TSQ Quantum GC

User Guide

70111-97151 Revision A September 2007

For Research Use Only

Not for use in Diagnostic Procedures
© 2007 Thermo Fisher Scientific Inc. All rights reserved.

Swagelok® is a registered trademark of the Crawford Fitting Company. Dranetz® is a registered trademark of
Dranetz Technologies, Inc. Styrofoam® is a registered trademark of Dow Chemical Company. Teflon® is a
registered trademark of E. I. du Pont de Nemours & Co. Tygon® is a registered trademark of Norton
Company. Dust-Off®is a registered trademark of Falcon® Safety Products. Micro-Blast™ is a trademark of
MicroCare® Corporation. Restek®is a registered trademark of Restek Corporation.

Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to use in the
product operation. This document is copyright protected and any reproduction of the whole or any part of this
document is strictly prohibited, except with the written authorization of Thermo Fisher Scientific Inc.
The contents of this document are subject to change without notice. All technical information in this
document is for reference purposes only. System configurations and specifications in this document supersede
all previous information received by the purchaser.
Thermo Fisher Scientific Inc. makes no representations that this document is complete, accurate or error-
free and assumes no responsibility and will not be liable for any errors, omissions, damage or loss that might
result from any use of this document, even if the information in the document is followed properly.
This document is not part of any sales contract between Thermo Fisher Scientific Inc. and a purchaser. This
document shall in no way govern or modify any Terms and Conditions of Sale, which Terms and Conditions of
Sale shall govern all conflicting information between the two documents.

Release history: Revision A, September 2007

Software revision: Xcalibur 2.0.5, Quantum 1.5

For Research Use Only. Not regulated for medical or veterinary diagnostic use by U.S. Federal Drug
Administration or other competent authorities.
 Regulatory Compliance
Thermo Fisher Scientific performs complete testing and evaluation of its products to ensure full compliance with
applicable domestic and international regulations. When the system is delivered to you, it meets all pertinent
electromagnetic compatibility (EMC) and safety standards as described below.

EMC Directive 89/336/EEC as amended by 92/31/EEC and 93/68/EEC

EMC compliance has been evaluated by TUV Rheinland of North America Inc.

EN 55011 1998, 1999, 2002 EN 61000-4-3 2002

EN 61000-3-2 1995, A1; 1998, A2; 1998, A14; 2000 EN 61000-4-4 1995, A1; 2000, A2; 2001
EN 61000-3-3 1998, 2001 EN 61000-4-5 1995, A1; 2001
EN 61326-1 1998, 2001, 2003 EN 61000-4-6 1996, A1; 2003
EN 61000-4-2 2001 EN 61000-4-11 1994, A1; 2001
CISPR 11 1998
FCC Class A, CFR 47 Part 15

Low Voltage Safety Compliance

Compliance with safety issues is declared under Thermo Fisher Scientific sole responsibility.
This device complies with Low Voltage Directive 73/23/EEC and harmonized standard EN 61010-1:2001.

Changes that you make to your system may void compliance with one or more of these EMC and safety standards.
Changes to your system include replacing a part or adding components, options, or peripherals not specifically
authorized and qualified by Thermo Fisher Scientific. To ensure continued compliance with EMC and safety standards,
replacement parts and additional components, options, and peripherals must be ordered from Thermo Fisher Scientific
or one of its authorized representatives.

FCC Compliance Statement

THIS DEVICE COMPLIES WITH PART 15 OF THE FCC RULES. OPERATION IS SUBJECT TO
THE FOLLOWING TWO CONDITIONS: (1) THIS DEVICE MAY NOT CAUSE HARMFUL
INTERFERENCE, AND (2) THIS DEVICE MUST ACCEPT ANY INTERFERENCE RECEIVED,
INCLUDING INTERFERENCE THAT MAY CAUSE UNDESIRED OPERATION.

CAUTION Read and understand the various precautionary notes, signs, and symbols contained inside
this manual pertaining to the safe use and operation of this product before using the device.
 Notice on Lifting and Handling of
Thermo Fisher Scientific San Jose Instruments
For your safety, and in compliance with international regulations, the physical handling of this Thermo Fisher Scientific
San Jose instrument requires a team effort to lift and/or move the instrument. This instrument is too heavy and/or
bulky for one person alone to handle safely.

Notice on the Proper Use of

Thermo Fisher Scientific San Jose Instruments
In compliance with international regulations: Use of this instrument in a manner not specified by Thermo Fisher
Scientific San Jose could impair any protection provided by the instrument.

Notice on the Susceptibility

to Electromagnetic Transmissions
Your instrument is designed to work in a controlled electromagnetic environment. Do not use radio frequency
transmitters, such as mobile phones, in close proximity to the instrument.
 WEEE Compliance
This product is required to comply with the European Union’s Waste Electrical &
Electronic Equipment (WEEE) Directive 2002/96/EC. It is marked with the following
symbol:

Thermo Electron has contracted with one or more recycling/disposal companies in each
EU Member State, and this product should be disposed of or recycled through them.
Further information on Thermo Electron’s compliance with these Directives, the
recyclers in your country, and information on Thermo Electron products which may
assist the detection of substances subject to the RoHS Directive are available at
[Link]/WEEERoHS.

WEEE Konformität
Dieses Produkt muss die EU Waste Electrical & Electronic Equipment (WEEE) Richtlinie
2002/96/EC erfüllen. Das Produkt ist durch folgendes Symbol gekennzeichnet:

Thermo Electron hat Vereinbarungen getroffen mit Verwertungs-/Entsorgungsanlagen in

allen EU-Mitgliederstaaten und dieses Produkt muss durch diese Firmen
wiederverwertet oder entsorgt werden. Mehr Informationen über die Einhaltung dieser
Anweisungen durch Thermo Electron, die Verwerter und Hinweise die Ihnen nützlich
sein können, die Thermo Electron Produkte zu identifizieren, die unter diese RoHS
Anweisung fallen, finden Sie unter [Link]/WEEERoHS.
 Conformité DEEE
Ce produit doit être conforme à la directive européenne (2002/96/EC) des Déchets
d'Equipements Electriques et Electroniques (DEEE). Il est marqué par le symbole
suivant:

Thermo Electron s'est associé avec une ou plusieurs compagnies de recyclage dans
chaque état membre de l’union européenne et ce produit devrait être collecté ou recyclé
par celles-ci. Davantage d'informations sur la conformité de Thermo Electron à ces
directives, les recycleurs dans votre pays et les informations sur les produits Thermo
Electron qui peuvent aider la détection des substances sujettes à la directive RoHS sont
disponibles sur [Link]/WEEERoHS.
CAUTION Symbol CAUTION VORSICHT ATTENTION PRECAUCION AVVERTENZA

Electric Shock: High Voltages capable Elektroschock: In diesem Gerät werden Choc électrique: L’instrument utilise des Descarga eléctrica: Este instrumento Shock da folgorazione. L’apparecchio è
of causing personal injury are used in the Hochspannungen verwendet, die tensions capables d’infliger des blessures utiliza altas tensiones, capaces de alimentato da corrente ad alta tensione
instrument. The instrument must be shut Verletzungen verursachen können. Vor corprelles. L’instrument doit être arrêté et producir lesiones personales. Antes de che puo provocare lesioni fisiche. Prima di
down and disconnected from line power Wartungsarbeiten muß das Gerät débranché de la source de courant avant dar servicio de mantenimiento al effettuare qualsiasi intervento di
before service is performed. Do not abgeschaltet und vom Netz getrennt tout intervention. Ne pas utiliser instrumento, éste debera apagarse y manutenzione occorre spegnere ed isolare
operate the instrument with the top cover werden. Betreiben Sie Wartungsarbeiten l’instrument sans son couvercle. Ne pas desconectarse de la línea de alimentacion l’apparecchio dalla linea elettrica. Non
off. Do not remove protective covers from nicht mit abgenommenem Deckel. Nehmen elensver les étuis protecteurs des cartes de eléctrica. No opere el instrumento sin sus attivare lo strumento senza lo schermo
PCBs. Sie die Schutzabdeckung von Leiterplatten circuits imprimés. cubiertas exteriores quitadas. No remueva superiore. Non togliere i coperchi a
nicht ab. las cubiertas protectoras de las tarjetas protezione dalle schede di circuito
de circuito impreso. stampato (PCB).
Chemical: Hazardous chemicals might be Chemikalien: Dieses Gerät kann Chimique: Des produits chemiques Química: El instrumento puede contener Prodotti chimici. Possibile presenza di
present in the instrument. Wear gloves gefährliche Chemikalien enthalten. Tragen dangereux peuven se trouver dans productos quimicos peligrosos. Utilice sostanze chimiche pericolose
when handling toxic, carcinogenic, Sie Schutzhandschuhe beim Umgang mit l’instrument. Proted dos gants pour guantes al manejar productos quimicos nell’apparecchio. Indossare dei guanti per
mutagenic, or corrosive/irritant chemicals. toxischen, karzinogenen, mutagenen oder manipuler tous produits chemiques tóxicos, carcinogenos, mutagenos o maneggiare prodotti chimici tossici,
Use approved containers and procedures ätzenden/reizenden Chemikalien. toxiques, cancérigènes, mutagènes, ou corrosivos/irritantes. Utilice recipientes y cancerogeni, mutageni, o
for disposing of waste oil. Entsorgen Sie verbrauchtes Öl corrosifs/irritants. Utiliser des récipients procedimientos aprobados para corrosivi/irritanti. Utilizzare contenitori
entsprechend den Vorschriften in den et des procédures homologuées pour se deshacerse del aceite usado. aprovo e seguire la procedura indicata per
vorgeschriebenen Behältern. débarrasser des déchets d’huile. lo smaltimento dei residui di olio.

Heat: Allow heated components to cool Hitze: Warten Sie erhitzte Komponenten Haute Temperature: Permettre aux Altas temperaturas: Permita que lop Calore. Attendere che i componenti
before servicing them. erst nachdem diese sich abgekühlt haben. composants chauffés de refroidir avant componentes se enfríen, ante de efectuar riscaldati si raffreddino prima di
tout intervention. servicio de mantenimiento. effetturare l’intervento di manutenzione.

Fire: Use care when operating the system Feuer: Beachten Sie die einschlägigen Incendie: Agir avec précaution lors de Fuego: Tenga cuidado al operar el Incendio. Adottare le dovute precauzioni
in the presence of flammable gases. VorsichtsmaBnahmen, wenn Sie das l’utilisation du système en présence de sistema en presencia de gases quando si usa il sistema in presenza di gas
System in Gegenwart von entzündbaren gaz inflammables. inflamables. infiammabili.
Gasen betreiben.

Eye Hazard: Eye damage could occur Verletzungsgefahr der Augen: Danger pour les yeux: Dex projections Peligro par los ojos: Las salicaduras de Pericolo per la vista. Gli schizzi di
from splattered chemicals or flying Verspritzte Chemikalien oder kleine chimiques, liquides, ou solides peuvent productos químicos o particulas que prodotti chimici o delle particelle presenti
particles. Wear safety glasses when Partikel können Augenverletzungen être dangereuses pour les yeux. Porter des salten bruscamente pueden causar nell’aria potrebbero causare danni alla
handling chemicals or servicing the verursachen. Tragen Sie beim Umgang mit lunettes de protection lors de toute lesiones en los ojos. Utilice anteojos vista. Indossare occhiali protettivi quando
instrument. Chemikalien oder bei der Wartung des manipulationde produit chimique ou pour protectores al mnipular productos si maneggiano prodotti chimici o si
Gerätes eine Schutzbrille. toute intervention sur l’instrument. químicos o al darle servicio de effettuano interventi di manutenzione
mantenimiento al instrumento. sull’apparecchio.

General Hazard: A hazard is present that Allgemeine Gefahr: Es besteht eine Danger général: Indique la présence Peligro general: Significa que existe un Pericolo generico. Pericolo non
is not included in the above categories. weitere Gefahr, die nicht in den d;un risque n’appartenant pas aux peligro no incluido en las categorias compreso tra le precedenti categorie.
Also, this symbol is used on the vorstehenden Kategorien beschrieben ist. catégories citées plus haut. Ce symbole anteriores. Este simbolo también se utiliza Questo simbolo è utilizzato inoltre
instrument to refer the user to instructions Dieses Symbol wird im Handbuch figure également sur l’instrument pour en el instrumento par referir al usuario a sull’apparecchio per segnalare all’utente
in this manual. auBerdem dazu verwendet, um den renvoyer l’utilisateur aux instructions du las instrucciones contenidas en este di consultare le istruzioni descritte nel
Benutzer auf Anweisungen hinzuweisen. présent manuel. manual. presente manuale.

When the safety of a procedure is in Wenn Sie sich über die Sicherheit eines Si la sûreté d’un procédure est incertaine, Cuando la certidumbre acerca de un Quando e in dubbio la misura di sicurezza
doubt, before you proceed, contact your Verfahrens im unklaren sind, setzen Sie avant de continuer, contacter le plus procedimiento sea dudosa, antes de per una procedura, prima di continuare, si
local Technical Support Organization for sich, bevor Sie fortfahren, mit Ihrer proche Service Clientèle pour les produits proseguir, pongase en contacto con la prega di mettersi in contatto con il
Thermo Electron San Jose Products. lokalen technischen de Thermo Electron San Jose. Oficina de Asistencia Tecnica local para Servizio di Assistenza Tecnica locale per i
Unterstützungsorganisation für Thermo los productos de Thermo Electron prodotti di Thermo Electron San Jose.
Electron San Jose Produkte in Verbindung. San Jose.
CAUTION Symbol CAUTION

Electric Shock: High Voltages capable

of causing personal injury are used in the
instrument. The instrument must be shut
down and disconnected from line power
before service is performed. Do not
operate the instrument with the top cover
off. Do not remove protective covers from
PCBs.

Chemical: Hazardous chemicals might be

present in the instrument. Wear gloves
when handling toxic, carcinogenic,
mutagenic, or corrosive/irritant chemicals.
Use approved containers and procedures
for disposing of waste oil.

Heat: Allow heated components to cool

before servicing them.

Fire: Use care when operating the system

in the presence of flammable gases.

Eye Hazard: Eye damage could occur

from splattered chemicals or flying
particles. Wear safety glasses when
handling chemicals or servicing the
instrument.

General Hazard: A hazard is present that

is not included in the above categories.
Also, this symbol is used on the
instrument to refer the user to instructions
in this manual.
When the safety of a procedure is in
doubt, before you proceed, contact your
local Technical Support Organization for
Thermo Electron San Jose Products.
 C

Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .v
Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Safety and Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Safety Precautions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .vi
Solvent and Gas Purity Requirements. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii
Service Philosophy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii
Level of Repair . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii
Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .viii

Chapter 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
Ionization Modes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Electron Ionization Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Chemical Ionization Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Ion Polarity Modes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Scan Modes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Q1MS and Q3MS Scan Modes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Product Scan Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Parent Scan Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Neutral Loss Scan Modes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Data Dependent Scan Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Scan Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Full Scan . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Selected Ion Monitoring . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Selected Reaction Monitoring . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
AutoSIM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Data Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Profile Data Type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Centroid Data Type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Mass/Charge Range. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

Chapter 2 Functional Description. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15

Autosampler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Gas Chromatograph . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Direct Sample Probes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Transfer Line. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Thermo Scientific TSQ Quantum GC User Guide i

Contents

Mass Spectrometer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Controls and Indicators . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Ion Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Inlet Valve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Ion Optics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Mass Analyzer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Ion Detection System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Vacuum System and Inlet Gasses Hardware . . . . . . . . . . . . . . . . . . . . . . . . . 37
Electronic Assemblies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
Data System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
Computer Hardware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
Data System / Mass Spectrometer / GC Interface . . . . . . . . . . . . . . . . . . . . . 45
Data System / Local Area Network Interface . . . . . . . . . . . . . . . . . . . . . . . . . 45

Chapter 3 System Shutdown, Startup, and Reset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .47

Shutting Down the System in an Emergency. . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Placing the System in Standby Mode. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
Shutting Down the System Completely. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Starting Up the System after a Complete Shutdown . . . . . . . . . . . . . . . . . . . . . 51
Restoring Power to the TSQ Quantum GC system . . . . . . . . . . . . . . . . . . . . 51
Starting Up the GC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
Starting Up the Data System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
Starting Up the Mass Spectrometer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
Starting Up the Autosampler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
Setting Up Conditions for Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
Resetting the Mass Spectrometer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
Resetting the Data System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Resetting the Data System by Using the Windows Shutdown and Restart
Procedure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Resetting the Data System by Turning the Personal Computer Off Then On 56
Turning Off Selected Mass Spectrometer Components . . . . . . . . . . . . . . . . . . . 56

Chapter 4 Tuning and Calibrating. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .59

Displaying the FC-43 Mass Spectrum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Running Auto Tune and Calibration. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Saving the Tune and Calibration Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Password Protection. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67

Chapter 5 Changing Ionization Modes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .69

Removing the Ion Volume . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
Installing the Ion Volume . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76

ii TSQ Quantum GC User Guide Thermo Scientific

 Contents

Chapter 6 Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .79

Cleaning Ion Source Components. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
Cleaning Ion Volumes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Cleaning Ion Source Lenses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Removing the Ion Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
Removing the Ion Source Lens Assembly . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
Disassembling the Ion Source Lens Assembly . . . . . . . . . . . . . . . . . . . . . . . . 87
Reassembling the Ion Source Lens Assembly . . . . . . . . . . . . . . . . . . . . . . . . . 89
Reinstalling the Ion Source Lens Assembly . . . . . . . . . . . . . . . . . . . . . . . . . . 89
Reinstalling the Ion Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
Replacing the Ion Source Filament . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
Dissassembling and Reassembling the Ion Source Completely. . . . . . . . . . . . . . 92
Cleaning Stainless Steel Parts. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
Cleaning Non-Stainless Steel or Hybrid Part . . . . . . . . . . . . . . . . . . . . . . . . . 97
Maintaining the Forepump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98
Adding Calibration Compound. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
Replacing the Ball Valve Seal. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
Removing and Installing a GC Capillary Column . . . . . . . . . . . . . . . . . . . . . . 104
Removing a GC Column. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
Installing a GC Column . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106

Chapter 7 Diagnostics and Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .111

Running the TSQ Quantum GC System Diagnostics . . . . . . . . . . . . . . . . . . . 111
Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
Communication Issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
Contamination Issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
Filament and Lens Control Issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
Heated Zone Issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
High Vacuum Issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
Linearity Issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
Power Supply Issues. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
Sensitivity Issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122
Stability Issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
Tuning Issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
Replacing a Fuse . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127
Replacing PCBs and Power Supplies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127

Chapter 8 Using the Direct Sample Probe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .129

Creating an Instrument Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
Creating a Sequence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132
Preparing the Probe and Inlet Valve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133
Preparing the Mass Spectrometer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133
Running the Sequence. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 136
Examining the Raw Data in Qual Browser . . . . . . . . . . . . . . . . . . . . . . . . . . . 140
Removing the Probe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141

Thermo Scientific TSQ Quantum GC User Guide iii

Contents

Chapter 9 Replaceable Parts and Consumables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .143

Accessory Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143
Chemicals Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .145

iv TSQ Quantum GC User Guide Thermo Scientific

 P

Preface
The Thermo Scientific TSQ Quantum GC™ system is a member of the TSQ™ Quantum
family of mass spectrometers.

