (ES), then
Spectrum (ES)].
2. Enter your Windows User name and Password.
If the Log on to field is not displayed, click Options>> to show the field.
3. Select the required Domain from the Log on to drop-down list.
By default, the Domain last logged on to is displayed.
NOTE: If all users are on the same Domain, there is no need to show the Log on to
field as the correct Domain will be listed. To avoid confusion, this field can be
hidden by clicking Options<<

Troubleshooting W indow s Login

There may be a number of reasons why you can't login using your Windows Login. Check
that each of the following is correct:

Your Windows administrator has added your name to the PKIUsers Group
(See Windows Login)

You have been assigned to at least one Group within Spectrum

(See Windows Login).

You have entered the correct User Name and Password, and selected the correct
Domain option from the Log on to drop-down list.

PE21CFR is still running. From the Start menu select Control Panel, and then select
Administrative Tools. Then select Services. In the Services dialog check that
PE21CFR is still running. If this has been paused or stopped you will be unable to
login to Spectrum.

Passw ord expiry

If whilst logging into Spectrum you get a message that your password is about to expire,
you can change your password. This change will be implemented by Windows as well as
Spectrum.

270 . Spectrum

Rem oving a User from the P KI Users W indow s Group

To remove a User from the PKIUsers Windows group:
1. From the Windows Start menu, select Control Panel then select the Performance
and Maintenance category.
2. Select the Control Panel icon named Administrative Tools.
3. Double-click on Computer Management.
The Computer Management dialog is displayed.
4. Double-click on Local Users and Groups.
5. Double-click on the Groups folder to see the list of available Groups on the PC.
6. Double-click on PKIUsers.
The PKIUsers Properties dialog is displayed.
7. To remove a user member from the Group, select the required member and then
click Remove.
The user is removed from the Group.

Spectrum Administration . 271

User Configuration in Spectrum

Spectrum can be configured to the needs of individual users. Items that may be
configured include menu options (by graying or hiding), and the toolbar and toolbox.
This topic describes how you use the User Configuration dialog to apply particular
configuration settings to an individual user.
Use the Users and Password Control dialog to enable or disable users, and to specify
whether or not the user should be a Spectrum administrator.

To apply particular configuration settings to a user:

1. From the Administration menu, select the User Configuration command.
The User Configuration dialog is displayed, which lists all users in its left hand pane.
2. Click on the name of the user you want to configure.
The tree expands to show the configuration categories for the user, namely the
Menus, Toolbar and Toolbox Configuration folders.
See also:
Configuring Menu items in Spectrum
Configuring the Toolbar and Toolbox in Spectrum
Configuration Files

Configuring M enu item s in Spectrum

Menu items not required by this user may be disabled. There are two ways to disable
menu items - you can choose to gray them so they cannot be selected, or choose to hide
them completely. Whether to gray or hide unwanted menu options is a global setting that
applies to all menu items - you cannot gray some menu items and hide others.

Setting global m enu properties

1. Select the user's Menus folder, then click Properties.
2. Choose Gray out from Menus (the default setting), or Hide completely from
menus.
This setting applies to all the menu items that you disable.

Disabling individual m enu item s

1. Select the user's Menus folder, then click the menu you want to amend.
2. Select the menu items to disable.
Before disabling menu items you may want to read some important considerations.

272 . Spectrum

Configuring the Toolbox & Toolbar in Spectrum

The toolbar and toolbox are configurable in exactly the same way. You can configure the
buttons this user should see, and specify the size and spacing of buttons.

Setting the size and spacing of buttons in the toolbar or toolbox

NOTE: Individual users can display or hide the captions from within Spectrum. You
cannot display or hide them here. The With Caption and Without Caption settings
enable you to specify two alternative button sizes and spaces. The sizes and
spaces that are used depends on whether the user chooses to display the
captions.
1. In the Toolbar or Toolbox folder, click on Properties.
2. In the Button Caption section, With Caption is selected (by default).
3. Click Font to set the font that will be used if the user switches the captions on.
4. In the Size/Positioning section, set the height (Button Height) and width (Button
Width) of the buttons, the interval between buttons (Button Interval) and the
spacer width (Spacer Width). These settings will be used when the user switches
the captions on.
5. In the Button Caption section, select Without Caption.
6. In the Size/Positioning section, set the height (Button Height) and width (Button
Width) of the buttons, the interval between buttons (Button Interval) and the
spacer width (Spacer Width). These settings will be used when the user switches
the captions off.

Adding or rem oving buttons from the Toolbar or Toolbox

1. In the Toolbar or Toolbox folder, click on Toolbar or Toolbox.
On the left side, the Standard Buttons section lists all the available buttons, while on
the right side, the Target Toolbar/Toolbox section displays the buttons in the toolbar
or toolbox for the group you are editing.
2. Edit the Target Toolbar/Toolbox by adding or removing buttons using the arrow
buttons. You can add a space to the toolbar by adding a Spacer, or start a new line
of buttons by adding a NewLine.

Spectrum Administration . 273

Creating your ow n button

You can create your own tool for use on the Toolbar or Toolbox, which can activate any
command or any executable program that can be run from within Windows.
1. In the Toolbar or Toolbox folder, click on Toolbar or Toolbox.
2. Click Define User Button
The User Button Definition dialog is displayed.
3. In Menu Item/Application, either choose a command from Menu List (by double
clicking the appropriate command), click Browse to choose an external application,
or type the command line for an application.
To enter a tooltip, type the tooltip at the end of the filename and path in Menu
Item/Application, between < and > symbols, for example <my tooltip>.
4. For the Bitmap Image File click Browse to choose a picture for the button. When
you have selected the bitmap (.bmp) or icon (.ico) file, the file source and file is
specified in Bitmap Image File.
NOTE: If you use a bitmap icon larger than 26x26 pixels the edges of the image may be
cropped.
5. In Button Caption, enter the caption to be displayed under the button, then click
OK.
NOTE: If you choose an application that has an icon and a caption associated with it, the
associated icon and caption appear in the dialog by default. You can either use
these defaults or change them.
The User Button Definition dialog closes. The new button now appears at the
bottom of the Standard Buttons list.
6. To add the new button to the target toolbar select it and click >.

274 . Spectrum

Group Configuration in Spectrum ES

A group is a set of configuration settings within Spectrum ES. Items that may be
configured include menu options (by graying or hiding), toolbars and toolboxes, and
other configuration settings such as default directories. These items are not configured
for individual users, but for groups of users. You specify which items an individual user
has access to by assigning the user to a group with the required settings.
This topic describes how you use the Group Configuration dialog to apply particular
configuration settings to a group.
Use the Users, Groups and Password Control dialog to create or delete groups, and to
assign group membership to users.

To apply particular configuration settings to a group:

1. From the Administration menu, select the Group Configuration command.
The Group Configuration dialog is displayed, which shows all the available groups in
its left hand pane.
2. Click on the name of the group that you want to configure.
The tree expands to show the configuration categories for the group, namely the
Menus, Toolbar, Toolbox, and Configuration folders.

Configuring M enu item s in Spectrum ES

When configuring Groups in Spectrum ES, Menu items not required by this group of users
may be disabled. There are two ways to disable menu items - you can choose to gray
them so they cannot be selected, or choose to hide them completely. Whether to gray or
hide unwanted menu options is a global setting that applies to all menu items - you
cannot gray some menu items for this group of users and hide others.