This TSQ Quantum GC User Guide contains a description of the modes of operation and
principle hardware components of your TSQ Quantum GC system. In addition, this manual
provides step-by-step instructions for cleaning and maintaining your mass spectrometer.

Related Documentation
In addition to this manual, Thermo Fisher provides the following for the TSQ Quantum GC:
• Preinstallation Requirements Guide

• Help available from within the software

Safety and Special Notices

Make sure you follow the precautionary statements presented in this guide. The safety and
other special notices appear in boxes.

Safety and special notices include the following:

CAUTION Highlights hazards to humans, property, or the environment. Each

CAUTION notice is accompanied by an appropriate CAUTION symbol.

IMPORTANT Highlights information necessary to prevent damage to software, loss of

data, or invalid test results; or might contain information that is critical for optimal
performance of the system.

Note Highlights information of general interest.

Tip Highlights helpful information that can make a task easier.

Thermo Scientific TSQ Quantum GC User Guide v

Preface

Safety Precautions
Observe the following safety precautions when you operate or perform service on the mass
spectrometer.
CAUTION Do Not Perform Any Servicing Other Than That Contained in the TSQ
Quantum GC User Guide. To avoid personal injury or damage to the instrument, do
not perform any servicing other than that contained in the TSQ Quantum GC User
Guide or related manuals unless you are qualified to do so.

CAUTION Shut Down the Mass Spectrometer and Disconnect It From Line Power
Before You Service It. High voltages capable of causing personal injury are used in the
instrument. Some maintenance procedures require that the mass spectrometer be shut
down and disconnected from line power before service is performed. Do not operate the
mass spectrometer with the top or side covers off. Do not remove protective covers from
PCBs.

CAUTION Respect Heated Zones. Treat heated zones with respect. The ion source and
transfer line might be very hot and might cause severe burns if they are touched. Allow
heated components to cool before you service them.

CAUTION Provide and Adequate Fume Exhaust System. It is your responsibility to

provide an adequate fume exhaust system. Samples and solvents that are introduced into
the TSQ Quantum GC will eventually be exhausted from the forepump. Therefore, the
forepump should be connected to a fume exhaust system. Consult local regulations for the
proper method of exhausting the fumes from your system.

CAUTION Use Care When Changing Vacuum Pump Oil. Treat drained vacuum pump
oil and pump oil reservoirs with care. Hazardous compounds introduced into the system
might have become dissolved in the pump oil. Always use approved containers and
procedures for disposing of waste oil. Whenever a pump has been operating on a system
used for the analysis of toxic, carcinogenic, mutagenic, or corrosive/irritant chemicals, the
pump must be decontaminated by the user and certified to be free of contamination
before repairs or adjustments are made by a Thermo Fisher San Jose Customer Support
Engineer or before it is sent back to the factory for service.

vi TSQ Quantum GC User Guide Thermo Scientific

 Preface

Solvent and Gas Purity Requirements

Use the highest purity solvents available. The TSQ Quantum GC mass spectrometer is
extremely sensitive to solvent impurities. Some solvent impurities are transparent to
UV/Visible detectors, but are easily detected by the TSQ Quantum GC mass spectrometer.
Liquid chromatography grade is the minimum acceptable purity. Higher grade solvents are
preferred. Distilled water is recommended. Deionized water contains chemicals and is not
recommended.

The following is a list of international sources that can supply high quality solvents:
Solvent Source Telephone Number

Mallinckrodt/Baker, Inc. Tel: (800) 582-2537

Fax: (908) 859-9370

Burdick & Jackson, Inc. Tel: (800) 368-0050

Fax: (616) 725-6216

E. M. Science, Inc. Tel: (800) 222-0342

Fax: (800) 336-4422

The TSQ Quantum GC mass spectrometer uses argon as a collision gas. The argon must be
high purity (99.995%). The required gas pressure is 135 ± 70 kPa (20 ± 10 psig). Thermo
Fisher has found that particulate filters are often contaminated and are therefore not
recommended.

Service Philosophy
Servicing the TSQ Quantum GC system consists of performing procedures required to
maintain system performance standards, prevent system failure, restore the system to an
operating condition, or all of the above. Routine and preventive maintenance procedures are
documented in this manual.

The user is responsible for routine and preventive maintenance during and after the warranty
period. Regular maintenance increases the life of the system, maximizes the up-time of your
system, and allows you to achieve optimum system performance.

Only a Thermo Fisher Scientific Customer Support Engineer can perform services not
described in this manual.

Level of Repair
Thermo Fisher Scientific’s service philosophy for the TSQ Quantum GC system calls for
troubleshooting to the lowest part, assembly, printed circuit board (PCB), or module listed in
the “Replaceable Parts” chapter of this manual.

Thermo Scientific TSQ Quantum GC User Guide vii

Preface

For mechanical failures: A mechanical assembly typically is to be repaired to the level of the
smallest item listed in the “Replaceable Parts” chapter of this manual.

For electronic failures: PCBs are not repaired to the component level except in certain cases of
fuses, relays, and so on. When these exceptions occur, component information can be found
in the “Replaceable Parts” chapter.

Contacting Us
There are several ways to contact Thermo Fisher Scientific.

Y To contact Technical Support

Phone 800-685-9535
Fax 561-688-8736
E-mail TechSupport.C+MS@[Link]
Knowledge base [Link]
Find software updates and utilities to download at [Link].

Y To contact Customer Service for ordering information

Phone 800-532-4752
Fax 561-688-8731
Web site [Link]/finnigan

Y To suggest changes to documentation or to Help

• Fill out a reader survey online at [Link]/lcms-techpubs.

• Send an e-mail message to the Technical Publications Editor at
[Link]-lcms@[Link].

viii TSQ Quantum GC User Guide Thermo Scientific

 1

Introduction
The TSQ Quantum GC™ is a member of the TSQ™ Quantum family of Thermo Scientific
mass spectrometers. The TSQ Quantum GC is an advanced analytical instrument that
includes a mass spectrometer and the Xcalibur™ data system. See Figure 1.

Contents
• Ionization Modes
• Ion Polarity Modes
• Scan Modes
• Scan Types
• Data Types
• Mass/Charge Range

In a typical analysis, a gas chromatograph (GC) introduces a sample. The GC separates the
sample into its various components. The components elute from the GC and pass into the
mass spectrometer where they are analyzed.

Thermo Scientific TSQ Quantum GC User Guide 1

1 Introduction

Figure 1. TSQ Quantum GC mass spectrometer, TriPlus autosampler, and TRACE GC Ultra gas
chromatograph

The TSQ Quantum GC mass spectrometer includes an electron ionization/chemical

ionization (EI/CI) ion source, ion optics, a triple-stage mass analyzer, and an ion detection
system, all of which are enclosed in a vacuum manifold. Ionization of the sample takes place
in the ion source. The specific process used to ionize the sample is known as the ionization
mode. The ion optics transmit the ions produced in the ion source into the mass analyzer,
where they are separated according to their mass-to-charge ratio. The polarity of the potentials
applied to the lenses in the ion source and ion optics determines whether positively charged
ions or negatively charged ions are transmitted to the mass analyzer. You can configure the
TSQ Quantum GC mass spectrometer to analyze positively or negatively charged ions (called
the positive or negative ion polarity mode).

The TSQ Quantum GC instrument’s triple-stage mass analyzer performs either one or two
stages of mass analysis:
• The TSQ Quantum GC system is operated as a conventional mass spectrometer with one
stage of mass analysis. The ion source ionizes the sample and the ion products are
subjected to mass analysis in the first rod assembly. The second and third rod assemblies
transmit the resulting mass-selected ions to the ion detection system.1

2 TSQ Quantum GC User Guide Thermo Scientific

 1 Introduction
Ionization Modes

• The TSQ Quantum GC system is operated as a tandem mass spectrometer with two
stages of mass analysis. The ion source ionizes the sample and the ion products are mass
analyzed by the first rod assembly. In this case, however, mass-selected ions exiting the
first rod assembly collide with an inert gas in the second rod assembly and fragment to
produce a set of ions known as product ions. (A chamber called the collision cell
surrounds the second rod assembly. The collision cell can be pressurized with an inert
gas.) The product ions undergo further mass analysis in the third rod assembly to detect
selected ions. Two stages of mass analysis yield far greater chemical specificity than a
single stage can achieve, because of the system’s ability to select and determine two
discrete but directly related sets of masses.

In a first stage of mass analysis the TSQ Quantum GC systems can be used to elucidate the
structures of pure organic compounds and the structures of the components within mixtures.
Furthermore, in a second stage of mass analysis, the mass spectrometer can fragment and
separate each ionic fragment of a molecule formed in the ion source to build up an entire
structure for the molecule, piece by piece. Thus, TSQ Quantum GC systems make
investigating all pathways for the formation and fragmentation of each ion in the mass
spectrum possible.

The two stages of mass analysis, with resultant reduction of chemical noise in the final mass
spectrum, allow for very selective and sensitive analysis.

Each sequence of single or triple-stage mass analysis of the ions is called a scan. The TSQ
Quantum GC mass spectrometer uses several different scan modes and different scan types to
filter, fragment, or transmit ions in the mass analyzer. Along with the ionization and ion
polarity modes, the ability to vary the scan mode and scan type affords the user great
flexibility in the instrumentation for solving complex analytical problems.

Ionization Modes
The specific process used to ionize the analyte is referred to as the ionization mode. You can
operate the TSQ Quantum GC mass spectrometer in either of two ionization modes:
• Electron ionization mode
• Chemical ionization mode

Electron Ionization Mode

In electron ionization (EI) mode, electrons are emitted by a heated, wire filament that has
electric current running through it, by thermionic emission. The filament and its reflector are
typically maintained at a -70 V potential relative to the ion source block. This potential

1 The instrument can also be used as a single-stage mass spectrometer by transmitting the ions through the first and

second rod assemblies followed by mass analysis in the third rod assembly.

Thermo Scientific TSQ Quantum GC User Guide 3

1 Introduction
Ionization Modes

accelerates the electrons through the ionization space, called the ion volume. These energetic
electrons interact with neutral, gas-phase analyte molecules present in the ion volume and
cause the analyte to lose an electron and produce a radical cation:
M + e - --> M+ + 2e -

Frequently, numerous cleavage reactions give rise to fragment ions, which provide structural
information about the analyte.

EI positive-ion mode is the only commonly used EI mode.

Chemical Ionization Mode

In chemical ionization (CI) mode, ionization of the sample molecules is a multi-step process:
1. Reagent gas is introduced into the CI ion volume at a flow (for methane) of about
2 mL/min, along with sample vapors typically present at partial pressures of less than
one-thousandth that of the reagent gas.
2. The energetic (typically 100 eV) electrons emitted by the heated filament interact to
ionize the reagent gas and form a plasma. This reaction also produces thermal electrons.
3. Reagent gas ions react with reagent gas molecules to form a variety of secondary ions that
are stable with respect to further reaction with reagent gas.
For example, for methane:
CH4 + e - ----> CH4+. + 2e -
CH4 + e - ----> CH3+ + e - + H-
CH4+. + CH4 ----> CH5+ +CH3.
CH3+ + CH4 ----> C2H5+ + H2
4. Positive sample ions are formed by one of the following:
• The transfer of a proton from a secondary reagent gas ion to a sample molecule
• The abstraction of an electron by a reagent gas ion
• An ion association reaction in which an adduct ion is formed between a reagent gas
ion and a sample molecule

In methane positive ion mode CI, the relevant peaks observed are MH+, [M+CH5]+, and
[M+C2H5]+; but mainly MH+.

In isobutane positive ion mode CI, the main peak observed is MH+.

In ammonia positive ion mode CI, the main peaks observed are MH+ and [M+NH4]+.

Negative sample ions are most commonly formed by one of the following:
• Sample molecules capture the secondary thermal electrons present in the ion source

4 TSQ Quantum GC User Guide Thermo Scientific

 1 Introduction
Ion Polarity Modes

• Electron transfer from ionized reagent gas (e.g. NH2-)

• Proton abstraction

Molecular ions observed in negative ion chemical ionization mass spectra are usually M- or
[M-H]-.

Ion Polarity Modes

You can operate the TSQ Quantum GC mass spectrometer in either of two ion polarity
modes: positive or negative. Both positively charged and negatively charged ions form in the
ion source of the mass spectrometer. The TSQ Quantum GC mass spectrometer can control
whether positive ions or negative ions are transmitted to the mass analyzer for mass analysis by
changing the polarity of the potentials applied to the ion source and ion optics. The ion optics
deliver the ions produced in the ion source, in a collimated beam, to the mass analyzer.

The information obtained from a positive-ion mass spectrum is different from and
complementary to the information from a negative-ion spectrum. Thus, the ability to obtain
both positive-ion and negative-ion mass spectra aids you in the qualitative analysis of your
sample. You can choose the ion polarity mode and ionization mode to obtain maximum
sensitivity for the particular analyte of interest.

Scan Modes
You can operate the TSQ Quantum GC mass spectrometer in a variety of scan modes. The
most commonly used scan modes can be divided into two categories: single mass
spectrometry (MS) scan modes and MS/MS scan modes. The scan modes in each category are
as follows:
• MS scan modes: Q1MS and Q3MS scan modes
• MS/MS scan modes: product scan mode, parent scan mode, Neutral Loss scan mode
• Data-dependent scan mode

The scan modes that can be employed depend on the number and type of rod assemblies and
the voltages applied to the rod assemblies.

The TSQ Quantum GC system mass analyzer has three rod assemblies.2 The first and third
rod assemblies, Q1 and Q3, are quadrupoles, and the second rod assembly, Q2, is a
square-profile quadrupole.
Rod assemblies can operate in either of two capacities:
• As ion transmission devices
2A rod assembly is a regular array of metal rods. Refer to “Mass Analyzer” on page 28 for a discussion of the rod
assemblies used on the TSQ Quantum GC instrument.

Thermo Scientific TSQ Quantum GC User Guide 5

1 Introduction
Scan Modes

• As mass analyzers

If only RF voltage is applied, a rod assembly serves as an ion transmission device that passes
all ions within a large range of mass-to-charge ratios (that is, virtually all ions present).

When you apply both RF and dc voltages to a rod assembly, the separation of ions of different
mass-to-charge ratios occurs. This separation allows the rod assembly to serve as a mass
analyzer.

On the TSQ Quantum GC mass spectrometer, the quadrupole rod assemblies can operate
with RF and dc voltages or with only RF voltage. That is, Q1 and Q3 can act either as mass
analyzers or ion transmission devices. The Q2 rod assembly operates exclusively with RF
voltage. Thus, Q2 is always an ion transmission device. For a summary of how the rod
assemblies function in several of the major scan modes, see Table 1.
.

Table 1. Summary of scan modes

Scan Mode Q1 quadrupole Q2 Collision Cell Q3 quadrupole
Q1MS Scana Pass all ionsb Pass all ions
Q3MS Pass all ions Pass all ions Scan
Product Setd Fragment ionsc, then pass Scan
all fragments
Parent Scan Fragment ions, then pass all Set
fragments
Neutral Loss Scan Fragment ions, then pass all Scan
fragments
aScan
= full scan or transmission of selected ions
bPass
all ions or fragments = pass ions or fragments within a wide range of mass-to-charge ratios
c
Fragment ions = collisions with argon gas cause ions to fragment
dSet = set to pass ions of a single mass-to-charge ratio or a set of mass-to-charge ratios

Q1MS and Q3MS Scan Modes

In the Q1MS and Q3MS scan modes, only one stage of mass analysis is performed. The mass
spectrum obtained is equivalent to the mass spectrum obtained from an instrument with a
single mass analyzer. In the one stage of analysis, ions formed in the ion source enter the
analyzer assembly. One of the mass analyzers (Q1 or Q3) is scanned to obtain a complete
mass spectrum. The other rod assemblies (Q2 and Q3, or Q1 and Q2, respectively) act as ion
transmission devices. In the Q1MS scan mode, Q1 is used as the mass analyzer; in the Q3MS
scan mode, Q3 is used as the mass analyzer.