Setting global m enu properties

1. In the Group Configuration dialog, select the Group's Menus folder, then click on
Properties.
2. Choose Gray out from Menus (the default setting), or Hide completely from
menus.
This setting applies to all the menu items that you disable.

Disabling individual m enu item s

1. In the Group Configuration dialog, select the Group's Menus folder, then click on
the menu you want to amend.
2. Select the menu items to disable.
Before disabling menu items you may want to read some important considerations.

Spectrum Administration . 275

I m portant M enu Configuration Considerations

Sub-m enus
The presentation of menu items within each configuration folder does not indicate the
hierarchical structure of the menus that are present in Spectrum. Certain items listed
within some of the menu folders are actually the sub-menu options of menu items.

If the menu item is disabled, then both the menu item and the sub-menu items in
Spectrum cannot be accessed. This applies whether the corresponding sub-menu
items have been marked as disabled or not.

If the menu item is enabled and some of the corresponding sub-menu items have
been disabled, then only the sub-menu items that have been left as enabled can be
accessed within Spectrum.

If the menu item and all sub-menu items have been disabled, then both the menu
item and the corresponding sub-menu items in Spectrum cannot be accessed.

Help m enu
In Spectrum ES, to ensure compliance with 21CFR Part 11, the Visit the PerkinElmer
Website command is permanently disabled regardless of this configuration setting

Instrument m enu
System Suitability, Validate Instrument, ASTM 0 and USP are sub-menu items of
Validate.
Enabling and disabling menu or sub-menu items in the absence of the appropriate
instrument has no effect. An example is ASTM 0 vs USP:
If a Spectrum 100 spectrometer is attached to Spectrum ES, then USP does not apply so
this is marked as disabled by default. For the Spectrum 100N, ASTM 0 does not apply
and this, like USP, is disabled by default. If ASTM 0 or USP is enabled, but the correct
instrument is not available then the software still treats these menu items as disabled.

Process m enu
Automatic Correction and Interactive Correction are sub-menu items of
Baseline Correction.
Automatic Smooth, Interactive Smooth and User Selected Smooth are sub-menu
items of Smooth.

276 . Spectrum

Setup m enu
System Suitability, Instrument, ASTM and USP are sub-menu items of Validation.
Show Toolbar and Show Toolbar Captions are sub-menu items of Toolbar.
Show Toolbox and Show Toolbox Captions are sub-menu items of Toolbox.

View m enu
Overlay and Split are sub-menu items of Overlay/Split Display.
Vertical Continuous, Vertical-Peak and Horizontal are sub-menu items of Cursor.

Window m enu
Horizontal and Vertical are sub-menu items of Tile.

Setup m enu
In Spectrum ES, to comply with 21CFR Part 11:
You may wish to prevent users from making any changes to the setup of an instrument
by disabling all Setup menu items.

Return to Configuring Menu items in Spectrum ES

Return to Configuring Menu items in Spectrum

Spectrum Administration . 277

Configuring the Toolbar & Toolbox in Spectrum ES

The toolbar and toolbox are configurable in exactly the same way, from the Group
Configuration dialog. You can configure the buttons this group of users should see, and
specify the size and spacing of buttons.

Setting the size and spacing of buttons in the toolbar or toolbox

NOTE: Individual users can display or hide the captions from within Spectrum. You
cannot display or hide them here. The With Caption and Without Caption settings
enable you to specify two alternative button sizes and spaces. The sizes and
spaces that are used depends on whether the user chooses to display the
captions.
1. In the Toolbar or Toolbox folder, click on Properties.
2. In the Button Caption section, With Caption is selected (by default).
3. Click Font to set the font that will be used if the user switches the captions on.
4. In the Size/Positioning section, set the height (Button Height) and width (Button
Width) of the buttons, the interval between buttons (Button Interval) and the
spacer width (Spacer Width). These settings will be used when the user switches
the captions on.
5. In the Button Caption section, select Without Caption.
6. In the Size/Positioning section, set the height (Button Height) and width (Button
Width) of the buttons, the interval between buttons (Button Interval) and the
spacer width (Spacer Width). These settings will be used when the user switches
the captions off.

Adding or rem oving buttons from the Toolbar or Toolbox

1. In the Toolbar or Toolbox folder, click on Toolbar or Toolbox.
On the left side, the Standard Buttons section lists all the available buttons, while on
the right side, the Target Toolbar/Toolbox section displays the buttons in the toolbar
or toolbox for the group you are editing.
2. Edit the Target Toolbar/Toolbox by adding or removing buttons using the arrow
buttons. You can add a space to the toolbar by adding a Spacer, or start a new
line of buttons by adding a NewLine.

278 . Spectrum

Creating your ow n button

You can create your own tool for use on the Toolbar or Toolbox, which can activate any
command or any executable program that can be run from within Windows.
1. In the Toolbar or Toolbox folder, click on Toolbar or Toolbox.
2. Click Define User Button
The User Button Definition dialog is displayed.
3. In Menu Item/Application, either choose a command from Menu List (by double
clicking the appropriate command), click Browse to choose an external application,
or type the command line for an application.
To enter a tooltip, type the tooltip at the end of the filename and path in Menu
Item/Application, between < and > symbols, for example <my tooltip>.
4. For the Bitmap Image File click Browse to choose a picture for the button. When
you have selected the bitmap (.bmp) or icon (.ico) file, the file source and file is
specified in Bitmap Image File.
NOTE: If you use a bitmap icon larger than 26x26 pixels the edges of the image may be
cropped.
5. In Button Caption, enter the caption to be displayed under the button, then click
OK.
NOTE: If you choose an application that has an icon and a caption associated with it, the
associated icon and caption appear in the dialog by default. You can either use
these defaults or change them.
The User Button Definition dialog closes. The new button now appears at the
bottom of the Standard Buttons list.
6. To add the new button to the target toolbar, select it and click >.
21CFR11: When operating in a 21CFR11 compliant environment, consider carefully the
implications of adding any applications to the toolbar or toolbox. Some
applications may allow users to access data files that they should otherwise
not be able to access.

Spectrum Administration . 279

Applying other Configuration settings in Spectrum ES

These Configuration settings may either be set here (that is, via the Spectrum
Administration Group Configuration command), or via the Spectrum Setup menu
Options command. If you set the configuration here, the corresponding dialog or setting
is not available in the Options dialog.
21CFR11: It is much more secure to set these options here than it is to allow users to
set them within Spectrum ES. When operating in a 21CFR11 compliant
environment, consider carefully whether to select Allow user to make
settings.
1. Click the Configuration folder to open it.
2. Select the category of settings that you want to work with:
Default Directories

GLP Lock

Process

Instrument Access

Procedures

Data Collection

Default Directories
Specifies the default directories for different types of file used in Spectrum ES. This
means that when you open or save a file, this directory is the one that is initially
displayed in the Open or Save dialog.
If you want each user to be able to set their own default directories from within
Spectrum ES, select Allow user to make settings. If you do this, the user can change
default directories by displaying the Setup menu, selecting Options, and then selecting
the File tab of the Options dialog. If you clear Allow user to make settings, the File tab
is unavailable in Spectrum ES.
21CFR11: The Windows NTFS filing system allows NT Administrators to set access
permissions to directories and files within the filing system. For example, it is
possible to set directory permissions to only allow files to be added and read,
but not deleted, renamed, executed or overwritten. When setting default
directories, consider carefully the permissions that a user needs to have when
writing data files within these directories and their subdirectories.
return to categories

GLP Lock
When GLP Lock is switched on, users are prevented from changing the Analyst and
Description information in the status information dialog for spectra that they have
collected previously. This information is added when the spectrum is collected, and may
not be changed afterwards.
If you want each user to be able to switch GLP Lock on or off in Spectrum ES, select
Allow user to make settings. If you do this, the user can change the GLP setting by
displaying the Setup menu, selecting Options, and then selecting the View tab of the
Options dialog. If you clear Allow user to make settings, the GLP Lock setting is
unavailable in Spectrum ES.
return to categories

280 . Spectrum

Process
You can specify settings for process commands in Spectrum ES. These settings apply
every time you process a spectrum using a command on the Process menu.
Overwrite Original

The spectrum to be processed will be replaced by the spectrum

that has been processed. No warning will be given. However, you
will be able to undo the action of the previous Process command
using the Undo command on the Process menu
21CFR11: This applies to spectra in memory, not those saved on
disk. Spectrum files on disk are prevented from being overwritten
by Spectrum ES and, ideally, by NTFS file permissions.

Auto Name

Spectrum ES will name the new spectrum with a unique name. It

consists of the original spectrum name with a new extension

User Name

A dialog will be displayed prompting you to enter a name for the

processed spectrum. If you enter a spectrum name that already
exists, you will be warned and given the option to enter another
name.

You can also specify which processes are included in a Data Tune-up. A Data Tune-up
is initiated from the Process menu by selecting Data Tune-up, and includes one or more
of the following:
Smooth

The spectrum is automatically smoothed.

Flat

The baseline of the spectrum is automatically flattened

Blank

Blank regions are automatically set in regions of the spectrum

where the noise is greater than the Noise Threshold.

NOTE: When all three data tune-up check boxes are clear (the default setup), the
message Data tune-up setup incomplete is displayed when you attempt to start a
Data tune-up.
If you want each user to be able to change these settings in Spectrum ES, select Allow
user to make settings. If you do this, the user can change these settings by displaying
the Setup menu, selecting Options, and then selecting the Process tab of the Options
dialog. If you clear Allow user to make settings, the Process tab is unavailable in
Spectrum ES.
return to categories

Spectrum Administration . 281

Instrum ent Access

The Instrument Access settings enable you to specify the level of access to instrument
controls that members of this group will have.
Routine access

Standard access

Advanced access

Users have very limited access to the instrument:

Access to only the Sample and Accessory tabs on the

Spectrum One Scan and Instrument Setup dialog;

Ability to monitor only Energy or Sample;

No access to the instrument setup functions.

Users do not have access to the following instrument controls:

The Advanced functions on the Instrument tab of the

Spectrum One Scan and Instrument Setup dialog, and the
Beam tab is only available if you enter the dialog from
Instrument on the Setup menu, not from Scan on the
Instrument menu;

The ability to monitor interferograms;

The Sampling Configuration, Data Collection and Adjustments

Toolbox dialogs.

Users have full access to all instrument control.

If you want each user to be able to change the access options in Spectrum ES, select
Allow user to make settings. If you do this, the user can change access settings by
displaying the Setup menu, selecting Options, and then selecting the Instrument tab of
the Options dialog. If you clear Allow user to make settings, the access settings are
unavailable in Spectrum ES.
return to categories

Procedures
You can specify the procedures that appear on the Procedures menu in Spectrum ES.
To add a procedure to the menu:
1. Enter the text to be displayed in the Procedures menu in Menu Text:
Precede the character that you choose to be underlined, and therefore activated by
the ALT + underlined letter keyboard shortcut, by an ampersand (&).
2. Enter the command line path of the procedure or application in Command Line:
OR
Click

to browse to the required drive path and file.

If you are adding a procedure that was created in Spectrum Procedures, type the
path and filename of the procedure, followed by <spectra>. When you run the
procedure from the Procedures menu, the selected spectra are input into the
procedure, in the same order as they are on the graph.
3. Click Add

282 . Spectrum
To remove a procedure from the menu:

Select the procedure you want to remove, then click Delete

If you want users in this group to be able to change the Procedures menu in Spectrum
ES, select Allow user to make settings. If you do this, the user can change the
Procedures setting by displaying the Setup menu, selecting Options, and then selecting
the Others tab of the Options dialog. If you clear Allow user to make settings, the
Procedures section of the Others tab is unavailable in Spectrum ES.
21CFR11: Adding your own procedures or applications to the Procedures menu is a
powerful feature, and one which may break 21CFR11 compliance if the
security aspects are not considered.
return to categories

Data Collection
You can specify how spectra collected in Spectrum ES are named.
If you select User Specified, then prior to scanning, the user enters the filename in the
Scan (or Instrument Setup) dialog on either the Scan tab or the Multiple Scan tab.
If you select Auto-Increment, you must also enter a Prefix for the filename. When the
user collects a spectrum, a filename is created automatically using the Prefix and an
autonumber. Every time a new spectrum is collected, the autonumber is increased by 1.
This results in a series of spectra with names such as [Link], [Link],
[Link] and so on.
You can also specify Auto-Save options for Spectrum ES. By default, Enable Auto-Save
is selected so, after data collection, Spectra are saved automatically in a binary Format.
21CFR11: The use of Auto-Save ensures that any spectra collected by Spectrum ES are
automatically saved to disk. We recommend that you use Auto-Save if you
wish to comply with 21CFR11. The recommended file format is binary so that
data files cannot be tampered with.
If you want each user to be able to change these settings in Spectrum ES, select Allow
user to make settings. If you do this, the user can change the settings by displaying
the Setup menu, selecting Options, and then selecting the Instrument tab of the Options
dialog. If you clear Allow user to make settings, these data collection settings are
unavailable in Spectrum ES.
return to categories

Spectrum Administration . 283

Adm inistration Audit Trail

NOTE: Applies to 21 CFR Part 11 compliant (ES) environments. The Administration Audit
Trail can only be viewed by users able to perform administration tasks.
The Administration Audit Trail records all changes to security settings in compliance with
21 CFR Part 11. All changes to users, groups and password settings are recorded.
1. Select View Admin Audit Trail from the Administration menu.
The Login History, Audit Trail and Summary dialog is displayed.
2. Select the Audit Trail tab.
The audit trail is displayed. For each change recorded, the following information is
given in the Audit Trail:
Function - the item that was changed, for example, Add New User
Previous Value - the state of the item before it was changed.
Numbers refer to instruments; see Summary
Current Value - the new state.
Numbers refer to instruments; see Summary
Full Name - the full name of the user who made the change
User Name - the login user name of the user who made the change
Computer - the name of the computer from which the change was made
Date Modified - the date and time of the change

Printing the Audit Trail

To print the Audit Trail click Print.

All the information currently held in the Audit Trail is printed.

Ex porting the Audit Trail

1. To export the Audit Trail click Export.
A Save As dialog is displayed.
2. Select the required destination and enter a filename.
The Audit Trail is exported as a *.csv file that can be opened, for example, in
Microsoft Excel.
NOTE: Exporting the Audit Trail does not clear the Audit Trail entries from the dialog.
However, you must export Audit Trail entries before they can be cleared.

284 . Spectrum

Clearing the Audit Trail

To clear the Audit Trail, click Clear Audit.