Product Scan Mode

Product scan mode performs two stages of analysis. In the first stage, ions formed in the ion
source enter Q1, which is set to transmit ions of one mass-to-charge ratio. Ions selected by
this first stage of mass analysis are called parent ions. (As a result, Q1 is referred to as the

6 TSQ Quantum GC User Guide Thermo Scientific

 1 Introduction
Scan Modes

parent mass analyzer, and the mass-to-charge ratio of ions transmitted by the parent mass
analyzer is referred to as the parent set mass.) Parent ions selected by Q1 then enter Q2,
which is surrounded by the collision cell.

Note When referring to the first, second, and third rod assemblies as pieces of
hardware, it is convenient to call them Q1, Q2, and Q3, respectively. However, when
discussing their function in MS/MS scan modes, it often adds clarity to refer to them as
the parent mass analyzer, collision cell (ion transmission device surrounded by the
collision cell), and product mass analyzer, respectively.

In the second stage of analysis, ions in the collision cell can fragment further to produce
product ions. Two processes produce product ions: by unimolecular decomposition of
metastable ions or by interaction with argon collision gas present in the collision cell. This
latter step is known as collision-induced dissociation (CID). Ions formed in the collision cell
enter Q3 (the product mass analyzer) for the second stage of mass analysis. Q3 is scanned to
obtain a mass spectrum that shows the product ions produced from the fragmentation of the
selected parent ion.

A mass spectrum obtained in the Product scan mode (product mass spectrum) is the mass
spectrum of a selected parent ion.

The Product scan mode is illustrated in Figure 2.

Figure 2. Illustration of Product scan mode

Q2
RF Only + Ar
Q1 Set Q3 Scanning

Q3 m/z

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1 Introduction
Scan Modes

Parent Scan Mode

The Parent scan mode also uses two stages of analysis. In the first stage, ions formed in the
ion source are introduced into the parent mass analyzer, which is scanned to transmit parent
ions sequentially into the collision cell.

In the second stage of analysis, in the collision cell, parent ions can fragment to produce
product ions by unimolecular decomposition of metastable ions or by collision-induced
dissociation. Ions formed in the collision cell enter the product mass analyzer, which
transmits a selected product ion. (The product set mass is the mass-to-charge ratio of ions
transmitted by the product mass analyzer.)

The resultant spectrum shows all the parent ions that fragment to produce the selected
product ion. Note that for a mass spectrum obtained in the Parent scan mode (parent mass
spectrum), data for the mass-to-charge ratio axis are obtained from Q1 (the parent ions),
whereas data for the ion intensity axis are obtained from Q3 (from monitoring the product
ion).

The Parent scan mode is illustrated in Figure 3.

Figure 3. Illustration of the Parent scan mode

Q2
RF Only + Ar
Q1 Scanning Q3 Set

Q1 m/z

8 TSQ Quantum GC User Guide Thermo Scientific

 1 Introduction
Scan Modes

Experiments that employ the parent scan mode (parent experiments) can be used in structure
and fragmentation studies as well as in survey analyses of mixtures. In general, parent
experiments detect all compounds that decompose to a common fragment. The experiments
are useful for the rapid detection of a series of structural homologs (for example, substituted
aromatics, phthalates, steroids, or fatty acids) that have a common fragment ion (for example,
m/z 149 for the phthalates).

Neutral Loss Scan Modes

In the Neutral Loss scan mode, the two mass analyzers (Q1 and Q3) are linked together so
that they are scanned at the same rate over mass ranges of the same width. The respective mass
ranges, however, are offset by a selected mass, such that the product mass analyzer scans a
selected number of mass units lower than the parent mass analyzer.

Thus, in the Neutral Loss scan mode, there are two stages of mass analysis. In the first stage,
the parent mass analyzer separates ions formed in the ion source by mass-to-charge ratio.
Then the ions are introduced sequentially into the collision cell.

In the second stage of analysis, ions admitted to the collision cell can fragment further by
metastable ion decomposition or by CID to produce product ions. The product mass analyzer
then separates these product ions by mass-to-charge ratio. Neutral Loss scan mode is
illustrated in Figure 4. Examples of compounds with a common neutral loss fragment appear
in Figure 5.

To detect an ion, between the time the ion leaves Q1 and enters Q3, it must lose a neutral
moiety whose mass (the neutral loss mass) is equal to the difference in the mass ranges being
scanned by the two mass analyzers. Thus, a neutral loss mass spectrum is a spectrum that
shows all the parent ions that lose a neutral species of a selected mass.

Note that a neutral gain (or association) experiment can also be performed in which the mass
range scanned by Q3 is offset by a selected mass above the mass range scanned by Q1.

For a neutral loss (or neutral gain) mass spectrum, as for a parent mass spectrum, data for the
mass-to-charge ratio axis are obtained from Q1 (the parent ion), whereas data for the ion
intensity axis are obtained from Q3 (the product ion being monitored).

Experiments that use the Neutral Loss scan mode (neutral loss experiments) are useful when a
large number of compounds are being surveyed for common functionality. Neutral moieties
are frequently lost from substituent functional groups (for example, CO2 from carboxylic
acids, CO from aldehydes, HX from halides, and H2O from alcohols).

Thermo Scientific TSQ Quantum GC User Guide 9

1 Introduction
Scan Modes

Figure 4. Illustration of the Neutral Loss scan mode

Q2
R F O nly + A r
Q1 Scanning Q3 = Q1 - ∆

Q1 m/z

Figure 5. Examples of compounds with a common neutral-loss fragment

NH2

N N

N H2 N N

HO N N

N
H2 N

N
N
H2 N N
N

10 TSQ Quantum GC User Guide Thermo Scientific

 1 Introduction
Scan Types

Data Dependent Scan Mode

The TSQ Quantum GC mass spectrometer uses the information in a data-dependent scan
mode experiment to make automatic decisions about the next step of the experiment without
input from a user. In data-dependent scan mode you specify criteria to select one or more ions
of interest on which to perform subsequent scans, such as MS/MS. You can approach the
setup of data-dependent experiments in either of two ways:
• If you have some idea of what the parent ion is, or if you expect a certain kind of parent,
you can set up a list of possible parent ions. Then, when one of the parent ions you
specified is detected, you can acquire product spectra and analyze the information.
Conversely, you can also set up a list of ions that you do not want selected for
fragmentation.
• If you have little information about your compound, you can set up the parameters of a
data-dependent experiment so that if the intensity of the ion signal is above a specified
threshold, the TSQ Quantum GC system generates product spectra. Later, you can
decide if the information is useful.

Because a data-dependent scan needs to use a target ion from a previous scan, the first scan
event cannot be a data-dependent scan.

Scan Types
TSQ Quantum GC systems can be operated with a variety of scan types. The most common
scan types are as follows:
• Full Scan
• Selected Ion Monitoring (SIM)
• Selected Reaction Monitoring (SRM)
• AutoSIM

Full Scan
The full-scan scan type provides a full mass spectrum of each analyte. With full scan, the
scanning mass analyzer is scanned from the first mass to the last mass, without interruption,
in a given scan time.

Full-scan experiments are used to determine or confirm the identity of unknown compounds
or the identity of each component in a mixture of unknown compounds. (Generally, a full
mass spectrum is needed to determine the identity of an unknown compound.)

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1 Introduction
Scan Types

The full-scan scan type gives you more information about an analyte than does SIM, but a full
scan does not yield the sensitivity that the other two scan types can achieve. With full scan,
you spend less time monitoring the signal for each ion than you do in SIM or SRM. Full scan
provides greater information but lower sensitivity than the other two scan types.

To use the SIM or SRM, you need to know what ions or reactions you are looking for before
you can perform an experiment with these scan types. Thus, you might use a full scan for SIM
to determine the identity of an analyte and to obtain its mass spectrum and a full scan for
SRM to determine the mass spectrum and product mass spectra for parent ions of interest.
Then, you might use SIM or SRM to do routine quantitative analysis of the compound.

Selected Ion Monitoring

Selected ion monitoring (SIM) monitors a particular ion or set of ions. SIM experiments are
useful in detecting small quantities of a target compound in a complex mixture when you
know the mass spectrum of the target compound. Thus, SIM is useful in trace analysis and in
the rapid screening of a large number of samples for a target compound.

Because SIM monitors only a few ions, it can provide lower detection limits and greater speed
than the full-scan modes. SIM achieves lower detection limits because more time is spent
monitoring significant ions that are known to occur in the mass spectrum of the target
analyte. SIM can achieve greater speed because it monitors only a few ions of interest; SIM
does not monitor regions of the spectrum that are empty or have no ions of interest.

SIM can improve the detection limit and decrease analysis time, but it can also reduce
specificity. Because SIM monitors only specific ions, any compound that fragments to
produce those ions will appear to be the target compound. The result could be a false positive.

Selected Reaction Monitoring

Selected reaction monitoring (SRM monitors a particular reaction or set of reactions, such as
the fragmentation of an ion or the loss of a neutral moiety.

SRM monitors a limited number of parent/product-ion pairs. In product-type experiments, a

parent ion is selected as usual, but generally only one product ion is monitored. SRM
experiments are normally conducted with the product scan mode.

As does SIM, SRM provides for the very rapid analysis of trace components in complex
mixtures. However, because SRM selects two sets of ions, it obtains specificity that is much
greater than what SIM can obtain. Any interfering compound would not only have to form
an ion source product (parent ion) of the same mass-to-charge ratio as the selected parent ion
from the target compound, but that parent ion would also have to fragment to form a product
ion of the same mass-to-charge ratio as the selected product ion from the target compound.

12 TSQ Quantum GC User Guide Thermo Scientific

 1 Introduction
Data Types

AutoSIM
In the scan type known as AutoSIM, the mass spectrometer automatically selects the most
intense masses (m/z values) in a survey scan, builds a SIM scan list for them, and then acquires
and records ion current at only these selected masses. AutoSIM scans can be performed on
any full scan in any scan mode, but not on data-dependent scans.

There might be times when the scan ranges of two (or more) selected masses overlap. If this
happens, both masses are placed in one SIM window. In Tune Master, the SIM table in the
Define Scan view displays the center mass for this new scan window, not each selected mass.

Data Types
You can acquire and display mass spectral data (intensity versus mass-to-charge ratio) with
the TSQ Quantum GC mass spectrometer in one of two data types:
• Profile data type
• Centroid data type

Profile Data Type

In the profile data type, you can see the shape of the peaks in the mass spectrum. Each atomic
mass unit is divided into many sampling intervals. The intensity of the ion current is
determined at each of the sampling intervals. The profile data type displays the intensity at
each sampling interval with the intensities connected by a continuous line. In general, use the
profile scan data type when you tune and calibrate the mass spectrometer so that you can
easily see and measure mass resolution.

Centroid Data Type

The centroid data type displays the mass spectrum as a bar graph and sums the intensities of
each set of multiple sampling intervals. This sum is displayed versus the integral center of
mass of the sampling intervals. In general, use the centroid scan data type for data acquisition
for faster scan speed. Data processing is also much faster for centroid data.

Mass/Charge Range
The TSQ Quantum GC mass spectrometer can operate in a mass/charge range of 10 to
3000 Da.

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 2

Functional Description
This chapter describes the principal components of the TSQ Quantum GC system and their
respective functions.

Contents
• Autosampler (optional)

• Gas Chromatograph

• Direct Sample Probes (optional)

• Transfer Line

• Mass Spectrometer

• Data System

A functional block diagram of the TSQ Quantum GC system is shown in Figure 6. A sample
transfer line connects the GC to the mass spectrometer. The autosampler and GC are installed
on the left side of the mass spectrometer.

In analysis by GC/MS, a sample is injected into a GC column. The sample is then separated
into its various components. The components elute from the GC column and pass through
the transfer line into the mass spectrometer where they are analyzed. You can also use a direct
sample probe to introduce sample into the mass spectrometer.

Electron ionization (EI) or chemical ionization (CI) ionize sample molecules upon entering
the mass spectrometer. The ion optics focus and accelerate the resulting sample ions into the
mass analyzer where they are analyzed according to their mass-to-charge ratios. An ion
detection system that produces a signal proportional to the number of ions detected then
detects the sample ions. The system electronics receive and amplify the ion current signal
from the ion detection system. That signal is then passed on to the data system for further
processing, storage, and display. The data system provides the primary TSQ Quantum GC
mass spectrometer user interface.

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2 Functional Description
Autosampler

Figure 6. Functional block diagram of the TSQ Quantum GC system

Sample flow
Electrical connection

Mass spectrometer Data system

Autosampler
(Optional)
Printer
(optional)

Instrument
Gas Ion Ion Mass Ion detection control Personal
chromatograph source optics analyzer system electronic computer
Transfer assemblies
line

Vacuum Video
system monitor

Autosampler
The (optional) Thermo Scientific TriPlus autosampler is used to inject samples automatically
into the GC inlet. With an autosampler, you can automate your GC/MS/MS analyses. The
TriPlus autosampler is shown in Figure 1 on page 2.

Autosampler Start/Stop signals with the TSQ Quantum GC mass spectrometer are provided
by contact closure.

You configure TriPlus autosampler from the data system computer. Select the TriPlus
instrument button in the Instrument Configuration window, which is available by choosing
Start > All Programs > Xcalibur > Instrument Configuration. Refer to Xcalibur Help for a
description of TriPlus configuration options.

You also use the data system to set up the TriPlus autosampler to inject samples. Choose
Start > All Programs > Xcalibur > Xcalibur and click Instrument Setup to open the
Instrument Setup window. Then, click the TriPlus icon to open the TriPlus Autosampler
page. Refer to the Help for instructions on running the TriPlus autosampler.

Refer to the documentation provided with the autosampler for maintenance procedures.

16 TSQ Quantum GC User Guide Thermo Scientific

 2 Functional Description
Gas Chromatograph

Gas Chromatograph
The Thermo Scientific TRACE GC Ultra gas chromatograph (GC)) separates a sample
mixture into its chemical components by gas chromatography. In gas chromatography, the
sample mixture is partitioned between a solid stationary phase and a mobile gas. The
stationary phase is adhered to the inside of a small-diameter glass tube: the capillary column.
The molecular structure of each component of the mixture determines in which order each
component elutes from the GC and enters the mass spectrometer. The TRACE GC Ultra gas
chromatograph is shown in Figure 1 on page 2.

Gas chromatography is widely used in analytical chemistry, though the high temperatures
used in GC make it unsuitable for high molecular weight biopolymers, frequently
encountered in biochemistry. It is well suited for use in the petrochemical, environmental
monitoring, and industrial chemical fields. It is also used extensively in chemistry research.

You configure TRACE GC Ultra gas chromatograph from the data system computer. Select
the TRACE GC Ultra instrument button in the Instrument Configuration window, which is
available by choosing Start > All Programs > Xcalibur > Instrument Configuration. Refer
to Xcalibur Help for a description of TRACE GC Ultra configuration options.

The TSQ Quantum GC mass spectrometer data system computer can directly control the
TRACE GC Ultra. Choose Start > Programs > Xcalibur > Xcalibur and click Instrument
Setup to open the Instrument Setup window. Click the TRACE GC Ultra icon to open the
TRACE GC Ultra page. Refer to the Help for instructions for operating the TRACE GC
Ultra.

Front-panel (keypad) operation of the GC and maintenance procedures for the GC are
described in the documentation provided with the GC. To replace the GC capillary column,
see “Removing and Installing a GC Capillary Column” on page 104.

Direct Sample Probes

With the (optional) direct sample probes you can introduce compounds directly into the ion
source without GC column separation. See Figure 7. The direct sample probes are ideal for
qualitative or semi-quantitative analysis of materials that don't require a GC column
separation, or are difficult, if not impossible, to elute chromatographically, such as solids. The
direct sample probes introduce samples directly into the ion source via a vacuum interlock. A
single controller box (Figure 7) with interchangeable probe tools makes it easy to select the
best method of sample introduction.

The direct sample probe system includes two probe tools:

• Direct exposure probe
• Direct insertion probe

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2 Functional Description
Transfer Line

The direct exposure probe (DEP) has a heated filament that rapidly vaporizes liquids or
solutions. The DEP is ideal for rapid molecular weight confirmation of liquids or solids
dissolved in a suitable solvent. The DEP can vaporize compounds with a high boiling point.

The direct insertion probe (DIP) has a temperature-controlled, heated capillary tube that
slowly vaporizes solid samples. You can use the DIP for rapid analysis of solids or trace
components in solid matrices, such as forensic samples or tissue.
Figure 7. Direct sample probe and controller

Transfer Line
The transfer line is the interface between the GC and mass spectrometer. The transfer line
heats the capillary column as it passes from the GC into the ion source in the mass
spectrometer. This prevents the sample from condensing. The transfer line includes an inlet
for calibration gas and CI gas.