You will be asked to confirm that you want to delete the Audit Trail log. All details
are removed.

NOTE: It is only possible to clear Audit Trail entries that have previously been exported.
If the Audit Trail contains additional entries since it was last exported, only those
entries that have been exported will be deleted. If none of the entries have been
exported, a warning message will be displayed when you attempt to clear the
Audit Trail.

Login History
NOTE: Applies to 21 CFR Part 11 compliant (ES) environments. The Login History can
only be viewed by users able to perform administration tasks.
1. Select View Admin Audit Trail from the Administration menu.
The Login History, Audit Trail and Summary dialog is displayed.
2. Select the Login History tab.
The login history is displayed. This details every login attempt, since the history was
last cleared, by:
Full Name - the full name of the user, or Not found if the user name entered did
not exist.
User Name - the user name entered, whether correct or not.
Computer - the name of the computer
Status - OK indicates that the user logged in with the correct password, Failed
indicates that a login was attempted with an incorrect password.
Logged In - date and time.
Logged Out - date and time.
NOTE: If a non-existent User Name is entered during login, a failed login attempt is
recorded. Not Found is entered in the Full Name field of the Login History, and
the incorrectly entered User Name is also recorded.
NOTE: There is no limit to the size of the Login History.

Spectrum Administration . 285

Printing the Login History

To print the Login History click Print.

All the information currently held in the Login History is printed.

Ex porting the Login History

1. To export the Login History click Export.
A Save As dialog is displayed.
2. Select the required destination and enter a filename.
The Login History is exported as a *.csv file and can be opened, for example, in
Microsoft Excel.
NOTE: Exporting the Login History does not clear the Login History details from the
dialog. However, you must export Login History entries before they can be
cleared.

Clearing the Login History

To clear the Login History, click Clear History.

You will be asked to confirm that you want to delete the Login History log. All Login
details are removed. The first Login details to appear after the Login has been
cleared will be the date and time that you log out.

NOTE: It is only possible to clear Login History entries that have previously been
exported. If the Login History contains additional entries since it was last
exported, only those entries that have been exported will be deleted. If none of
the entries have been exported, a warning message will be displayed when you
attempt to clear the Login History.

286 . Spectrum

Sum m ary
NOTE: Applies to 21 CFR Part 11 compliant (ES) environments. The Summary can only
be viewed by users able to perform administration tasks.
1. The document created by this command records a summary of the security status of
the application.
2. Select View Admin Audit Trail from the Administration menu.
The Login History, Audit Trail and Summary dialog is displayed.
3. Select the Summary tab.
The Summary records all information about the security settings:

Application - records the application for which this Summary applies.

Password control - records the Login type, Windows group, Maximum

password age, Minimum password age, Minimum password length, Password
uniqueness, Lockout count and Lockout duration.

Permissions - records the number of permissions, then lists each permission

with the number of users to which it applies.

Instruments - records the number of instruments attached to the application,

including a notional instrument named 'Work Offline'. Each instrument is then
listed with a number that is used to identify the instrument on the Audit Trail.

Users - records the number of users, including a default user for each group.
It then records each Username, Full name, Status, Last login, the Groups the
user belongs to, and the Permissions of that group.

Groups - records the number of groups. For each Group it records the Group
Name, the Users in the Group, and the Instruments the group has permission
to use.

Printing the Sum m ary

To print the Summary click Print.

All the information is printed.

Ex porting the Sum m ary

1. To export the Summary click Export.
A Save As dialog is displayed.
2. Select the required destination and enter a filename.
The summary is exported as a *.csv file and can be opened, for example, in
Microsoft Excel.

Spectrum Administration . 287

Spectrum Audit Trail

NOTE: Applies to 21 CFR Part 11 compliant (ES) environments. The Spectrum Audit Trail
command is only available to users able to perform administration tasks.
The Spectrum Audit trail records any changes made to the software's configuration in an
active database. You can periodically archive the active database, so that old data is
moved to an archive database. The archive database is closed and cannot be reused as
the active database. There is only one active database but, over time, you create a
number of archive databases.
1. Select the View Spectrum Audit Trail command from the Administration menu.
The Spectrum Audit Trail dialog is displayed, together with the records in the active
database:
ID - the audit trail record number
User ID - the identity of the user that made the change
File Name - the filename for the group settings applicable to that user
Time - the date and time of the change
PC ID - the name of the computer used to make the change
Heading - the name of the collection of configuration settings where the change
can be found
Category - the type of audit trail record
Item - the name of the configuration that was changed
Change Type - allowed values for the configuration that was changed
Old Value - the previous value applied to the configuration that was changed
New Value - the value applied when the configuration change was made.
2. To view any archived records, open the Related Archives folder in the left-hand
pane of the Spectrum Audit Trail dialog, then select the name of the archive
database from those listed.
The records in the archive database are displayed.
Hint:

If you cannot see the Related Items tree, click on the Active Database icon to
refresh the left pane.

If you cannot display a particular archive database using the link in the Related
Items tree, the archive database may have been moved to another secure location.
See: Displaying an Archive database stored elsewhere

The record entry controls in the right pane are never available; there are no
circumstances when records can be entered or changed manually.

288 . Spectrum

Archiving the Active database

To archive the current active database used by the Spectrum Audit Trail:
NOTE: This action cannot be undone and a warning dialog will be presented each time
the archiving action is undertaken.
1. In the Spectrum Audit Trail dialog, select the Archive Active Database command
from the Actions menu, or click the

button.

2. Click Yes to confirm that you want to archive the active database.
Records in the active database are moved to a new archive database file stored in
the same location as the active database. A Cap Record is added so that the archive
cannot be used as the active database.
A new Archive appears in the Related Archives folder. The name Archive is followed
by a number that is incremented by one each time an archive database is created.
The most recently archived records are in the Archive followed by the highest
number. For example: Archive 1 links to the first archive database; Archive 10 links
to the tenth archive database.

Displaying an Active database stored elsew here

If an archive database file has been moved since its creation, it cannot be read using the
pointer in the Related Archives folder in the left pane of the Spectrum Audit Trail dialog.
Instead:
3. Select the Open Audit Database command from the File menu, or the click the
button.
The Open file dialog opens.
4. Browse to and select the appropriate Audit*.mdb file, where * represents a numeric
security code.
The Spectrum Audit Trail dialog displays the contents of the archive database.
NOTE: Typically, the path to archived audit database files is:
C:\Documents and Settings\All Users\Application
Data\PerkinElmer\SpectrumES\Audit*.mdb
Although C:\Documents and Settings\All Users\Application Data is hidden by
default, audit files can be copied, or moved to another secure location for longterm storage.

Spectrum Administration . 289

P rinting an Audit database

Three File menu commands (or their equivalent buttons) govern how the Spectrum Audit
Trail database is printed, namely: Print
Print Preview

, Print Options

, and

The page orientation (landscape or portrait, set in the Print dialog as a printer
Preference) affects the Print Preview display, and may affect which Print Options you
choose.

To select a printer and page orientation:

1. Select the Print command from the File menu, or the click the

button.

The Print dialog opens.

2. Select the printer you wish to use, click Preferences, then choose Landscape or
Portrait on the Page tab.
3. Close the Printing Preferences and Print dialogs.

To form at the records for printing:

1. Select the Print Options command from the File menu, or the click the
button.
The Audit Print Options dialog opens.
2. Enter any Header Text required, then format the records for your printer by:
Checking or un-checking the Print options,
Selecting appropriate Margin sizes,
Selecting appropriate fonts and colors.
3. When you are happy with your selections, click OK.

To preview your print:

Select the Print Preview command from the File menu, or click the

button.

The records are displayed as they will be printed.

To start printing:

Click the Print button in either the Print

or the Print Preview

dialogs.

290 . Spectrum

Ex porting an Audit database

To export an audit database from the Spectrum Audit Trail dialog:
1. View the active or archive audit database that you want to export.
2. Select the Export Audit Database command from the File menu, or click the
button.
The Save As dialog opens.
A file saved in the comma separated value (.csv) text file format can be read by many
spreadsheet and database applications.

Creating & Using a new Active database

To create a new Active database:
1. In the Spectrum Audit Trail dialog, select the Create Active Audit Database
command from the Actions menu, or the click the

button.

A Warning dialog states that 'This action cannot be undone, continue ?'
2. Click Yes to confirm that you want to create a new active audit database.
The Open file dialog opens.
3. Browse to the location where you would like the active database to be kept, enter a
filename for the new active audit database, then click Open
The current active audit database is archived.
The new active audit database file is created, and used from this point on.
Provided the archived database files have not been moved, the pointers in the
Related Archives folder remain valid.

To use the new active database:

1. Select the Select Active Audit Database command from the Actions menu, or the
click the

button.

A Warning dialog states that 'This action cannot be undone, continue ?'
2. Click Yes to confirm that you want to use another active audit database.
The Open file dialog opens.
3. Browse to and select the active database, then click Open
The current active audit database is archived.
The selected active audit database is used from this point on.
Provided the archived database files have not been moved, the pointers in the
Related Archives folder remain valid.
NOTE: An archive database includes a Cap Record and Archive Reference that places its
contents within a longer sequence of records. As such, it cannot be selected as
the Active Audit database; the Error message 'An archive database cannot be
selected to be the active' is displayed.

Spectrum Administration . 291

I nstrum ent and Accessory Configuration

Before collecting spectra, a Spectrum administrator must install, test and configure an
instrument, and install and test any accessories used.
In Spectrum ES, the Spectrum administrator must also assign the instrument to one or
more appropriate groups of users.

I nstalling an I nstrum ent

To install a new instrument, the Spectrum administrator must Log In and elect to Work
Offline.
1. From the Administration menu, select Instrument and Accessory Configuration.
A sub-menu is displayed.
2. Select Add Instrument.
The Instrument Install Wizard is displayed.
3. Click Next.
The Instrument Details page is displayed.
4. Enter the Instrument Name.
This may be Spectrum 400, Spectrum 100, Spectrum 100N, or a name to distinguish
your instrument from another resource connected to the network.
5. Enter the IP Address then click Next.
NOTE: The Use Factory Default button enters a default IP address. If used, make sure
this address is compatible with the IP address scheme used by your network; and
is not used by an existing network resource, such as another PerkinElmer
spectrometer.
6. When the Instrument Configuration Disk page is displayed, insert the Configuration
Files CD (or floppy disk for older instruments) that was shipped with the instrument.
7. Navigate to the configuration file and then click Copy Configuration.
The Test Configuration page is displayed. This automatically tests the connection
and configuration of the new instrument. If any of the tests fail, you cannot
proceed.
8. When the Test Configuration page displays Completed, check that the information
is correct.
9. Remove the configuration CD and then click Next.
The Test the performance of your instrument page is displayed.

292 . Spectrum
10. If you want to test the performance of the instrument, click Next.
If you do not want to test the performance of the instrument, click Skip.
If your instrument is a Spectrum 100 Series, the software performs a series of
instrument performance tests.
If your instrument is a Spectrum 400 Series, the Performance Tests Setup dialog is
displayed. If you want to perform the tests in a particular order, to perform tests for
a particular configuration, or to cancel some tests, edit the settings using the
drop-down lists, and then click OK.
11. When the tests are complete, click View Log if you want to see the results of the
performance tests in more detail.
If you want to view the results of the performance tests later, the log is stored at
C:\Program Files\PerkinElmer\ServiceIR\<Instrument Serial Number>\Performance
Tests xxx\[Link] (where xxx is an incremental number).
12. Click Next.
If your instrument is a Spectrum 100 Series, the Collect ASTM Reference Spectra
page is displayed.
If your instrument is a Spectrum 400 Series, the Collect ASTM Reference Spectra
page is not displayed if the ASTM spectra were collected during the Performance
Tests.
13. To collect ASTM Reference Spectra, click Next.
If you do not want to collect ASTM Reference Spectra, click Skip to move to the
Finish page.
If your instrument is a Spectrum 400 Series, it may need to change the data
collection range before collecting spectra.
14. When the ASTM0 Reference Spectra Collection is complete, click View Log if you
want to see the results in more detail.
If you want to view the results later, the log is stored at C:\Program
Files\PerkinElmer\ServiceIR\<Instrument Serial Number>\Performance Tests
xxx\[Link] (where xxx is an incremental number).
15. Click Next.
The Finish page is displayed.
16. Click Finish to complete the installation.
If the source, beamsplitter, or detector on your Spectrum 400 was changed to
facilitate testing, you are given an opportunity to return the instrument to its
original setup.
17. Click Yes or No as required.

Spectrum Administration . 293

Rem oving an I nstrum ent

To remove an instrument, the Spectrum administrator must Log In and elect to Work
Offline.
1. From the Administration menu, select Instrument and Accessory Configuration.
A sub-menu is displayed.
2. Select Remove Instrument
The Remove Instrument dialog is displayed.
3. Select the instrument to remove from the drop-down list, then click OK.
You are asked to confirm the deletion.
4. Click Yes.
The instrument is removed from the list of Available instruments.

Adding Accessories
This procedure allows you to configure and test an existing combination of instrument
and accessory, or to configure and test a new combination of instrument and accessory.
1. From the Administration menu, select Instrument and Accessory Configuration.
A sub-menu is displayed.
2. Select Add Accessories.
The Instrument Install Wizard is displayed.
3. Select the instrument on which the accessory will be installed, and then click Next.
The Install Accessories page is displayed.
4. Fit the accessory you want to install into the instrument as described in its Users
Guide.
Typically, you remove the current accessory from the instrument, then slide in the
new accessory, making sure that it is properly connected. When an accessory has
been fitted into the instrument it is automatically recognized by the Spectrum
software.
5. Click Next.
The Insert Accessory dialog is displayed. If the new accessory is an external
reflectance accessory on a Spectrum 400, follow steps 6 and 7. If your instrument is
a Spectrum 100, or a Spectrum 400 with no external accessory fitted, a simplified
dialog is displayed. In this case continue with step 8.
6. If an external accessory is fitted, select the accessory you want to install.
7. Select the Mode (wavelength range), in which you want to test the accessory.
The current instrument mode is marked by a * and the standard operating mode of
the accessory by a +.
If you do not select the current wavelength range, a wavelength range change will
be performed before testing begins.
NOTE: Depending on the beamsplitters and detectors fitted, the instrument requires
some time to equilibrate after changing ranges and before Performance Testing
can continue.