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 2 Functional Description
Mass Spectrometer

Figure 8. Transfer line

GC end

Inlet for calibration

gas and CI gas

Mass spectrometer
ion source end

Mass Spectrometer
The TSQ Quantum GC mass spectrometer provides sample ionization and mass analysis of
samples introduced from a gas chromatograph or direct insertion probe. The mass
spectrometer uses a triple-quadrupole mass analyzer with an ion source external to the mass
analyzer. Several important features of the TSQ Quantum GC mass spectrometer are as
follows:
• High sensitivity and resolution
• m/z 10 to 3000 mass range

• EI and CI ionization modes

• Positive and negative ion polarity modes

• MS and MS/MS scan modes

• Full-scan, SIM, SRM, AutoSIM, and data-dependent scan types

The mass spectrometer includes the following components:

• Controls and Indicators

• Ion Source

• Ion Optics

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2 Functional Description
Mass Spectrometer

• Mass Analyzer

• Ion Detection System

• Vacuum System and Inlet Gasses Hardware

• Electronic Assemblies

• Data System

Controls and Indicators

Five light-emitting diodes (LEDs) are located at the upper right side of the front panel of the
mass spectrometer. See Figure 9.

The Power LED illuminates green whenever power is supplied to the vacuum system and
electronic assemblies of the mass spectrometer.

The Vacuum LED illuminates yellow when the turbomolecular pump is nearly at speed (80%
of its operating speed of 750 MHz) and it is safe to turn on the ion gauge. The Vacuum LED
is off if the turbomolecular pump is not at speed. The Vacuum LED illuminates green
whenever the pressure in the analyzer chamber, as measured by the ion gauge, is at or below
the value required to enable high voltages to the mass analyzer. See Table 2.
Figure 9. Front panel LEDs of the mass spectrometer

Power Vacuum Communication

System Scan

Table 2. Maximum allowed pressure to turn on high voltages

Carrier gas Ar collision gas Maximum pressure (Torr)
He Off 6 × 10-6
He On 5 × 10-5
H2 Off 5 × 10-5
H2 On 1 × 10-4

The Communication LED illuminates yellow when the mass spectrometer and the data
system are trying to establish a communication link. The Communication LED illuminates
green when the Ethernet communication link between the mass spectrometer and the data
system has been made.

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 2 Functional Description
Mass Spectrometer

The System LED illuminates yellow whenever the mass spectrometer is in Standby—that is,
high voltage is not supplied to the ion source, mass analyzer, or ion detection system, but the
mass spectrometer power is on. The System LED illuminates green whenever the high voltage
is enabled and the system is in the On state. High voltage is enabled if the analyzer chamber is
below the values listed in Table 2.

The Scan LED flashes blue whenever the mass spectrometer is on and is scanning ions.

The System Power Off button, located on the front of the electronics module, turns off power
to the mass spectrometer, gas chromatograph, and autosampler. See Figure 10. You must use
the main power circuit breaker, located on the back of the electronics module, to restore
power to the mass spectrometer, gas chromatograph, and autosampler.

CAUTION In an emergency, to shut off all power to the mass spectrometer, gas
chromatograph, and autosampler, press the System Power Off button located at the front
of the instrument.

Figure 10. Front panel System Power Off button

System

System Power Off

The main power circuit breaker switch (labeled Main Power) is located on the power panel at
the back of the electronics module. See Figure 11. In the Off (O) position, the circuit breaker
removes all power to the mass spectrometer, gas chromatograph, and autosampler. In the On
(|) position, power is supplied to the mass spectrometer, gas chromatograph, and autosampler.
In the standard operational mode, the circuit breaker is kept in the On (|) position.

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2 Functional Description
Mass Spectrometer

Figure 11. Rear power panel of the electronics module

Power In GC Power Out Quantum Power Out A/S Power Out

! !
V~230 V~230 V~230 V~230
Hz, 30A MAX 50/60 Hz, 16A MAX 50/60 Hz, 10A MAX 50/60 Hz, 2A MAX

The mass spectrometer main power circuit breaker switch (labeled Main Power) is located on
the mass spectrometer power panel in the lower corner of the right-side panel of the mass
spectrometer. See Figure 12. In the Off position, the circuit breaker removes all power to the
mass spectrometer, including the vacuum pumps. In the On position, power is supplied to the
mass spectrometer. In the standard operational mode, the circuit breaker is kept in the On
position.

The electronics service switch (labeled Electronics) is located next to the main power circuit
breaker on the mass spectrometer power panel (Figure 12). In the Service Mode position the
switch removes power to all components of the mass spectrometer other than the vacuum
system. The Operating Mode position supplies power to all non-vacuum system components
of the mass spectrometer.

The vacuum service switch (labeled Vacuum) is located next to the electronics service switch
on the mass spectrometer power panel (Figure 12). In the Service Mode position the switch
removes power to all components of the vacuum system, including the forepump,
turbomolecular pump, and turbomolecular pump controller. The switch in the Operating
Mode position supplies power to all vacuum system components of the mass spectrometer.

The System Reset button is also located on the mass spectrometer power panel. Pressing the
System Reset button takes the 5 V logic to ground and causes the embedded computer on the
System Control PCB to reboot. The TSQ Quantum GC mass spectrometer software is then
reloaded from the data system. See “Resetting the Mass Spectrometer” on page 54 for
information on how to reset the mass spectrometer.

Three LEDs are located on the power panel: The Pump On LED is green when the rough
pump current sensor detects current to the forepump. The LED is off when the rough-pump
current sensor does not detect current to the forepump. If the current sensor detects a loss of
current when the TSQ Quantum Access is on, the vacuum system vents.

The Vent Valve Closed LED is green whenever the vent valve current sensor detects current
through the vent valve and the vent valve is closed. The LED is off when the vent valve is
open.

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 2 Functional Description
Mass Spectrometer

The Ethernet Link OK LED is green when the System Control PCB is communicating with
the data system PC. The LED is off when there is no communication between the System
Control PCB and the data system PC.
Figure 12. Right-side power panel of the mass spectrometer

Pum p O n

Electronics Vacuum

Qualified
Service
Personnel
Only

!
Ion Source
The ion source forms gas phase sample ions from sample molecules that elute from the GC or
are introduced by the direct sample probe. You can operate the ion source in either the
electron ionization (EI) or chemical ionization (CI) mode.

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2 Functional Description
Mass Spectrometer

Figure 13. Ion source

Magnets and
magnet yoke

Filament
EI/CI Source PCB
Ion source block

Heater ring
Lens L1, L2, L3,
and L4 assembly

The ion volume, located in the center of the ion source, is the site where electrons interact
with sample or reagent gas molecules to form ions. Three exchangeable ion volumes and ion
volume holders are available for use in the ion source. See Figure 14. The choice of ion
volume depends on the ionization mode. The EI ion volume is open on the analyzer end, with
a relatively large electron entrance hole. The closed EI ion volume has a smaller ion exit hole
than the EI ion volume. This results in a higher pressure of analyte, and greater sensitivity, but
less dynamic range. The CI ion volume is closed on the analyzer end, except for a small ion
exit hole and a relatively small electron entrance hole. In the CI mode it is important to
maintain a relatively high reagent gas pressure.

The ion source block holds the ion volume in its center. Samples are introduced from the GC
capillary column through an aperture on the side of the ion source block and then into the ion
volume. Gases for calibration or chemical ionization enter the ion volume through a gas inlet
tube.

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 2 Functional Description
Mass Spectrometer

Figure 14. EI (left), closed EI (center), and CI (right) on volumes and holders

Electron
entrance hole

Ion exit
hole (front)

GC effluent, CI gas, cal

gas entrance hole
Electron exit hole

Cartridge heaters heat the ion source block to minimize the rate at which deposits form on the
ions source block and ion volume. The ion source block is also heated to assist in the rapid
temperature equilibration of the ion source block and ion volume after the filament is turned
on. In EI mode, the ion source is typically maintained at 150 oC to 220 oC. However, lower
or higher temperatures are sometimes used for certain applications. In the CI mode, the ion
source is typically maintained at 180 oC to 200 oC. The ion source heater is feedback
controlled.

The filament assembly, positioned in a recess at the top of the ions source block, contains the
filament, reflector, and electron lens. The filament is a rhenium wire that is electrically heated
to produce electrons by thermionic emission. The reflector repels electrons emitted by the
filament away from the filament toward the ion volume. The filament and its reflector are
maintained at a negative potential relative to the ion volume. The electron lens prevents
positive ions from traveling up the electron beam. In turn, this prevents positive ions from
leaving the ion volume through the electron entrance hole. The difference in potential
between the filament and the ion volume determines the electron energy.

Two permanent magnets are held in a magnet yoke in the proper position above and below
the ion source block. The permanent magnets collimate the electron beam and cause the
beam to spiral through the ion volume. This ensures optimum ionization of the sample.

Four ion source lenses, designated L1, L2, L3, and L4, extract the ions formed in the ion
source and transmit them to the ion optics. The lens L2 voltage is mass dependent. Lenses L1
and L3 voltages are constant and equal in magnitude. The lens L4 voltage depends on the
lowest mass. In positive ion mode, the lenses are adjusted to a negative potential, and in
negative ion mode, the lenses are adjusted to a positive potential. The arrangement of the
lenses and their spacers enables quick and efficient pump-out of the ion source.

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2 Functional Description
Mass Spectrometer

Inlet Valve
The inlet valve, which is attached to the front of the vacuum manifold, is a vacuum-sealed
valve that allows you to change ion volumes or insert the direct exposure probe without
venting the mass spectrometer to atmosphere. You use the insertion/removal (I/R) tool to
insert or remove ion volumes. See Figure 15. The forepump evacuates the inlet valve.

The ball valve is a ball with a hole in it, and it is located between the vacuum manifold and
the inlet valve block. The ball valve is open when the hole in the ball is aligned with the
opening between the vacuum manifold and the inlet valve. The ball valve lever opens and
closes the ball valve. When the ball valve is closed, it prevents the vacuum manifold from
venting to atmosphere.
Figure 15. Inlet valve, I/R tool, guide bar, and ball valve lever

Inlet valve

I/R tool

Guide bar

Ball valve lever

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 2 Functional Description
Mass Spectrometer

Ion Optics
The ion optics focus the ions produced in the ion source and transmit them to the mass
analyzer. The ion optics includes the Q0 quadrupole and lenses L11 and L12.

The Q0 quadrupole is a square array of square-profile rods that acts as an ion transmission
device. See Figure 16. An RF voltage applied to the rods gives rise to an electric field that
guides the ions along the axis of the quadrupole. The Q0 offset voltage increases the
translational kinetic energy of ions emerging from the ion source.
Figure 16. Q0 quadrupole

Figure 17 gives a cross-sectional view of the transfer line, ion source, and Q0 quadrupole.

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2 Functional Description
Mass Spectrometer

Figure 17. Cross-sectional view of the transfer line, ion source, and Q0 quadrupole
Ion source lens
Q0 quadrupole assembly Ion source ion volume

Transfer line

Capillary column

The L11 and L12 lenses are metal disks with a circular hole in the center through which the
ion beam can pass. Together they act as a two-element cone lens. An electrical potential can
be applied to the lens to accelerate (or decelerate) ions as they approach the lens and to focus
the ion beam as it passes through the lens. The value ranges between 0 and ±300 V. Lenses
L11 and L12 also act as a vacuum baffle between the Q0 quadrupole chamber and the mass
analyzer chamber.

Mass Analyzer
The mass analyzer separates ions according to their mass-to-charge ratio and then passes them
to the ion detection system. The mass analyzer on the TSQ Quantum GC consists of three
quadrupole rod assemblies (Q1, Q2, and Q3) and three lens sets.

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 2 Functional Description
Mass Spectrometer

The mass analyzer is discussed in detail in the following subtopics:

• Quadrupole Rod Assemblies

• RF and DC Fields Applied to the Quadrupoles

• Mass Analysis
• Collision Cell and CID Efficiency

• Quadrupole Offset Voltage

• Mass Analyzer Lenses

Quadrupole Rod Assemblies

The three rod assemblies used in the TSQ Quantum GC mass spectrometer are numbered
from the ion source end of the manifold and are designated Q1, Q2, and Q3. Q1 and Q3 are
quadrupoles that enable high-resolution scans without signal loss.

Q1 and Q3 are square arrays of precision-machined and precision-aligned, hyperbolic-profile

round rods. Q1 or Q3 are shown in Figure 18. Quartz spacers act as electrical insulators
between adjacent rods.
Figure 18. Q1 or Q3 quadrupole

Q2 is a square-profile quadrupole rod assembly. Q2 always acts as an ion transmission device.

The Q2 quadrupole rods are bent through a 90-degree arc. In addition to reducing the
footprint of the instrument, this prevents the transmission of unwanted neutral species to the
detector and dramatically lowers the noise level in the data. Q2 has become synonymous with
the term collision cell. Technically, the collision cell is the chamber that encloses Q2 where
collision-induced dissociation can take place if the argon collision gas is present. See
Figure 19.

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2 Functional Description
Mass Spectrometer

Figure 19. Collision cell, Q2 quadrupole, and lenses

Lenses L21, L22, Lenses L31, L32,
and L23 and L33

RF and DC Fields Applied to the Quadrupoles

In a quadrupole rod assembly, because rods opposite each other in the array connect
electrically, the four rods can be considered as two pairs of two rods each. Ac and dc voltages
are applied to the rods and these voltages are ramped during the scan. Voltages of the same
amplitude and sign are applied to the rods of each pair. However, the voltages applied to the
different rod pairs are equal in amplitude but opposite in sign. See Figure 20.
Figure 20. Polarity of the RF and dc voltages applied to the rods of the Q1 and Q3 mass analyzers

RF voltage
+ dc voltage

RF voltage 180° out of phase

– dc voltage

The ac voltage applied to the quadrupole rods is of constant frequency (1.123 MHz). The RF
voltage applied to the rods varies from 0 to 10 000 V P/P, and the dc voltage varies from 0 to
±840 V. Voltages of the same amplitude and sign are applied to each rod pair. However, the
voltages applied to the other rod pair are equal in amplitude but opposite in sign.

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 2 Functional Description
Mass Spectrometer

Because the frequency of this ac voltage is in the radio frequency range, it is referred to as RF
voltage. In Figure 21, the solid line represents the combined RF and dc voltage applied to one
rod pair, and the dashed line represents the combined RF and dc voltage applied to the other
rod pair. The ratio of RF voltage to dc voltage determines the ability of the mass spectrometer
to separate ions of different mass-to-charge ratios.

The first and third quadrupole rod assemblies (Q1 and Q3 quadrupoles) can act as mass
analyzers or as ion transmission devices. When both RF and dc voltages are applied, Q1 and
Q3 function as mass analyzers. When only RF voltage is applied, they act as ion transmission
devices. In the ion transmission mode, the quadrupole rod assemblies allow ions in a wide
window of mass-to-charge ratios to pass.

The square quadrupole rod assembly (Q2) operates in the ion transmission mode only.
Surrounding Q2 is a collision cell where collision-induced dissociation (CID) can take place if
the argon collision gas is present in the cell.
Figure 21. Magnitude of the RF and dc voltages applied to the rods of the Q1 and Q3 mass
analyzers

10,000 V P/P
840 V DC VOLTAGE

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2 Functional Description
Mass Spectrometer

Mass Analysis
The mass analyzers (Q1 and Q3) are square arrays of precision-machined and
precision-aligned round-profile rods. The rods are charged with a variable ratio of RF voltage
and dc voltage (Figure 21). These potentials give rise to an electrostatic field that gives stable
oscillations to ions with a specific mass-to-charge ratio and unstable oscillations to all others.

At any given instant, one particular set of RF and dc voltage values is being applied to the
mass analyzer rods. Under these conditions, only ions of one mass-to-charge ratio (for
example, m/z 180) are maintained within bounded oscillations as their velocity carries them
through the mass analyzer. During this same time, all other ions undergo unbounded
oscillations. These ions strike one of the rod surfaces, become neutralized, and are pumped
away, or they are ejected from the rod assembly.

Then, at a later time, both RF and dc voltages change, and ions of the next mass-to-charge
ratio (for example, m/z 181) are allowed to pass, while all other ions (including m/z 180)
become unstable and undergo unbounded oscillations. This process continues, with ions of
one mass-to-charge ratio after another being transmitted, as the RF and dc voltages change in
value. At the end of the scan, the RF and dc voltages are discharged to zero, and the process is
repeated.

The potentials on the quadrupole rods can be changed rapidly and precisely. The RF and dc
voltages in the TSQ Quantum GC mass spectrometer can be scanned over the full mass range
of the system, m/z 10 to 3000, in 0.85 s.

The more closely the electrostatic field generated by a set of quadrupole rods approximates a
hyperbolic geometry, the better their operating characteristics are. As a result, the precision
quadrupole rods of the TSQ Quantum GC mass spectrometer provide excellent sensitivity,
peak shape, resolution, and high mass transmission.

Collision Cell and CID Efficiency

In the MS/MS scan modes, the TSQ Quantum GC applies a large voltage of opposite
polarity to the rod pairs between scans, which empties the collision cell. This process ensures
that no ions remain in the collision cell from scan to scan.

The collision cell quadrupole rod assembly (Q2), which always acts as an ion transmission
device, is a quadrupole array of square-profile rods. A variable RF voltage charges the rods,
which creates an electrostatic field that gives stable oscillations to ions in a wide window of
mass-to-charge ratios.

The collision cell surrounds Q2 and is usually pressurized from about 1 × 10-3 to
4 × 10-3 Torr with argon collision gas. The collision cell is where collision-induced
dissociation takes place.

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 2 Functional Description
Mass Spectrometer

CID is a process in which an ion collides with a neutral atom or molecule and then, because
of the collision, dissociates into smaller fragments. The mechanism of dissociation involves
converting some of the translational kinetic energy (TKE) of the ion into internal energy. This
collision places the ion in an excited state. If the internal energy is sufficient, the ion
fragments.