294 . Spectrum
8. Click Continue.
Some accessories (for example the Universal ATR), are shipped with a CD
containing, for example, reference spectra generated during manufacture. In these
cases the Copy Accessory Files page is displayed, which prompts you for the
configuration CD supplied with the accessory.
9. Navigate to the configuration file, and then click Copy Accessory Data.
The Install Accessories page is displayed.
The software performs a series of accessory performance tests. You may be
prompted to remove the accessory briefly, and then replace it. This is to clear the
beam path while a background spectrum is collected.
If your instrument is a Spectrum 400 Series, it may need to change the data
collection range before collecting spectra.
10. When the accessory tests and calibrations tests are complete you can install another
accessory, if required, by clicking Another Accessory.
You are returned to the start of the installation wizard.
11. Click View Log if you want to see the test results in more detail.
If you want to view the results of the accessory tests later, the log is stored at
C:\Program Files\PerkinElmer\ServiceIR\<Instrument Serial Number>\Performance
Tests xxx\[Link] (where xxx is an incremental number).
12. Click Next when you do not want to install any more accessories.
The Finish page is displayed.
13. Click Finish to complete the installation.
If the source, beamsplitter, or detector on your Spectrum 400 was changed to
facilitate testing, you are given an opportunity to return the instrument to its
original setup.
14. Click Yes or No as required.

Spectrum Administration . 295

Legacy File Converter

NOTE: Applies to 21 CFR Part 11 compliant environments. Only Spectrum ES
administrators can convert legacy data files.
21 CFR Part 11 technical compliance mandates very high levels of data integrity and
security. To ensure that Spectrum ES only accesses and uses data acquired on a 21 CFR
Part 11 compliant system, a data security checksum has been added to the spectrum
data file generated from an Enhanced Security software application.
Spectra without this 21 CFR Part 11 checksum will not be read into the Enhanced
Security software and cannot be processed. This feature stops data from older data
systems from being automatically used in new compliant systems.
To allow users access to their legacy data a Conversion Utility has been included in the
Administration menu. This allows users to add a data security checksum to all spectra in
a directory of legacy spectra.
NOTE: Use of the utility should be highly controlled and spectra that are converted
should have full supporting GxP provenance as part of their audit trail.

To Convert Legacy Data:

1. Select Legacy File Converter from the Administration menu.
The Legacy File Converter dialog is displayed.
2. For the Source Path, click Browse and on the file selector displayed, select the
Source Path for the directory containing the legacy data.
On first use, the suggested path is:
C:\Documents and Settings\Operating System User Name\CheckSumInput
If needed, use Explorer to create this folder. Generally, the default path is the last
path used.
3. For the Destination Path, click Browse and on the file selector displayed, select the
Destination Path for the directory containing the converted data.
On first use, the suggested path is:
C:\Documents and Settings\Operating System User Name\CheckSumOutput
If needed, use Explorer to create this folder. Generally, the default path is the last
path used.
4. Click Next.
The data is copied and a checksum is added to each file, then the new files are
written to the destination directory with _cs appended to each filename. The original
data files are untouched.
5. To view information about the conversion, click View Log.
A log file is displayed.

296 . Spectrum

I m porting and ex porting Quant m ethods

The packages used to develop Quant methods are not 21 CFR Part 11 compliant, so it is
unlikely that they will be installed on the same PC as Spectrum ES.
To use one or more Quant Methods in Spectrum ES, you export them from the Quant PC
as a zip file, and then import this file into Spectrum ES. Only Spectrum ES administrators
can import Quant methods.
Spectrum includes the Quant Transfer Utility to facilitate the export of Quant methods for
use in a 21 CFR Part 11 compliant environment.
Where 21 CFR Part 11 compliance is not important, the Beers Law Quant, Spectrum
Quant+, or Spectrum QuantC packages can be installed with Spectrum Standard. Where
a Quant product and Spectrum are installed on the same PC, you simply browse to the
required method file.
NOTE: The installation of the Beers Law Quant, Spectrum Quant+, or Spectrum QuantC
packages with Spectrum ES is not prohibited. You are simply warned that their
installation may invalidate your 21CFR11 environment.

To im port a Quant m ethod into Spectrum ES:

1. Select Quant Import from the Administration menu
The Quant Import dialog is displayed.
2. Click Add Zipfile To List
The Open dialog is displayed.
3. Browse to and select the PerkinElmer Quant Zip File you want to import, then click
Open.
The filename (of the form [Link]) is added to the Source Files list.
4. Continue adding, and removing, PE Quant Zip files until all the methods you want to
import are listed, the click Next.
The Quant methods are extracted. If a method already exists, you are asked to
decide whether you want it to be overwritten.
5. Click View Log to read how your actions have been recorded by the system.
6. When you have completed importing methods, click Exit.
7. The imported methods are now available for use with Spectrum ES.

Spectrum Administration . 297

To ex port a Quant m ethod from Spectrum :

1. Click the Windows Start button then select All Programs > PerkinElmer Applications
> Quant Export
The Quant Transfer Utility is displayed.
2. Select the package used to create the method from the Source: Quant Type dropdown list.
The path displayed in the Source: Methods Directory field is updated to show the
default folder used by that package, and the methods available listed In the
Methods: field.
If the method you want to export is stored elsewhere, click the
browse dialog.

button to open a

3. The path displayed in the Transfer File: Destination Path field is to

//pel_data/QExport, the default folder used for exporting Quant methods.
If you want to export the zipped method file to another location, click the
to open a browse dialog.

button

4. Click Next.
The method is zipped into [Link] and placed in the destination folder, together
with a log file named name_ExportLog__date_time.txt
A Copy Process dialog monitors the tranfer, and informs you when the transfer is
complete.
5. Click View Log
The log file records the date and time that the named method was transferred from
which location, to which destination.
6. Click Exit to close the Quant Transfer Utility.
The Quant method is now available for import into Spectrum ES.

298 . Spectrum

Spectrum M enus

300 . Spectrum

M enus
These are the menus available in the Spectrum software. Click on the menu name to list
the commands available.
File
Edit
View
Process
Instrument
Setup
Administration
Procedures
Window
Help

Spectrum Menus . 301

File M enu
These are the commands available in the File menu. To learn more about a command,
click on its name.
New

Ctrl+N

Open

Ctrl+O

Save

Ctrl+S

Save As
Close
Rename
Status
Print
Print Setup...
Copy to Report
Exit

Ctrl+P

302 . Spectrum

Edit M enu
These are the commands available in the Edit menu. To learn more about a command,
click on its name.
Cut

Ctrl+X

Copy

Ctrl+C

Paste

Ctrl+V

Paste Spectra
Delete
Report Viewer

Del

Spectrum Menus . 303

View M enu
These are the commands available in the View menu. To learn more about a command,
click on its name.
Optimize
Format View
Overlay/Split Display

>

Cursor

>

Radar Display
Previous Range
Autorange X

Ctrl+R

Autorange Y

Ctrl+Y

Autoscale Y
Cancel Autoscale
Cancel Offset
Full Scale
Select All
Label Cursor
Label Peaks
Clear All Peak Labels
Add / Edit Text...
Spectrum Browser...

Ctrl+A

304 . Spectrum

Process M enu
These are the commands available in the Process menu. To learn more about a
command, click on its name.
Undo

Ctrl+Z

Data Tune-up
Absorbance
Transmittance
Kubelka-Monk
ConvertX...
Difference
Baseline Correction

>

Smooth

>

Deconvolution...
Spectral Calculator...
Normalize...
Abex...
Derivative...
Interpolate...
Blank...
Kramers-Kronig...
ATR Correction...
Compare
IR Search
Interactive Interpretation...
Quant Prediction...
Peak Area / Height...
Peak Table...