Three expression convey the efficiency of the CID process:

• Collection efficiency

• Fragmentation efficiency
• Overall CID efficiency

Collection efficiency: The ion flux ratio measured at the exit of the collision cell and at its
entrance. With no collision gas present, the TSQ Quantum GC obtains virtually 100 percent
collection efficiency. Collection efficiency is a mass-dependent parameter. For example, with
mid-range collision gas pressure, the collection efficiency might vary from about 50 percent
for comparatively less massive ions (which are more prone to scatter) up to 75 percent for
comparatively more massive ions (which are less prone to scatter).

Fragmentation efficiency: The fraction of the ion flux at the exit of the collision cell that
results from fragmented ions. Fragmentation efficiency depends directly on the stability of the
ion and indirectly on the mass of the ion. The more stable the ion, the less likely a given
collision will fragment the ion. The more massive the ion, the greater its ability to distribute
the vibrational energy imparted by a collision. As a result, ion fragmentation might decrease.

With a mid-range collision gas pressure, fragmentation efficiency might vary from 15 percent
to 65 percent for various compounds. As the collision gas pressure increases, the
fragmentation efficiency for all compounds approaches 100 percent due to multiple collisions.
The collection efficiency decreases, however, due to scattering.

Overall CID efficiency: The product of the collection efficiency and the fragmentation
efficiency. The overall CID efficiency exhibits a maximum with intermediate pressure. As the
pressure is increased beyond the optimum value, more and more collisions take place, the
probability of scattering increases, and fewer and fewer ions pass through the collision cell.
This results in the collection efficiency decreasing. The fragmentation efficiency also decreases
as the pressure is decreased from its optimum value, because fewer and fewer collisions take
place.

Quadrupole Offset Voltage

The quadrupole offset voltage is a dc potential applied to the quadrupole rods in addition to
the ramping dc voltage. The offset voltage applied to the two rod pairs of the assemblies is
equal in amplitude and equal in sign. The quadrupole offset voltage accelerates or decelerates
ions and, therefore, sets theTKE of the ions as they enter the quadrupole rod assembly.

Thermo Scientific TSQ Quantum GC User Guide 33

2 Functional Description
Mass Spectrometer

In general, for a given experiment, the TSQ Quantum GC has fixed offset voltages for Q1
and Q2. However, in MS/MS experiments, the quadrupole offset voltage applied to Q3
usually varies as a scan proceeds. The TSQ Quantum GC automatically computes the Q3
quadrupole offset voltage necessary and then varies the voltage, as appropriate, as each scan
proceeds.

The offset voltage applied to Q2 (which contains the collision cell) is responsible for the
collision energy. The collision energy is the difference in potential between the ion source
(where parent ions are formed) and Q2 (where they collide with collision gas). As the offset
voltage on Q2 increases, the TKE of the parent ions also increases. As a result, increases in the
Q2 offset voltage increase the energy of ion/Ar collisions. The collision energy is generally set
to one value for an entire scan and can be set from 0 to ±200 V.

Before obtaining any mass spectra, the TSQ Quantum GC tunes Q1 in the Q1MS scan mode
(Q2 and Q3 RF voltage only), and tunes Q3 in the Q3MS scan mode (Q1 and Q2 RF
voltage only). During tuning, the TSQ Quantum GC determines the optimum quadrupole
offset voltage for Q1 and for Q3.

Mass Analyzer Lenses

The TSQ Quantum GC system mass analyzer has three lens sets. See Figure 19 on page 30.
Those between Q1 and Q2 are designated L21, L22, L23; those between Q2 and Q3 are
designated L31, L32, L33; and the lens between Q3 and the ion detection system is
designated as L4 (or exit lens). All of the lenses have circular holes in their centers through
which the ion beam passes.

The lens assemblies also retain the three rod assemblies to ensure accurate and automatic axial
alignment of the rod assemblies.

The L2x lens set (between Q1 and Q2) and the L3x lens set (between Q2 and Q3) serve these
functions:
• To minimize the amount of collision gas that enters the mass analyzers (Q1 and Q3)
from the collision cell (Q2). (For high-mass transmission, it is important to maintain a
low pressure in the mass analyzers.)
• To retain the collision gas. Lenses L23 and L3 form two of the walls of the collision cell,
so they tend to hold the collision gas in the collision cell. The collision gas escapes,
however, through the same lens holes through which the ion beam passes.
• To prevent gas from entering the mass analyzers. Lenses L22 and L21 on one side of Q2
and lenses L32 and L33 on the other side of Q2 act as baffles to help prevent the gas that
escapes from the collision cell from entering the mass analyzers.
• To shield Q1 from the RF voltage applied to Q2 and vice versa (L2x lens set) and to
shield Q3 from the RF voltage applied to Q2 and vice versa (L3x lens set).

34 TSQ Quantum GC User Guide Thermo Scientific

 2 Functional Description
Mass Spectrometer

• To focus the ion beam. The three lenses between Q1 and Q2 (and those between Q2 and
Q3) together form a three-element aperture lens. The first and third lenses are generally
set to similar or identical values and the central lens is set to a value different (either
higher or lower) from the other two.

The voltage applied to each of the lenses can vary from about -300 to +300 V. Typically,
however, the voltage applied to the first and third elements of the L2x lens set is somewhat
greater than the quadrupole offset voltage applied to Q1. Because the Q1 quadrupole offset
voltage is generally set to about ±5 V (depending on the charge of the ions of interest), the
voltage applied to lenses L21 and L23 is typically about -10 V for positive ions and +10 V for
negative ions. The voltage applied to the central lens of the L2x lens set is typically about
±225 V.

In the Q3MS scan mode, the voltage applied to the lenses of the L3x lens set is about the same
as that applied to the corresponding lens in the L2x lens set. Note, however, that in the
MS/MS scan modes, the voltage applied to the L3x lens set automatically varies with the
quadrupole offset voltage applied to Q3. As the Q3 quadrupole offset voltage ramps, the
voltages applied to the lenses ramp correspondingly.

Lens L4 is located between Q3 and the ion detection system. L4 is held at ground potential.
Its purpose is to shield Q3 from the high voltage applied to the ion detection system and to
shield the ion detection system from the high RF voltages applied to Q3.

Ion Detection System

The TSQ Quantum GC mass spectrometer is equipped with a high-sensitivity, off-axis ion
detection system. This system produces a high signal-to-noise ratio and allows for voltage
polarity switching between positive ion and negative ion modes of operation. The ion
detection system includes a 15 kV conversion dynode and a channel electron multiplier. The
ion detection system is located at the rear of the vacuum manifold behind the mass analyzer.

The conversion dynode is a concave metal surface located at a right angle to the ion beam.
The TSQ Quantum GC applies to the conversion dynode a potential of +15 kV for negative
ion detection or -15 kV for positive ion detection. When an ion strikes the surface of the
conversion dynode, one or more secondary particles are produced. These secondary particles
can include positive ions, negative ions, electrons, and neutrals. When positive ions strike a
negatively charged conversion dynode, the secondary particles of interest are negative ions and
electrons. When negative ions strike a positively charged conversion dynode, the secondary
particles of interest are positive ions. The curved surface of the conversion dynode focuses
these secondary particles and a voltage gradient accelerates the particles into the electron
multiplier.

The electron multiplier includes a cathode and an anode. The cathode of the electron
multiplier is a lead-oxide, funnel-like resistor. The high voltage ring applies a potential of up
to -2.5 kV to the cathode. The exit end of the cathode (at the anode) is near ground potential.

Thermo Scientific TSQ Quantum GC User Guide 35

2 Functional Description
Mass Spectrometer

The anode of the electron multiplier is a small cup located at the exit end of the cathode. The
anode collects the electrons produced by the cathode. The anode screws into the anode
feedthrough in the base plate.

Secondary particles from the conversion dynode strike the inner walls of the electron
multiplier cathode with sufficient energy to eject electrons. The ejected electrons are
accelerated farther into the cathode, drawn by the increasingly positive potential gradient.
The funnel shape of the cathode causes the ejected electrons not to travel far before they again
strike the inner surface of the cathode, which causes the emission of more electrons. A cascade
of electrons is then created that finally results in a measurable current at the end of the
cathode where the anode collects the electrons. The current collected by the anode is
proportional to the number of secondary particles striking the cathode.
Figure 22. Ion detection system, showing the electron multiplier (top) and conversion dynode
(bottom)

Typically, the electron multiplier is set to a gain of about 3 × 105 (that is, for each ion or
electron that enters, 3 × 105 electrons exit) in MS mode and 2 × 106 in MS/MS mode. The
electrometer circuit converts the current that leaves the electron multiplier via the anode to a
voltage and the data system records the voltage.

36 TSQ Quantum GC User Guide Thermo Scientific

 2 Functional Description
Mass Spectrometer

The ion detection system of the TSQ Quantum GC mass spectrometer increases signal and
decreases noise. The high voltage applied to the conversion dynode results in a high
conversion efficiency and increased signal. That is, for each ion striking the conversion
dynode, many secondary particles are produced. The increase in conversion efficiency is more
pronounced for more massive ions than it is for less massive ions.

Because of the off-axis orientation of the ion detection system relative to the mass analyzer,
neutral molecules from the mass analyzer tend not to strike the conversion dynode or electron
multiplier. As a result, noise from neutral molecules is reduced.

Vacuum System and Inlet Gasses Hardware

The vacuum system evacuates the region around the ion source, ion optics, mass analyzer, and
ion detection system. The principal components of the vacuum system include the following:
• Vacuum Manifold

• Turbomolecular Pump

• Forepump

• Convectron®® Gauges

• Ion Gauges

The inlet gasses hardware controls the flow of collision gas, CI reagent gas, calibration
compound, and air (during venting) into the mass spectrometer. The inlet gasses hardware
includes the following components:
• Vent Valve

• Collision Gas Flow Control Valves

• Calibration Compound and CI Reagent Gas Flow Control

Figure 23 shows a functional block diagram of the vacuum system and inlet gasses hardware.

Thermo Scientific TSQ Quantum GC User Guide 37

2 Functional Description
Mass Spectrometer

Figure 23. Functional block diagram of the vacuum system and inlet gasses hardware
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Vacuum Manifold
The vacuum manifold encloses the ion source, ion optics, mass analyzer, and ion detection
system assemblies. The vacuum manifold is a thick-walled, aluminum chamber with two
removable side cover plates, with openings on the front, sides, and top, and various electrical
feedthroughs and gas inlets.

The main vacuum manifold is divided into two chambers by a baffle. See Figure 24. The high
vacuum port of the turbomolecular pump evacuates the region inside the first chamber, called
the analyzer region, to less than 10-5 Torr. The turbomolecular pump then discharges into the
forepump through the foreline.

The region inside the second chamber, called the Q0 quadrupole region, is evacuated to
1 mTorr by the interstage port of the turbomolecular vacuum pump.

A second vacuum manifold houses the ion source, which is open to the Q0 quadrupole
chamber. The interstage port of the turbomolecular pump evacuates the ion source region.

38 TSQ Quantum GC User Guide Thermo Scientific

 2 Functional Description
Mass Spectrometer

Figure 24. Vacuum manifold (interior)

O-ring Ion gauge Turbomolecular pump

Collision cell chamber Analyzer chamber Baffle Ion gauge

Q0 quadrupole chamber Ion source chamber

When CID is turned on, the collision cell chamber, inside the analyzer chamber, has a user
controlled argon pressure of between 1 and 4 mTorr. The forepump evacuates the argon in
the collision cell when CID is turned off.

The vacuum manifold has the following feedthroughs and inlets:

• A feedthrough for the high voltage for the conversion dynode

• A feedthrough for the high voltage for the electron multiplier

• A feedthrough for the ion current signal from the anode of the electron multiplier

• Two feedthroughs for the Q1 quadrupole RF voltage

• Two feedthroughs for the Q3 quadrupole RF voltage

• A feedthrough for the Q2 quadrupole RF voltage

Thermo Scientific TSQ Quantum GC User Guide 39

2 Functional Description
Mass Spectrometer

• A feedthrough for lens L21, L22, L23, L31, L32, and L33 voltages

• A feedthrough for the Q0 quadrupole RF voltage

• A vacuum connection for measuring the pressure in the analyzer region with the ion
gauge
• An argon gas inlet into the collision cell

• A vent gas inlet

Two removable side cover plates on the left side of the vacuum manifold allow access to the
Q0 ion optics, mass analyzer, and ion detection system. Two electrically conductive O-rings
provide a vacuum-tight seal between the side cover plates and the vacuum manifold.

Turbomolecular Pump
A Leybold TW220/150/15S double-inlet turbomolecular pump provides the vacuum for the
ion source, Q0 quadrupole region, and analyzer region of the vacuum manifold. The
turbomolecular pump mounts onto the top of the vacuum manifold (Figure 24).

The turbomolecular pump has two pumping inlets:

• A high-vacuum inlet at the top of the rotor stack, which evacuates the analyzer chamber

• An interstage inlet about halfway down the rotor stack, which evacuates the ion source
and Q0 quadrupole chambers

The turbomolecular pump is controlled by a Leybold TDS controller and powered by a

+24 V dc (250 W) power supply. The mass spectrometer circuit breaker switch and the
vacuum service switch, but not the electronics service switch, turn power for the
turbomolecular pump off and on. A fan draws air in from the front of the instrument cools
the pump.

Power to the turbomolecular pump shuts off if the foreline pressure, as measured by the
Convectron gauge, is too high, or if the turbomolecular temperature is too high.

Forepump
An Edwards E2M30 forepump (or roughing pump) establishes the vacuum necessary for the
proper operation of the turbomolecular pump. The forepump also evacuates the inlet valve
and the collision cell. The pump has a maximum displacement of 650 L/min and maintains a
minimum pressure of approximately 1 Pa (0.01 Torr).

The forepump is connected to the turbomolecular pump by a section of reinforced PVC

tubing. The power cord of the forepump is plugged into the outlet labeled Forepump on the
power panel (see Figure 12 on page 23). This outlet supplies power to the pump and is
controlled by the main power circuit breaker switch and vacuum service switch, not by the
electronics service switch.

40 TSQ Quantum GC User Guide Thermo Scientific

 2 Functional Description
Mass Spectrometer

CAUTION Always plug the forepump power cord into the outlets labeled Forepump on the
right side power panel of the mass spectrometer. Never plug it directly into a wall outlet.

Convectron® Gauges®

A Convectron gauge measures the pressure in the inlet valve and the foreline, which connects
the turbomolecular pump and the forepump. A second Convectron gauge measures the
pressure of argon collision gas in the collision cell.

The Convectron gauge uses a Wheatstone bridge with a temperature dependent resistor to
measure pressure down to a fraction of a milliTorr. The voltage present at the top of the
bridge depends on how fast the resistor can radiate heat, which is related to the pressure. The
pressure measured by the Convectron gauge is monitored by vacuum protection circuitry on
the Source PCB, which in turn is monitored by the embedded computer on the System
Control PCB. The vacuum protection circuitry detects whether the foreline pressure is too
high for the proper operation of the turbomolecular pump.

Ion Gauges
A Granville-Phillips® 342™ mini ion gauge measures the pressures in the analyzer region of
the vacuum manifold and the Q0/ion source region. The ion gauge produces energetic
electrons that cause the ionization of molecules in the ion gauge. Positive ions formed in the
ion gauge are attracted to a collector. The collector current is related to the pressure in the
vacuum manifold. The ion gauge is also involved in vacuum protection.

Vent Valve
The vent valve, located in the area of Q2, allows the vacuum manifold to be vented to air that
has been filtered through a sintered nylon filter. The vent valve is a solenoid-operated valve,
which is controlled by the Vent Delay PCB. When the solenoid is energized, the vent valve
closes. If the power fails or the main power circuit breaker is placed in the Off (O) position, a
4-farad capacitor located in the Power Entry Module keeps the solenoid in the closed position
for several minutes. If power is not restored in this time, then the solenoid opens and the
system is vented with filtered air. The vent valve closes after power is restored to the mass
spectrometer.

Collision Gas Flow Control Valves

The collision gas flow control valves control the flow of argon collision gas into and out of the
Q2 collision cell. A solenoid valve acts to shut off argon gas flow to the cell. The collision gas
pressure is regulated by a proportional valve that is controlled by the data system. You can set
the collision gas pressure (0 to 4 milliTorr) in the Define Scan view of the Tune Master
window.

Thermo Scientific TSQ Quantum GC User Guide 41

2 Functional Description
Mass Spectrometer

Ions enter the Q2 collision cell, collide with the argon collision gas, and then, because of the
collision, dissociate into smaller fragments. See “Collision Cell and CID Efficiency” on
page 32.

Argon enters the mass spectrometer through a 1/8-in. port on the left side of the mass
spectrometer.

A second proportional valve allows the forepump to evacuate the Q2 collision cell of argon
and waste gasses when CID is turned off. The TSQ Quantum GC mass spectrometer
automatically opens and closes the collision gas evacuation valve, depending on whether Q2 is
acting as an ion transmission device or a collision cell.

Calibration Compound and CI Reagent Gas Flow Control

The calibration compound gas flow control valve controls the flow of calibration compound
gas into the ion source, via the transfer line. The calibration gas flow can be either high or
low. Normally low flow is used, but high flow might be necessary for negative ion CI
calibration.

The CI gas flow control valve controls the flow of chemical ionization reagent gas into the ion
source, via the transfer line. The maximum CI gas flow rate is about 4 mL/min, depending on
the gas.

Electronic Assemblies
The electronic assemblies that control the operation of the mass spectrometer are distributed
among various PCBs and other modules located in the tower, in the embedded computer,
and on or around the vacuum manifold of the mass spectrometer.

The Power Entry Module provides mass spectrometer power control, a contact closure
interface, vent valve control, an Ethernet 100 base-T connection from the System Control
PCB to the data system PC, a mechanical pump failure protection circuit (linked to vent valve
control), a system reset button, status LEDs, and service ports. The right-side power panel,
shown in Figure 12 on page 23, is part of the Power Entry Module.

The Power Entry Module accepts line power, filters it, and provides it to various components
of the mass spectrometer. The Power Module includes the following components:
• Main power circuit breaker switch

• Surge suppressor
• Line filter

• Electronics service switch

• Vacuum service switch

42 TSQ Quantum GC User Guide Thermo Scientific

 2 Functional Description
Mass Spectrometer

The “brains” of the TSQ Quantum GC mass spectrometer is the System Control PCB. The
System Control PCB and embedded computer include the following:
• PowerPC processor

• Serial Peripheral Interconnect (SPI) bus

• I/O coprocessor
• Super Harvard Architecture Computer (Sharc) bus

• Scan generator DSP

• Acquisition processor DSP

• Interbus bridge

• 100 base-T Ethernet port

The RF voltage generation electronic assemblies produce the Q0, Q1, Q2, and Q3 RF
voltages that enable ion transmission and mass analysis. All RF voltages are controlled by the
Analyzer Control PCB and the System Control PCB.

The Q1 and Q3 RF voltage amplifier circuits are identical, and the circuits for Q0 and Q2 are
similar.

The RF voltage generation electronic assemblies include the following components:

• RF oscillator
• RF Voltage Amplifier PCB
• Low Pass Filter PCB
• RF voltage coil
• RF voltage detector
• Mass DAC
• Integrating amplifier

The ion detection system electronic assemblies provide high voltage to the electron multiplier
and conversion dynode of the ion detection system. They also receive the electron multiplier
output current signal, convert it to a voltage (by the electrometer circuit), and pass it to the
embedded computer.

The ion detection system electronic assemblies include the following:

• Electron multiplier power supply
• Conversion dynode power supply
• Electrometer PCB
• Acquisition DSP

Thermo Scientific TSQ Quantum GC User Guide 43

2 Functional Description
Data System

The Analyzer Control PCB contains circuitry for controlling and monitoring the operation of
the ion source, ion optics, mass analyzer, and ion detection system. These circuits are in turn
monitored by the PowerPC processor of the System Control PCB via the SPI bus.

The Analyzer Control PCB controls and monitors the RF voltages for Q0, Q1, Q2, and Q3
quadrupoles. It also has lens voltage drivers that convert ±330 V dc power from the DC Rod
Driver PCB to dc voltages that are applied to the lenses

Data System
The data system controls and monitors the TSQ Quantum GC mass spectrometer. The data
system also processes data that the TSQ Quantum GC mass spectrometer acquires. The data
system is composed of the following:
• Computer Hardware

• Data System / Mass Spectrometer / GC Interface

• Data System / Local Area Network Interface

Computer Hardware
The data system computer has the following major features:
• Intel® Pentium® IV processor
• High capacity hard disk drive
• Recordable/rewriteable CD drive
• Primary Ethernet port (data system to mass spectrometer)
• Secondary Ethernet port (data system to local area network)
• High performance video graphics card
• CDRW drive
• DVD drive
• 1280×1024 resolution color monitor
• Keyboard and mouse

For more information about the computer, refer to the appropriate manuals.

44 TSQ Quantum GC User Guide Thermo Scientific

 2 Functional Description
Data System

Data System / Mass Spectrometer / GC Interface

The data system computer contains a 100 base-T Ethernet adapter (called the primary
Ethernet adapter) that is dedicated to data system/mass spectrometer/GC communications.
This primary Ethernet adapter communicates with the mass spectrometer and GC modules
via a 10/100 base-T Ethernet switch. The Ethernet adapter on the mass spectrometer resides
on the System Control PCB. A twisted pair, Ethernet cable connects the primary Ethernet
adapter of the data system to the Ethernet switch, which is connected to the Ethernet
connector on the power panel of the mass spectrometer and to the GC.

Data System / Local Area Network Interface

The data system computer contains a secondary Ethernet adapter. This secondary Ethernet
adapter is not involved in data system/mass spectrometer or GC communications. You can
use this secondary Ethernet adapter to access your local area network.

Thermo Scientific TSQ Quantum GC User Guide 45

 3

System Shutdown, Startup, and Reset

Many maintenance procedures for the TSQ Quantum GC system require that the mass
spectrometer be shut down completely. In addition, you can place the TSQ Quantum GC
mass spectrometer in standby mode if the system is not to be used for 12 hours or more.

Contents
• Shutting Down the System in an Emergency

• Placing the System in Standby Mode

• Shutting Down the System Completely

• Starting Up the System after a Complete Shutdown

• Resetting the Mass Spectrometer

• Resetting the Data System

• Turning Off Selected Mass Spectrometer Components

Shutting Down the System in an Emergency

You can turn off all power to the mass spectrometer, gas chromatograph, and autosampler by
pressing the System Power Off button, located on the front of the electronics module, or the
main power circuit breaker, located on the rear of the electronics module. You can turn on the
system power only with the main power circuit breaker on the rear of the electronics module
and not the System Power Off switch.

Y To turn off the mass spectrometer in an emergency

CAUTION Press the System Power Off button located on the front of the electronics
module. See Figure 25. The System Power Off button turns off all power to the mass
spectrometer (including the vacuum pumps), gas chromatograph, and autosampler.
Although removing power abruptly does no harm to any component within the
system, under normal conditions do not shut down the system with the System Power
Off button. For the recommended procedure, see “Shutting Down the System
Completely” on page 49.

Thermo Scientific TSQ Quantum GC User Guide 47

3 System Shutdown, Startup, and Reset
Placing the System in Standby Mode

Figure 25. System Power Off button on the front of the electronics module

System Power
Off button

Figure 26. Power panel on the rear of the electronics module

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V~230 V~230 V~230 V~230
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Placing the System in Standby Mode

If you are not going to use the TSQ Quantum GC system for a short period of time, such as
overnight or over weekends, it does not need to be shut down completely. When you are not
going to operate the system for 12 hours or more, you can leave the system in standby mode.

Y To place the TSQ Quantum GC system in standby mode

1. Wait until data acquisition, if any, is complete.

2. From the Quantum Tune Master window, choose Control > Standby (or click the
On Off Standby
On/Standby button) to put the mass spectrometer in standby.

When you choose Control > Standby, the TSQ Quantum GC system turns off the
electron multiplier, the conversion dynode, the ion source filament and lenses (but not
the heater), and the mass analyzer and ion optics RF voltages. See Table 4 on page 57 for

48 TSQ Quantum GC User Guide Thermo Scientific

 3 System Shutdown, Startup, and Reset
Shutting Down the System Completely

the On/Off status of mass spectrometer components when the mass spectrometer is in
standby mode. The System LED on the front panel of the mass spectrometer illuminates
yellow when the system is in standby.

3. Leave the mass spectrometer power on.

4. Leave the GC power on with column flow.

5. Leave the autosampler power on.

6. Leave the data system power on.

Shutting Down the System Completely

Shut down the TSQ Quantum GC system completely only if it is to be unused for an
extended period or if it must be shut down for a maintenance or service procedure. For a short
period of time, such as overnight or over weekends, you can place the system in standby
mode. See “Placing the System in Standby Mode.”

Y To shut down the TSQ Quantum GC system completely

1. Cool the GC, transfer line, and ion source:

• GC oven 30 oC
• Injector off
• Transfer line off
• Ion source 30 oC
Note If you do not plan to change the column or perform maintenance on the gas
chromatograph, you do not have to lower the injector temperature.

2. From the Quantum Tune Master window, choose Control > Standby (or click the
On/Standby button) to put the mass spectrometer in standby.

3. Place the electronics service switch, located on the right-side power panel, in the Service
Mode.

Thermo Scientific TSQ Quantum GC User Guide 49

3 System Shutdown, Startup, and Reset
Shutting Down the System Completely

Figure 27. Right-side power panel of the mass spectrometer

Pum p O n

Electronics Vacuum

Qualified
Service
Personnel
Only

!
4. Place the vacuum service switch, located on the right-side power panel, in the Service
Mode position.

5. Place the mass spectrometer main power circuit breaker switch, located on the right-side
power panel, in the Off position. When you place the main power circuit breaker switch
in the Off position, the following occurs:

• All power to the mass spectrometer is turned off. (All LEDs on the front panel of the
mass spectrometer are off.)

• A capacitor on the Vent Delay PCB provides power to the vent valve for two to four
minutes (to allow the turbomolecular pump to spin down). After the capacitor
discharges, power to the vent valve solenoid shuts off. When power to the vent valve
solenoid shuts off, the vent valve opens and the vacuum manifold vents to filtered air.
You can hear a hissing sound as the air passes through the air filter.

• After about two minutes, the pressure of the vacuum manifold reaches atmospheric
pressure.

6. Unplug the power cord for the mass spectrometer.

CAUTION Allow heated components to cool before servicing them.

50 TSQ Quantum GC User Guide Thermo Scientific

 3 System Shutdown, Startup, and Reset
Starting Up the System after a Complete Shutdown

Note If you plan to perform routine or preventive system maintenance on the mass
spectrometer only, you can leave the argon, data system, GC, and autosampler on. In
this case, the shutdown procedure is complete. However, if you do not plan to
operate your system for an extended period of time, Thermo Fisher Scientific
recommends that you turn off the GC, data system, and autosampler as described in
steps 7 through 12 below.

7. Turn off the GC. Follow the procedure described in the manual that came with the GC.

8. Turn off the autosampler by using the main power on/off switch.
9. Press the System Power Off button (Figure 25) to remove all power from the TSQ
Quantum GC system.
10. If the TSQ Quantum GC is not to be used for an extended period, turn off the argon
collision gas supply at the tank.

11. Turn off the data system:

a. Choose Start > Shut Down from the Windows® task bar. The Shut Down Windows
dialog box appears.
b. To start the Windows shutdown procedure, select Shut down and click OK.

12. Turn off the (optional) printer by using the on/off switch.

Starting Up the System after a Complete Shutdown

Start the TSQ Quantum GC system after it has been shut down completely by doing the
following:
• Restoring Power to the TSQ Quantum GC system
• Starting Up the GC
• Starting Up the Data System

• Starting Up the Mass Spectrometer

• Starting Up the Autosampler (autosampler is optional)

• Setting Up Conditions for Operation

Restoring Power to the TSQ Quantum GC system

Y To restore power to the TSQ Quantum GC system

Place the main power circuit breaker, located on the rear of the electronics module
(Figure 26), in the On position.

Thermo Scientific TSQ Quantum GC User Guide 51

3 System Shutdown, Startup, and Reset
Starting Up the System after a Complete Shutdown

Starting Up the GC

Y To start the GC

Follow the startup procedure described in the manual that came with the GC. Verify that the
gas chromatograph is on and there is carrier gas flowing through the column into the mass
spectrometer.

Starting Up the Data System

Y To start the data system

1. Turn on the monitor, computer, and printer.

2. Observe the Windows startup procedure on the monitor and press

CONTROL+ALT+DELETE when you are prompted to do so. To complete the startup
procedure, click OK or enter your password (if you have one) in the Logon Information
dialog box.

Starting Up the Mass Spectrometer

Y To start the mass spectrometer

CAUTION If you turn on the mass spectrometer without column flow, air can
damage the GC column. This large air leak into the TSQ Quantum GC also causes
the ion source to require cleaning.

1. Turn on the flow of argon at the tank if it is off.

Note The data system must be running before you start the mass spectrometer. The
mass spectrometer will not operate until it receives software from the data system.

2. Make sure that the mass spectrometer main power circuit breaker switch, located on the
right side power panel (Figure 27), is in the Off (O) position and the electronics service
switch and the vacuum service switch are both in the Service Mode position.

3. Plug in the power cord for the mass spectrometer.

4. Place the mass spectrometer main power circuit breaker switch in the On (|) position.
When you place the main power circuit breaker switch in the On (|) position, power is
supplied to those mass spectrometer components that are not affected by the vacuum
service switch and the electronics service switch.

5. Place the vacuum service switch in the Operational position.

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 3 System Shutdown, Startup, and Reset
Starting Up the System after a Complete Shutdown

6. Place the electronics service switch in the Operational position. When you place the
electronics service switch in the Operational position, the following occurs:

• The Power LED on the mass spectrometer front panel illuminates green to indicate
that power is provided to the mass spectrometer electronics. (The electron multiplier,
conversion dynode, ion source, and mass analyzer and ion optics RF voltages remain
off.)

• The embedded computer reboots. After several seconds the Communication LED on
the front panel illuminates yellow to indicate that the data system and the mass
spectrometer have started to establish a communication link.

• After several more seconds, the Communication LED illuminates green to indicate
that the data system and the mass spectrometer have established a communication
link. Software for the operation of the mass spectrometer is then transferred from the
data system to the mass spectrometer.

• After three minutes, the System LED illuminates yellow to indicate that the software
transfer from the data system to the mass spectrometer is complete and that the
instrument is in standby.

• The Vacuum LED on the front panel of the mass spectrometer remains off until the
turbomolecular pump reaches 80 percent of its operational speed of 750 Hz. At this
time the ion gauge is turned on and the Vacuum LED illuminates yellow. The
Vacuum LED illuminates green, and the high voltage can be turned on, only if the
pressure in the mass analyzer region of the vacuum manifold is less than the
appropriate value listed in Table 3.

Table 3. Maximum allowed pressure to turn on high voltage

Carrier gas Ar collision gas Maximum pressure (Torr)
He Off 6 × 10-6
He On 5 × 10-5
H2 Off 5 × 10-5
H2 On 1 × 10-4

Figure 28. Front panel LEDs of the mass spectrometer

Power Vacuum Communication

System Scan

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3 System Shutdown, Startup, and Reset
Resetting the Mass Spectrometer

If you have an autosampler, go to “Starting Up the Autosampler” on page 54. If you do not
have an autosampler, go to “Setting Up Conditions for Operation” on page 54.

Starting Up the Autosampler

Y To start the autosampler

Place the main power switch on the autosampler in the On position. If necessary,
configure the autosampler. For procedures for placing sample vials, preparing solvent and
waste bottles, installing syringes, and so on, refer to the manual that came with the
autosampler.

Setting Up Conditions for Operation

Y To set up your TSQ Quantum GC mass spectrometer for operation

1. Before you begin data acquisition with your TSQ Quantum GC system, allow the system
to pump down for at least one hour. Operation of the system with excessive air and water
in the vacuum manifold can cause reduced sensitivity, tuning problems, and reduced
lifetime of the electron multiplier.

2. Ensure that the argon pressure is within the operational limits [argon: 135 ±70 kPa
(20 ±10 psig)].
Note Air in the argon line must be purged or given sufficient time to be purged for
normal TSQ Quantum GC mass spectrometer performance.

3. Look at the Instrument Information Center or Status view in the Quantum Tune Master
window. Check that the pressure measured by the ion gauge is below about 3 × 10-6 Torr
(2 × 10-5 Torr with H2 carrier gas) with the collision gas turned off.
Note You do not need to calibrate and tune the TSQ Quantum GC mass
spectrometer each time you restart the TSQ Quantum GC system. To tune and
calibrate the TSQ Quantum GC, see Chapter 4, “Tuning and Calibrating.”

Resetting the Mass Spectrometer

If communication between the mass spectrometer and data system computer is lost, it might
be necessary to reset the mass spectrometer using the Reset button on the right-side power
panel. Pressing the System Reset button creates an interrupt in the embedded computer. This
causes the embedded computer to restart in a known (default) state. See Figure 27 on page 50
for the location of the System Reset button.

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 3 System Shutdown, Startup, and Reset
Resetting the Data System

The procedure given here assumes that the mass spectrometer and data system computer are
both powered on and operational. If the mass spectrometer, data system computer, or both
are off, go to “Starting Up the System after a Complete Shutdown” on page 51.

Y To reset the mass spectrometer

Press the System Reset button located on the right-side power panel. Make sure the
Communication LED is extinguished before releasing the System Reset button. When you
press the Reset button, the following occurs:
• An interrupt on the embedded computer causes the CPU to reboot. All LEDs on the
front panel of the mass spectrometer are off except the Power LED.

• After several seconds, the Communication LED illuminates yellow to indicate that the
data system and the mass spectrometer are starting to establish a communication link.

• After several more seconds, the Communication LED illuminates green to indicate that
the data system and the mass spectrometer have established a communication link.
Software for the operation of the mass spectrometer is then transferred from the data
system to the mass spectrometer.

• After three minutes the software transfer is complete. The System LED illuminates either
green to indicate that the instrument is functional and the high voltages are on, or yellow
to indicate that the instrument is functional, and it is in standby.

Resetting the Data System

There are two ways to reset the data system:
• Resetting the Data System by Using the Windows Shutdown and Restart Procedure

• Resetting the Data System by Turning the Personal Computer Off Then On

Resetting the Data System by Using the Windows Shutdown and Restart Procedure

If possible, use the Windows shutdown and restart procedure to shut down and restart the
data system so that Windows can properly close programs and save changes to files.

Y To reset the data system by using the Windows shutdown and restart procedure

1. Choose Start > Shut Down from the Windows task bar. The Shut Down Windows
dialog box appears.

2. Select Restart and click OK to start the Windows shutdown and restart procedure.
3. Observe the Windows shutdown and restart procedure on the monitor. Press
CTRL+ALT+DELETE when you are prompted to do so. To complete the shutdown and

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3 System Shutdown, Startup, and Reset
Turning Off Selected Mass Spectrometer Components

restart procedure, click OK or enter your password (if you have one) in the Logon
Information dialog box.