Spectrum Menus . 305

I nstrum ent M enu

These are the commands available in the Instrument menu. To learn more about a
command, click on its name.
Scan
Monitor
Validate
Halt

>

(not selectable in the FIR range)

306 . Spectrum

Setup M enu
These are the commands available in the Setup menu. To learn more about a command,
click on its name.
Instrument...
Instrument Validation...

>

IR Search...
Compare...
Quant...
Area / Height...
Report Template
Learn...
Options...
Toolbar

>

Toolbox

>

(not selectable in the FIR range)

Spectrum Menus . 307

Adm inistration M enu

This section of the help includes topics on the administration tasks associated with
Spectrum and Spectrum ES (Enhanced Security).
NOTE: Only users that have permission to perform administration tasks in Spectrum
have access to the Administration menu. For other users, this menu is not
displayed.
Spectrum ES implements the very high levels of data integrity and security mandated for
21 CFR Part 11 technical compliance, so has an enhanced Administration command set
compared to Spectrum.
In Spectrum ES, each user must have a password. You configure the level of access
required by groups of users, then grant users appropriate group membership. Spectrum
ES also includes audit trails for both user administration and software configuration, and
controls access to legacy files and methods.
In Spectrum, user password control is much less strict, and you configure the level of
access required by each user.

Adm inistration for Spectrum

These are the commands available in the Administration menu for Spectrum. To learn
more about a command, click on its name.
Setup Users...
User Configuration...
Instrument and Accessory
Configuration

>

Adm inistration for Spectrum ES

These are the commands available in the Administration menu for Spectrum ES. To learn
more about a command, click on its name.
Setup Users and Groups...
Group Configuration...
View Admin Audit Trail...
View Spectrum Audit Trail...
Instrument and Accessory
Configuration
Legacy File Converter...
Quant Import...

>

308 . Spectrum

Procedures M enu
These are the commands available in the Procedures menu. To learn more about a
command, click on its name.
[no procedures]

Spectrum Menus . 309

W indow M enu
These are the commands available in the Windows menu. To learn more about a
command, click on its name.
Cascade
Tile
Arrange Icons
Close All
1 Graph #1

>

310 . Spectrum

Help M enu
These are the commands available in the Help menu. To learn more about a command,
click on its name.
Contents and Index...
Learning Spectrum...
IR Assistant...
About...

F1

I ndex
2
2nd Derivative .............................137

A
Abex ............................100, 101, 248
Abscissa
contract .................................... 33
expand ...................................... 33
Abscissa ....................................... 33
Abscissa Test ................189, 193, 204
Abscissa Units
choose ...................................... 54
Abscissa Units ............................... 54
Abscissa Units ..............................136
Absorbance ........................ 53, 55, 57
Accessory
controlling ................................159
Accessory ....................................159
Accessory ....................................160
Accessory ....................................161
Accessory ....................................162
Accessory ....................................163
Accessory ....................................164
Accessory ....................................166
Accessory ....................................168
Accessory ....................................170
Accessory ....................................175
Accessory ....................................189
Accessory ....................................209
Add
comments ................................243
description ....................... 121, 122
Learn Mode Script .....................247
pauses .....................................247
Spectrum .................................. 21
steps ........................................243
Add .............................................. 21
Add .............................................. 76
Add .............................................121
Add .............................................243
Add .............................................247
Adjustments Toolbox180, 181, 183, 184,
185, 186, 187, 209
Administration
Audit ................................ 284, 286
Legacy ............................. 295, 296
Administration ..............................284
Administration ..............................286
Administration ..............................295
Administration ..............................296
Administration menu ............ 295, 296

Aligning ....................................... 183

Annotations ...................................24
apodization .................................. 132
APV ...................... 143, 189, 193, 197
Archive ......................... 189, 193, 197
Area/Height ...................................93
Arrange Icons ...................... 220, 247
Assistant ..................................... 227
ASTM Level 0 ............................... 197
ATR Correction ...............60, 109, 248
Auto Check ................... 189, 193, 197
Auto Data Interval ....................... 131
Auto Name .................................. 235
Auto Setup .................................. 189
Auto Zero Automatic .................... 100
Autocheck .................... 189, 193, 197
Auto-increment ............................ 177
Automatic Baseline Correction.........49
Automatic Precision Validator 189, 193
Autorange .................. 29, 31, 36, 234
Autorange Y ............... 31, 32, 36, 234
Autoscale ......................................31
Autoscale Y............................ 31, 101
AVI ...................... 138, 143, 184, 197
AVI Calibration ............................. 184
Axes Units .....................................24

B
Background ... 153, 154, 177, 189, 205
Baseline Correction .........49, 109, 248
Beampath ..................... 189, 193, 197
Beamsplitter .. 144, 146, 147, 155, 197
Beer's Law ....................... 63, 87, 296
Blank................................... 103, 110
Blank Regions .............................. 103
Block Average .............................. 115
Boxcar ................................... 95, 132

C
Calibrating ........................... 189, 193
Cancel31, 32, 174, 175, 221, 222, 239,
242, 243
Cancel Autoscale ...................... 31, 32
Cancel Offset ........................... 31, 32
Cascade ...................................... 220
Centerburst ......................... 155, 183
Clear All Peak Labels ......................42
Clipboard ..................................... 174
Close All .............................. 213, 241
Closing Files ................................ 213
Clutch ................................. 161, 162
CO2 ...............................29, 101, 103

312 . Spectrum
CO2 Blanking ................................ 71
CO2/H2O Suppression ................. 138
Collecting .................................... 177
Colors .................................. 214, 234
Comments............................ 121, 243
Compare ................................. 59, 71
Compare Setup.............................. 71
Configuration ................. 23, 148, 175
Confirm Deletes .....212, 221, 222, 234
Contamination ...................... 189, 205
Contamination spectra ................. 189
ConvertX ....................................... 54
Copy To Clipboard ....................... 174
Corrected HeNe Wavenumber ...... 181
Correlation .................................... 71
Cursors ......................................... 40

D
Data ............................................. 52
Data Collection ..................... 177, 209
Data Collection Setup ................... 177
Data Interval .................... 54, 59, 131
Data Server .......................... 221, 222
Data Tune-up ................. 48, 232, 248
Deconvolution ....................... 95, 111
Default Mode............................... 234
Default Printer ............................. 214
Default Range ............................. 155
Default TextFont.......................... 234
Default View Template ................. 234
Define Login ................................ 247
Define Toolbar............................. 247
Define Toolbox ............................ 247
Derivative ..................................... 57
Description ................... 121, 175, 234
Detectors .................................... 144
Difference ............................. 55, 112
Diffuse Reflectance Accessory ...... 163
Discrimination ............................... 71
Display Modes ............................... 35

E
Edit menu ...........19, 38, 42, 232, 302
Editing ................................. 243, 248
Energy ......................... 125, 155, 209
Euclidean Search ........................... 76
Exiting ......................... 212, 221, 222
Expand Y ...................................... 33
Expert Search ................................ 76

F
File menu . 23, 43, 174, 217, 221, 222,
301
Files ....................... 24, 212, 214, 233
Filters ........................................... 71
Filterwheel ................... 138, 143, 184

Fit-for-purpose ..................... 189, 193

Fonts .....................................26, 234
FOP ............................. 122, 168, 177
Format View............................ 24, 55
Full Range................................... 155
Full Scale ...................................... 36

G
GLP Lock..................................... 234
Graph Colors ................................. 26
Graph Templates ....................23, 217
Graph Window ................... 71, 76, 87
Grid ........................................ 24, 26
Grow box ...................................... 30

H
H2O Blanking ................................ 71
H2O Weighting .............................. 71
Halt ..................................... 154, 183
HATR Accessory .......................... 161
Height .................................... 93, 94
Height Options .............................. 94
History .. 109, 110, 111, 112, 113, 114,
115, 116
Horizontal ATR ............................ 161
Horizontal Cursor ........................... 40

I
Icons .......................................... 220
Instrument ... 121, 125, 129, 131, 132,
134, 135, 138, 140, 144, 146, 147,
148, 177, 183, 193, 209, 236
Instrument Access Level 121, 125, 148
Instrument Alias .......................... 205
Instrument menu . 121, 125, 148, 189,
193, 197, 209, 248, 305
Instrument options ...................... 236
Instrument Performance Validation189
Instrument Settings Files ............. 174
Instrument setup .. 144, 146, 147, 155,
159, 163, 170, 174
Instrument Validation ... 193, 204, 205
Instrument Validation Report ....... 205
Instrument Validation Setup .. 189, 193
Instrument Validation Tests ......... 193
Intensity Weighting ....................... 71
Interactive Baseline Correction ....... 49
Interactive Correction .................... 49
Interactive Interpretation ........79, 248
Interactive Smooth ...................... 112
Interferogram centerburst ............ 183
Interferograms ...... 131, 134, 155, 209
Interleaved ................................. 160
Interpolate .............................59, 113
Interpretation ................................ 76

Index . 313
Interval ............ 26, 59, 189, 193,
Interval APV.......... 189, 193, 197,
IPV ...................................... 189,
IR Assistant ......................... 226,
IR Expert .................. 29, 48, 140,
IR Search .............................. 76,

197
205
193
227
175
248

J
J-stop .................................. 138, 147

K
Kramers-Kronig .............. 64, 113, 248
Kubelka-Munk ... 52, 63, 114, 125, 248

L
Label cursor .................................. 40
Labelling ......... 23, 26, 40, 42, 84, 237
Labelling peaks ............................. 42
Laser Wavenumber ......................181
Learn Mode .......... 226, 239, 243, 248
Learn Mode script 239, 241, 242, 243,
247, 248
Libraries ....................................... 76
Liquid Sipper Accessory ........ 170, 175
Login ...........................................205
Look Ahead..................................139

M
Maintenance ................................180
M-Distance ................................... 87
Monitor ........................................155
Move spectra between graphs........ 20

N
New graph ............................. 21, 217
New graph template .....................217
NIR Fiber Optic Probe ....122, 168, 177
NIR Tablet Autosampler.121, 122, 166
NIRA ................................... 121, 164
Noise Threshold ...........................235
Noise weighting ............................ 71
Normalize ............................ 100, 114
Norton Beer Apodization ...............132

O
Offset ........................................... 32
Optimize ....................................... 29
Ordinate label ............................... 24
Ordinate scale .................... 31, 32, 33
Other options ...............................238
Overlay........................................129
Overlay/Split display ............... 35, 129
over-pressure clutch .....................162
Overwrite original .........................235

P
Page layout ................................. 214
Page orientation........................... 214
Pan Y ............................................33
Panning .........................................33
Paste................................. 19, 38, 39
Paste spectra .................................19
Pasting spectra ..............................19
Pasting text ...................................38
Pathlength ............................. 60, 170
Peak Area ................................ 93, 94
Peak Area/height ................... 93, 248
Peak Area/Height Setup .................93
Peak Cursor ........................... 84, 237
Peak Labels ...................................42
Peak Match ....................................76
Peak Options ......................... 84, 237
Peak Table ............... 76, 84, 237, 248
Performance Validation......... 189, 193
Phase Correction .......................... 134
Possible Structural Units ........... 76, 79
Prediction Report ...........................87
Preview ................ 121, 122, 161, 162
Previous Range ..............................36
Print
Graph ...................................... 214
Instrument Settings File ............ 174
Print ............................................ 174
Print ............................................ 214
Print Report .................. 189, 193, 197
Print Setup .................................. 214
Procedures .................................. 238
Process menu48, 49, 52, 53, 54, 55, 60,
63, 64, 71, 76, 79, 87, 95, 99, 100,
101, 103, 235, 248, 304
Process Options ........................... 235
PSUs ....................................... 76, 79

Q
Quality Checks ..................... 140, 175
Quant .................................... 87, 296
Quant Export ............................... 296
Quant Import............................... 296
Quant Prediction .................... 87, 248
Quant Setup .......................... 87, 296

R
Radar Display .......................... 30, 36
Range ............................24, 189, 193
Ready-for-Work ................... 189, 193
Reference band ........................... 181
Relocate Centerburst .................... 183
Rename............................... 212, 219
Report Builder........................ 43, 214
Report options ...............................76

314 . Spectrum
Report Template .. 43, 76, 87, 93, 214,
247
Report Viewer ............................. 205
Rescale ..............................29, 31, 36
Resolution ................................... 129
Resolution Weighting ..................... 71
RMS ............................. 189, 193, 205
Routine Access Users ................... 209

S
Sample ........................ 121, 122, 175
Sample Shuttle ..................... 125, 160
Sample Slide ............................... 159
Sampling Configuration ................ 209
Save All................................ 221, 222
Save As ... 23, 174, 175, 217, 219, 243
Scale ............................................ 26
Scan number ............................... 125
Scan Progress ...................... 153, 154
Scan Range ................................. 135
Scan speed .......................... 135, 197
Scan type .................................... 160
Search
choosing .................................... 76
Search .......................................... 76
Search libraries .............................. 76
Select All ................................. 22, 32
Setup menu 23, 43, 71, 76, 84, 87, 93,
94, 121, 125, 144, 146, 147, 148,
177, 180, 181, 183, 184, 189, 193,
197, 209, 231, 232, 233, 234, 235,
236, 237, 238, 306
Show toolbar ............................... 247
Show Toolbar Captions ................ 247
Show Toolbox ...................... 231, 247
Show Toolbox Captions ......... 231, 247
Smooth ................................. 94, 115

Spectral Calculator .......... 99, 116, 248

Spectrum Browser ......................... 21
Spectrum Procedures ................... 238
Split Display .................................. 35
Standard Access Users ................. 209
Summary info.............................. 174
System Suitability . 175, 177, 189, 204,
205
System Suitability tests ................ 189

T
Text........................................ 38, 39
Throughput .......................... 189, 205
Toolbox ...................................... 231
Transmittance ............................... 53

U
Universal ATR Accessory .............. 162
USP ............................................ 200

V
Validation.............. 189, 193, 197, 200
Vertical Cursor............................... 40
View menu . 21, 22, 24, 29, 31, 32, 35,
36, 40, 42, 48, 129, 303

W
Wavenumber Calibration .............. 181
Window menu .......... 38, 43, 220, 309
Windowed mode ......................... 234

Z
Zoom ......................... 30, 36, 55, 101