Note The communications link between the data system and the mass spectrometer
should automatically reestablish after you reset the data system. When this occurs the
Communication LED on the front panel of the mass spectrometer illuminates yellow and
then green. If the system is unable to reestablish the communications link, press the
System Reset button on the power panel of the mass spectrometer.

Resetting the Data System by Turning the Personal Computer Off Then On

If you are unable to reset the data system by using the Windows shutdown and restart
procedure, proceed as follows:
1. Press the Power button on the personal computer to turn the personal computer off.

2. After several seconds, press the Power button on the personal computer to turn the
personal computer on.

3. Observe the Windows XP startup procedure on the monitor and press

CTRL+ALT+DELETE when you are prompted to do so. To complete the shutdown and
restart procedure, click OK or enter your password in the Logon Information dialog box.

4. When the shutdown and restart procedure has completed, choose

Start > All Programs > Xcalibur > Quantum Tune to display the Quantum Tune
Master window.
Note The communications link between the data system and the mass spectrometer
should automatically reestablish after you reset the data system. When this occurs the
Communication LED on the front panel of the mass spectrometer illuminates yellow and
then green. If the system is unable to reestablish the communications link, press the
System Reset button on the right-side power panel of the Power Entry Module of the
mass spectrometer.

Turning Off Selected Mass Spectrometer Components

There are different ways that you can turn off some or all of the mass spectrometer
components:
• Turn off individual mass spectrometer components from the Quantum Tune Master
window. Turning off individual mass spectrometer components might be necessary when
you are troubleshooting or when you are running certain diagnostic procedures.

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 3 System Shutdown, Startup, and Reset
Turning Off Selected Mass Spectrometer Components

• Place the mass spectrometer in standby mode. Standby is the normal condition to leave
the mass spectrometer in when it is not in use. Choose Control > Standby (or toggle the
On/Standby button) from the Quantum Tune Master window to place the mass
spectrometer in standby.

• Place the mass spectrometer in the Off condition. The Off condition is similar to
Standby, except all high voltage components of the mass spectrometer are turned off.
Choose Control > Off from the Quantum Tune Master window to place the mass
spectrometer in the Off condition.

• Place the electronics service switch in the Service Mode position. The electronics service
switch turns off all components in the mass spectrometer other than the +24 V power
supply, forepump, turbomolecular pump, Vent Delay PCB, and fans.

• Place the vacuum service switch in the Service Mode position. The vacuum service switch
turns off all vacuum system components, including the +24 V power supply, forepump,
turbomolecular pump, Vent Delay PCB, and fans.

• Place the right-side power panel circuit breaker switch in the Off position. Placing the
right-side power panel circuit breaker switch in the Off position removes all power to the
mass spectrometer, including the vacuum system.

• Press the System Power Off button. Pressing the System Power Off button removes all
power to the mass spectrometer, gas chromatograph, and autosampler.

Table 4 summarizes the on/off status of mass spectrometer components, voltages, and gas
flows.
Table 4. On/Off status of mass spectrometer components and voltages (Sheet 1 of 2)
Standby Off Electronics Vacuum service MS Main power
service switch in switch in circuit breaker
Mass spectrometer component
Service Mode Service Mode switch in Off
position position position
Electron multiplier Off Off Off Off Off
Conversion dynode Off Off Off Off Off
Mass analyzer RF voltage Off Off Off Off Off
Mass analyzer dc offset voltage Off Off Off Off Off
Q0 ion optics RF voltage Off Off Off Off Off
Q0 ion optics dc offset voltage Off Off Off Off Off
Ion source filament Off Off Off Off Off
Ion source heater On On Off Off Off
Ion source lenses Off Off Off Off Off
Argon collision gas Off Off Off Off Off

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3 System Shutdown, Startup, and Reset
Turning Off Selected Mass Spectrometer Components

Table 4. On/Off status of mass spectrometer components and voltages (Sheet 2 of 2)

Standby Off Electronics Vacuum service MS Main power
service switch in switch in circuit breaker
Mass spectrometer component
Service Mode Service Mode switch in Off
position position position
Vent valve Closed Closed Closed Open Open
(after 2 to 4 min) (after 2 to 4 min)
Turbomolecular pump On On On Off Off
Forepump On On On Off Off
Vent Delay PCB On On On On Off
Embedded computer On On Off On Off
Turbomolecular pump controller On On On Off Off
Power supply, electron multiplier Off Off Off On Off
and conversion dynode
Power supply, 8 kV Off Off Off On Off
PS1 power supply, +24 V On On On Off Off
PS2 power supply, +5, ±15, On On Off Off Off
±24 V dc
PS3 power supply, +36, On On Off Off Off
-28 V dc
Fan, turbomolecular pump On On On Off Off
Fan, above manifold On On On Off Off
Fan, center wall On On On Off Off
Convectron gauge, foreline On On On On Off
Convectron gauge, collision cell On On Off On Off
Ion gauge On On Off Off Off

58 TSQ Quantum GC User Guide Thermo Scientific

 4

Tuning and Calibrating

Tune parameters are instrument parameters that affect the intensity of the ion signal.
Calibration parameters are instrument parameters that affect the mass accuracy and resolution
of the mass spectrum. Tune and calibrate the Quantum GC automatically with Quantum
Tune Master. Quantum Tune Master uses FC-43 as the tuning and calibration compound.
FC-43 resides in a vial inside the mass spectrometer.

Contents
• Displaying the FC-43 Mass Spectrum
• Running Auto Tune and Calibration
• Saving the Tune and Calibration Report
• Password Protection

Record the ion signal intensity of FC-43 (see Figure 29) just after you tune and calibrate the
mass spectrometer. Periodically check the FC-43 ion signal. Re-tune and calibrate the mass
spectrometer if the FC-43 ion signal falls below 50% of the tuned value. Also, re-tune and
calibrate after switching between EI and CI modes or between positive and negative polarity
modes.
Note You may need to calibrate more often if you operate in H-SRM mode (as opposed
to SRM mode only).

Table 5 lists typical peaks that are observed in the FC-43 mass spectrum in EI, positive
polarity mode.

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4 Tuning and Calibrating
Displaying the FC-43 Mass Spectrum

Table 5. Typically observed FC-43 peaks in EI, positive polarity mode

m/z 69
m/z 100
m/z 114
m/z 119
m/z131
m/z 169
m/z 219
m/z 264
m/z 314
m/z 352
m/z 402
m/z 414
m/z 464
m/z 502
m/z 614

Displaying the FC-43 Mass Spectrum

The first step in tuning and calibrating the Quantum GC mass spectrometer is to display the
FC-43 mass spectrum.

Y To display the FC-43 mass spectrum

1. Choose Start > All Programs > Xcalibur > Quantum Tune to open the Tune Master
window.
2. Choose Workspace > System Tune and Calibration to display the System Tune and
Calibration workspace (Figure 29).
3. Choose a polarity mode. In this example the mass spectrometer is in positive polarity
mode. If necessary, toggle the polarity button.
Positive Negative Note For EI negative polarity mode, you might have to set the calibration gas flow to
high.

4. Select Scan Type: Full Scan and Scan Mode: Q1MS.

5. Enter a First Mass and a Last Mass to define the displayed range. In this example we use
m/z 50 and 600.

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 4 Tuning and Calibrating
Displaying the FC-43 Mass Spectrum

6. Click the Calibration Gas button in the Tune Master toolbar to turn on the flow of
calibration gas into the ion source.

.......... .Cal Gas Off ...........On

7. Click the Filament button in the Tune Master toolbar to turn on the filament.

..........Filament Off. . ....... On

8. Choose Control > On to start the mass spectrometer scanning.

If your mass spectrum looks very different from the one in Figure 29, see “Diagnostics and
Troubleshooting” on page 111.
Figure 29. System Tune and Calibration Workspace, showing the FC-43 mass spectrum in EI, positive polarity mode before
tuning and calibrating

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4 Tuning and Calibrating
Running Auto Tune and Calibration

Running Auto Tune and Calibration

Run the tune and calibration procedure after you obtain a good FC-43 ion signal.

Y To tune and calibrate your mass spectrometer automatically in the EI, positive ion
mode
1. Display the FC-43 positive ion mass spectrum as described in the previous section.
2. In the Compound list, select FC43 pos. ions. This automatically selects the positively
charged FC-43 ions to be used for automatic tuning and calibrating.
3. Select Auto Tune - Calibration to specify a full tune and calibration.
4. Select Both to tune and calibrate both the first and third quadrupoles.
5. Click Start to start the automatic tuning and calibration procedure.
The Status box displays real-time messages about the system tune and calibration so that
you can monitor the progress of each sub-procedure. After a sub-procedure is complete,
the result is reported (for example, whether it passed or failed). At the end of the entire
procedure, it displays a summary.
• If errors occur during the automatic tuning and calibration procedure, go to step 6.
• If the automatic tuning and calibration procedure finishes without errors, go to
step 7.
6. If errors occur during the automatic tuning and calibration procedure, restore the
previous mass spectrometer device settings and perform the tuning and calibration
procedure again by completing the following steps:
a. To restore the prior tuning and calibration settings, click Undo.
b. To reload the prior tuning and calibration settings to the mass spectrometer, click
Accept.
c. Troubleshoot and correct the problem that caused the tuning and calibration
procedure to fail. See “Tuning Issues” on page 125.
d. Go to step 5 and restart the tuning and calibration procedure.

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 4 Tuning and Calibrating
Running Auto Tune and Calibration

Figure 30. System Tune and Calibration Workspace during an automatic tune and calibration

7. Click Accept to accept the results of the tuning and calibration procedure.
After you accept the results of the tuning and calibration procedure, a message box asks
whether you want to copy the positive ion tuning and calibration settings to the negative
ion mode.
• If you have already tuned and calibrated the instrument successfully in the negative
ion mode, click No. (Do not copy the positive ion mode parameters to the negative
ion mode.)
• If you have not tuned and calibrated the instrument in the negative ion mode,
click Yes.
Note If you intend to perform high-sensitivity, negative-ion mass spectrum
analysis, Thermo Fisher Scientific recommends that you also perform a full tune
and calibration of the instrument in the negative ion mode.

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4 Tuning and Calibrating
Saving the Tune and Calibration Report

8. Save the calibration file as follows:

a. Click Save Calib. As to open the Save Calibration File dialog box.
b. In the File Name box, enter a name for your calibration file.
c. Click Save to save the calibration file. The Save As dialog box appears.
9. Save the tune method file as follows:
a. In the File Name box, enter a name for your tune method file.
b. Click Save to save the tune method file.

The mass spectrometer is now tuned and calibrated in the positive ion mode.

Saving the Tune and Calibration Report

You can save the information that appears in the Status box and in the parameter
optimization plots as a PDF file. Examples of status information and parameter optimization
plots from the tune and calibration report follow.

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 4 Tuning and Calibrating
Saving the Tune and Calibration Report

Figure 31. Tune and calibration report, status page

Quantum Tune Master - Tune and Calibration

Results from System Tune and Calibration using FC43 Pos. Ions:
Q1 and Q3 Tuning & Calibrating
10:55:29: Tuning and Calibrating Q1
10:55:39: Tuning Q1MS at mass 69.00 m/z
10:55:41: Opening resolution
10:55:42: Adjusting resolution
10:56:02: The adjusted resolution is -13.33 at the width 0.78
10:56:02: Coarse resolution done - Quick calibration
10:56:07: The adjusted calibration of mass 69.0 is -0.88
10:56:08: Averaging Stopping Curve...
10:56:12: Q1 Quadrupole Offset set to -0.85 for all reswidths
10:56:14: Optimizing Lens 2 for ion 69.00 m/z
10:56:20: Previous Setting = -7.00, New Setting = -0.80
10:56:20: Maximum Intensity = 1.04e+06
10:56:20: 322 % Improvement
10:56:20: Optimizing Lens 4 for ion 69.00 m/z
10:56:26: Previous Setting = -10.00, New Setting = -46.55
10:56:26: Maximum Intensity = 1.61e+06
10:56:26: 60 % Improvement
10:56:26: Optimizing Lens 1-1 for ion 69.00 m/z
10:56:32: Previous Setting = -5.00, New Setting = -0.86
10:56:32: Maximum Intensity = 1.93e+06
10:56:32: 15 % Improvement
10:56:32: Optimizing Lens 1-2 for ion 69.00 m/z
10:56:38: Previous Setting = -21.90, New Setting = -5.00
10:56:38: Maximum Intensity = 2.43e+06
10:56:38: 41 % Improvement
10:56:38: Optimizing Lens 2-1 for ion 69.00 m/z
10:56:45: Previous Setting = -8.45, New Setting = 3.92
10:56:45: Maximum Intensity = 2.56e+06
10:56:45: 17 % Improvement
10:56:45: Tuning Q1MS at mass 501.97 m/s
10:56:47: Opening resolution
10:56:48: Adjusting resolution
10:57:04: The adjusted resolution is -14.38 at the width 0.78
10:57:04: Coarse resolution done - Quick calibration
10:57:10: The adjusted calibration of mass 502.0 is -0.16
10:57:11: Averaging Stopping Curve...
10:57:16: Q1 Quadrupole Offset set to -2.00 for all reswidths
10:57:18: Optimizing Lens 2 for ion 501.97 m/z
10:57:24: Previous Setting = -7.00, New Setting = -2.70
10:57:24: Maximum Intensity = 2.97e+05
10:57:24: 223 % Improvement
10:57:24: Optimizing Lens 1-2 for ion 501.97 m/z
10:57:30: Previous Setting = -50.14, New Setting = -51.11
10:57:30: Maximum Intensity = 4.35e+05
10:57:30: 6 % Improvement
10:57:30: Optimizing Lens 2-1 for ion 501.97 m/z

Signature: __________________________________________

May 09, 2007 11:17:28 Page 1 of 10

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4 Tuning and Calibrating
Saving the Tune and Calibration Report

Figure 32. Tune and calibration report, parameter optimization plots

Quantum Tune Master - Tune and Calibration

Optimizing Lens 2 for Q1MS Optimizing Lens 2 for Q3MS

Previous Setting Previous Setting
Optimum Setting Optimum Setting
100 100

80 80
R e la t iv e Int e ns it y

R e la t iv e Int e ns it y
60 60

40 40

20 20
Mass 501.97m/z : 223 % Improvement Mass 501.97m/z : 281 % Improvement
Mass 218.99m/z : 94 % Improvement Mass 218.99m/z : 57 % Improvement
Mass 69.00m/z : 322 % Improvement Mass 69.00m/z : 235 % Improvement
0 0
-50 -40 -30 -20 -10 0 -50 -40 -30 -20 -10 0
Lens 2 Voltage (V) Lens 2 Voltage (V)
May 9, 2007 May 9, 2007

Optimizing Lens 4 for Q1MS Optimizing Lens 1-1 for Q1MS

Previous Setting Previous Setting
Optimum Setting Optimum Setting
100 100

80 80
R e la t iv e Int e ns it y

R e la t iv e Int e ns it y
60 60

40 40

20 20

Mass 69.00m/z : 60 % Improvement Mass 69.00m/z : 15 % Improvement

0 0
-50 -40 -30 -20 -10 0 -10 -8 -6 -4 -2 0
Lens 4 Voltage (V) Lens 1-1 Voltage (V)
May 9, 2007 May 9, 2007

Optimizing Lens 1-1 for Q3MS Optimizing Lens 1-2 for Q1MS
Previous Setting Previous Setting
Optimum Setting Optimum Setting
100 100

80 80
R e la t iv e Int e ns it y

R e la t iv e Int e ns it y

60 60

40 40

20 20
Mass 501.97m/z : 6 % Improvement
Mass 218.99m/z : No Improvement
Mass 69.00m/z : 6 % Improvement Mass 69.00m/z : 41 % Improvement
0 0
-10 -8 -6 -4 -2 0 -250 -200 -150 -100 -50 0
Lens 1-1 Voltage (V) Lens 1-2 Voltage (V)
May 9, 2007 May 9, 2007

Y To save the tune and calibration report

1. In the System Tune and Calibration Workspace, click Save Report. The Save As dialog
box appears.
2. Enter the name and the path of the report, and click Save.

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 4 Tuning and Calibrating
Password Protection

Password Protection
You can password protect the secure workspaces in Tune Master. The workspaces you can
protect are System Tune and Calibration, Full Instrument Control, and Diagnostics.

Three levels of protection are possible:

• No protection—All operators can access all workspaces.
• Automatic protection—Tune Master uses the default password, lctsq, to protect the
secure workspaces.
• Custom password protection—The Key Operator (or Laboratory Administrator or
Manager) can select a password to protect the secure workspaces.

If your TSQ Quantum GC system has been password protected, you need to obtain the
password before you can access the secure workspaces (including the System Tune and
Calibration workspace). If the instrument password is lost, you need to reinstall the TSQ
Quantum GC software to reset the default password (lctsq).

Thermo Scientific TSQ Quantum GC User Guide 67

 5

Changing Ionization Modes

You can operate the TSQ Quantum GC in either EI or CI ionization mode. Changing
ionization modes requires changing ion volumes. It is not necessary to shut down the mass
spectrometer to change ion volumes.

The following sections describe how to change the ionization mode.

Contents
• Removing the Ion Volume

• Installing the Ion Volume

Removing the Ion Volume

Tools Needed
• Gloves, clean, lint- and powder-free
• Insert/removal (I/R) tool and guide bar

Frequency
When you change ionization modes or as needed to clean the ion volume

Y To remove the ion volume

1. Install the guide bar.

a. With the guide ball track facing left, insert the guide bar into the entry housing.
See Figure 33.
b. Push the guide bar in as far as it will go; then rotate it 90° clockwise to lock the guide
bar in the entry housing.

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5 Changing Ionization Modes
Removing the Ion Volume

Figure 33. Insertion/removal (I/R) tool and guide bar

I/R tool

Guide ball
Guide ball
hole

First stop Guide ball Guide bar Bayonet lock

track

2. Prepare the inlet valve and I/R tool for insertion.

a. Make sure the inlet valve is closed. Figure 34 shows the inlet valve lever is down for
closed.
b. Loosen the inlet valve knob counter-clockise and remove the inlet valve plug. The
inlet valve plug prevents air from entering the vacuum manifold in case the inlet valve
is inadvertently opened.
c. Turn the I/R tool to the unlock position , which indicates the I/R tool is
in position to accept the ion volume.

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 5 Changing Ionization Modes
Removing the Ion Volume

Figure 34. Inlet valve components

Inlet valve
knob

Inlet valve
plug

Entry
housing

Inlet valve lever

(down is closed,
up is open)

3. Choose Start > All Programs > Xcalibur > Quantum Tune to open the Tune Master
window.

4. Click the Probe button in the Tune Master toolbar. The Insert Probe message
appears (Figure 35).
Figure 35. Insert Probe message

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5 Changing Ionization Modes
Removing the Ion Volume

5. Inset the I/R tool into the inlet valve.

a. Insert the guide ball into the guide ball hole.
b. Slide the I/R tool forward into the inlet valve until the guide ball is at the guide bar’s
first stop (see Figure 36).
c. Tighten the inlet valve knob clockwise to ensure a leak-tight seal.

Figure 36. I/R tool at the first stop on guide bar and the inlet valve knob tightened

I/R tool First stop of Inlet valve knob

guide bar

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 5 Changing Ionization Modes
Removing the Ion Volume

6. Click OK. The forepump evacuates the inlet valve. Wait until the safe to insert probe
message appears, and then click OK.
Figure 37. Safe to insert the probe message

7. Once evacuation is complete, pull the inlet valve lever up to open the inlet valve.
Figure 38. I/R tool at first stop and inlet valve lever up

I/R tool First stop of Inlet valve lever

guide bar

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5 Changing Ionization Modes
Removing the Ion Volume

8. Remove the ion volume.

a. Slide the I/R tool into the vacuum manifold until the tip of the I/R tool is fully
inserted into the ion volume holder. The head of the arrow on the I/R tool
(Figure 40), when viewed through the window of the ion source manifold, should
not be visible.

Figure 39. I/R tool inserted into the inlet valve

b. Turn the I/R tool handle counterclockwise to put the I/R tool into lock position
. Listen for a click, which indicates that the handle is fully engaged in
the lock position and is holding the ion volume.
c. Withdraw the I/R tool (with the ion volume attached) until the guide ball reaches the
first stop (see Figure 38).
d. Pull the lever down to close the inlet valve.

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 5 Changing Ionization Modes
Removing the Ion Volume

CAUTION Do not withdraw the I/R tool beyond the point where the guide ball
reaches the first stop in the guide bar. Close the inlet valve first. Otherwise, the
system vents to the atmosphere.

e. Loosen the inlet valve knob by turning it counterclockwise to release the seal.
f. Continue withdrawing the I/R tool completely from the inlet valve by sliding the I/R
tool through the guide ball track in the guide bar.

CAUTION Because the ion volume might be too hot to touch, let it cool to room
temperature before handling it.

9. Remove the ion volume from the I/R tool. See Figure 40.
a. Wearing clean gloves, press the ion volume forward into the tip of the I/R tool and
rotate it to disconnect the bayonet pins from the pin guides.
b. Pull the ion volume out of the I/R tool.
Figure 40. Ion volume, ion volume holder, and I/R tool

Bayonet
Arrow Bayonet pin lock Arrow I/R tool

Bayonet pin
guide

Ion volume holder

Spring washer

Ion volume

10. To clean the ion volume, use the instructions in “Cleaning Stainless Steel Parts” on
page 95. If you are cleaning a CI ion volume, be sure to clean out the small electron
entrance hole. Aluminum oxide can get trapped in this hole, which can adversely affect
sensitivity. Use a dental pick or old syringe needle to clean the hole.

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5 Changing Ionization Modes
Installing the Ion Volume

Installing the Ion Volume

You install an ion volume after cleaning or to change ionization modes.

Y To install the ion volume

Note Wear clean, lint- and powder- free gloves when you handle a clean ion volume.

1. Place the clean ion volume on the I/R tool with the arrows aligned. See Figure 40.

CAUTION Make sure the arrows on the I/R tool and ion volume are aligned to avoid
damage to the ion source.

2. Turn the I/R tool handle to the lock position .

3. Install the guide bar.

a. With the guide ball track facing left, insert the guide bar into the entry housing (see
Figure 33).
b. Push the guide bar in as far as it will go, and then rotate it 90° clockwise to lock the
guide bar in the entry housing.
4. Prepare the inlet valve for insertion.
a. Make sure the inlet valve is closed. Figure 34 shows the inlet valve lever is down for
closed.
b. Remove the inlet valve plug. The inlet valve plug prevents air from entering the
vacuum manifold in case the inlet valve is inadvertently opened.

5. Choose Start > All Programs > Xcalibur > Quantum Tune to open the Tune Plus
window.

6. Click the Probe button in the Tune Master toolbar. The Insert Probe message
appears. See Figure 35.

7. Inset the I/R tool into the inlet valve.

a. Insert the guide ball into the guide ball hole.
b. Slide the I/R tool forward into the inlet valve until the guide ball is at the guide bar’s
first stop. See Figure 36.
c. Tighten the inlet valve knob clockwise to ensure a leak-tight seal.

8. Click OK. The forepump evacuates the inlet valve. Wait for the safe to insert probe
message to appear (Figure 37); then click OK.

9. Once evacuation is complete, pull the inlet valve lever up to open the inlet valve.

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 5 Changing Ionization Modes
Installing the Ion Volume

10. Install the ion volume.

a. Slide the I/R tool and ion volume assembly into the vacuum manifold until the ion
volume assembly is fully inserted and seated into the ion source block. Listen for a
click, which indicates that the ion volume has connected with the ion source block.
b. Turn the I/R tool handle to the unlock position to release the ion
volume from the I/R tool.
Figure 41. Ion volume seated in the ion source block

Ion source block

Ion volume

11. Verify that the ion volume is fully seated in the ion source block:

• Withdraw the I/R tool away from the ion volume about 2.5 cm (1 in.), and turn the
I/R tool handle to the lock position.

• Slide the I/R tool back into the vacuum manifold until the end of the I/R tool just
touches the ion volume.

• Test that the I/R tool does not go into the inlet valve completely, which indicates that
the ion volume is seated properly.

12. Remove the I/R tool.

a. Withdraw the I/R tool until the guide ball reaches the first stop (see Figure 38).
b. Close the inlet valve by pulling the inlet valve lever down (see Figure 36).

CAUTION Do not withdraw the I/R tool beyond the point where the guide ball
reaches the first stop in the guide bar. Close the inlet valve first. Otherwise, the
system vents to the atmosphere.

c. Loosen the inlet valve knob by turning it counter-clockwise.

d. Continue withdrawing the I/R tool completely from the inlet valve by sliding the I/R
tool through the guide ball track in the guide bar.

13. Remove the guide bar by rotating it 90° counter-clockwise and sliding it out of the entry
housing.

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5 Changing Ionization Modes
Installing the Ion Volume

14. Replace the inlet valve plug. Orient the plug to indicate whether an EI or CI ion volume
is installed.

15. Tighten the inlet valve knob clockwise to create a leak-tight seal.
16. (Optional) To prevent the inlet valve from being opened accidentally, pull free and
remove the inlet valve lever.

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 6

Maintenance
This chapter describes routine maintenance procedures that you must perform to ensure
optimum performance of the instrument. Optimum performance of the TSQ Quantum GC
mass spectrometer depends on the maintenance of all parts of the instrument. You are
responsible for maintaining your system properly by performing the system maintenance
procedures on a regular basis.
Note When you perform maintenance procedures, be methodical; always wear clean,
lint-free gloves when handling the components of the ion source; always place the
components on a clean, lint-free surface; and never overtighten a screw or use excessive
force.

Table 6 lists routine and infrequent mass spectrometer maintenance procedures. For
instructions on maintaining the GC or autosampler, refer to the manual that comes with the
GC or autosampler.
Table 6. Maintenance procedures (Sheet 1 of 2)
Mass Spectrometer Procedure
Procedure Frequency
Component Location
Ion source Cleaning the ion volume As needed* Page 82
Ion source Cleaning the lenses As needed* Page 83
Ion source Cleaning entire ion As needed* Page 90
source
Ion source Replacing the filament or If the filament fails Page 90
other components
Inlet valve Replacing the ball valve If there is an air leak Page 102
seal in the inlet valve
Calibration compound Adding calibration If Tune error Page 99
compound message indicates
low intensity of
calibration gas ions
Gas chromatograph Replacing the capillary If chromatographic Page 104
column separation is bad
Q0 ion optics Cleaning Q0 quadrupole As needed*
and lenses L11 and L12**

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6 Maintenance

Table 6. Maintenance procedures (Sheet 2 of 2)

Mass Spectrometer Procedure
Procedure Frequency
Component Location
Mass analyzer Cleaning Q1, Q2, and As needed*
Q3 quadrupoles and
lenses**
Forepump Purging pump oil If pump oil is Manufacturer’s
cloudy documentation
Forepump Adding oil If pump oil level is Manufacturer’s
low documentation
Forepump Changing oil Every 4 months or if Manufacturer’s
pump oil is cloudy documentation
and discolored
Ion detection system Replacing electron If noise in spectrum
multiplier assembly** is excessive or
proper electron
multiplier gain
cannot be achieved
Electronic modules Replacing electronic If electronic module
module** fails
PCBs Replacing PCB** If PCB fails
*The frequency of cleaning the components of the mass spectrometer depends on the types and amounts of
samples and solvents that are introduced into the instrument. Cleaning of the Q0, Q1, Q2, and Q3 quadrupoles is
rarely (if ever) required.
**A Thermo Fisher Scientific Field Service Engineer should perform this maintenance procedure.

Contents
• Cleaning Ion Source Components

• Replacing the Ion Source Filament

• Maintaining the Forepump

• Adding Calibration Compound

• Replacing the Ball Valve Seal

• Removing and Installing a GC Capillary Column

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 6 Maintenance
Cleaning Ion Source Components

Cleaning Ion Source Components

An important part of maintaining your TSQ Quantum GC is making sure that the ion source
components are clean. Follow the cleaning procedures in this section to clean stainless steel
and non-stainless steel parts.

When your TSQ Quantum GC is clean and in good working order, perform benchmark tests
and record the results. When the tested performance of your system decreases significantly
from your benchmark test results, clean the ion volume. If this does not restore performance,
clean the lenses.

How often you clean the ion source depends on the types and amounts of samples and
solvents you introduce into the system. In general, the closer a component is to the sample
introduction point, the more rapidly the component becomes dirty. For example, you clean
the ion volume more often than other parts. If you just want to change or clean the ion
volumes, you do not need to shut down the system.

Most parts can be removed and disassembled by hand. Make sure you have all the tools
needed before starting each procedure.

Figure 42 shows an exploded view of the ion source assembly.

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Figure 42. Ion source assembly, exploded and assembled views

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 6 Maintenance
Cleaning Ion Source Components

Cleaning Ion Volumes

You do not need to vent the TSQ Quantum GC to atmosphere to clean the ion volume.

Y To clean the ion volume

1. Remove the ion volume. See “Removing the Ion Volume” on page 69.

CAUTION Burn Hazard. The ion volume might be hot. Allow the ion volume to cool
to room temperature before touching it.

2. Clean the ion volume. See “Cleaning Stainless Steel Parts” on page 95. If you are cleaning
a CI ion volume, be sure to clean out the small electron entrance hole. Aluminum oxide
can get trapped in this hole, which can adversely affect sensitivity. Use a dental pick or old
syringe needle to clean the hole.
3. Reinstall the ion volume. See“Installing the Ion Volume” on page 76.

Cleaning Ion Source Lenses

If cleaning the ion volume does not restore system performance, clean the ion source lenses.
Note Lens L4 requires cleaning less often than lens L1, L2, and L3.

Y To clean the ion source lenses

1. Shut down and vent the system. See “Shutting Down the System Completely” on
page 49.

CAUTION Shock Hazard. Unplug the TSQ Quantum GC before proceeding.

CAUTION Burn Hazard. The ion source might be hot. Allow the ion source to cool to
room temperature before touching it.

2. Remove the ion source. See “Removing the Ion Source” on page 84.
3. Remove the ion source lens assembly from the ion source and disassemble it. See
“Removing the Ion Source Lens Assembly” on page 86.
4. Clean the lenses and the spacers. See “Cleaning Stainless Steel Parts” on page 95 and
“Cleaning Non-Stainless Steel or Hybrid Part” on page 97, respectively.

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6 Maintenance
Cleaning Ion Source Components

5. Reassemble the ion source lens assembly and install it onto the ion source. See
“Reassembling the Ion Source Lens Assembly” on page 89.
6. Reinstall the ion source into the mass spectrometer. See “Reinstalling the Ion Source” on
page 89.
7. Restart the system. See “Starting Up the System after a Complete Shutdown” on page 51.

Removing the Ion Source

Remove the ion source to clean the lenses or replace the filament.

Tools Needed
• Gloves, cleanroom grade (P/N 23827-0008 and 23827-0009)
• Lint-free cloth

Frequency
As needed to perform ion source maintenance

Y To remove the ion source

CAUTION Do not remove the ion source without first pulling back the capillary
column, or else the capillary column might break.

1. Shut down and vent the TSQ Quantum GC. See “Shutting Down the System
Completely” on page 49.

CAUTION Shock Hazard. Unplug the TSQ Quantum GC before proceeding.

2. Pull back the capillary column.

a. Lower the oven, injector, and transfer line temperatures to 30 °C and allow them to
cool before continuing.

CAUTION Burn Hazard. The GC oven, injector, and transfer line are hot. Allow
them to cool to room temperature before touching them.

b. Once the oven, injector, and transfer line are cool, turn off the gas chromatograph.
c. Loosen the transfer line nut. See Figure 54 on page 105.
d. Pull back the column. (You can first mark the column’s position with white out or
something similar.)

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 6 Maintenance
Cleaning Ion Source Components

3. Prepare a clean work area by covering the area with lint-free cloth.
4. Undo the two latches that secure the lid of the ion source vacuum manifold, and open the
lid.
5. Disconnect the connectors from the lead pins at the EI/CI Source PCB, lens L1, L2, L3
assembly, and lens L4 assembly. See Figure 43.
Figure 43. EI/CI ion source

Q0 quadrupole mount

Lens L4 connector
Lens L1,L2,L3 connector

EI/CI Source PCB connector

Thumbscrew

Transfer line

Thumbscrew

CAUTION Burn Hazard. The ion source might be hot. Allow the ion source to cool
to room temperature before touching it.

Note Wear clean, lint- and powder- free gloves when you handle the ion source.

6. While holding the ion source assembly, loosen the two thumbscrews that secure the ion
source assembly to the Q0 quadrupole.

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Cleaning Ion Source Components

7. Pull the ion source assembly away from the Q0 quadrupole and 2 mm to the right to clear
the transfer line bellows.
8. Slide the ion source off the magnet yoke.
9. Place the ion source and magnet yoke on a clean, lint-free cloth.
10. Close the lid of the ion source vacuum manifold.

Removing the Ion Source Lens Assembly

The ion source lens assembly includes lens L1, L2, L3, and L4. You must remove and
disassemble the ion source lens assembly to clean the lenses. A retainer clip fastens the lens
assembly to the ion source block.

To remove the ion source lens assembly

1. Wearing clean, lint- and powder- free gloves, unscrew the threaded hexagonal standoff
and remove the retainer clip that secures the lens assembly to the ion source block.
See Figure 44.
2. Pull the lens assembly out of the ion source.
3. Place the ion source and lens assembly on a clean surface.
Figure 44. Lens assembly removed from the ion source

Lens
assembly

Ion source

Retainer clip

Threaded
standoff

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 6 Maintenance
Cleaning Ion Source Components

Disassembling the Ion Source Lens Assembly

Y To disassemble the lens assembly

1. Pull the L1, L2, L3 lens assembly from the L4 lens assembly.
Figure 45. Ion source lens assembly separated into L1, L2, L3 lens assembly (left) and L4 lens
assembly (right)

L1, L2, L3 lens L4 lens

assembly assembly

2. Disassemble the L1, L2, L3 lens assembly.

a. Remove the lens clip by pinching the ends with your fingers or a pair of tweezers.
b. Remove the lenses and spacers from the lens holder.
c. Place the components on a clean surface.

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Cleaning Ion Source Components

Figure 46. L1, L2, L3 lens assembly, exploded and assembled views

3. Disassemble the L4 lens assembly.

a. Remove the lens clip by pinching the ends with your fingers or a pair of tweezers.
b. Remove the lens L4 from the lens holder.
c. Place the components on a clean surface.
Figure 47. L4 lens assembly, exploded view

Lens clip

Lens L4

Lens holder

Note To clean the ion source lenses, follow the procedure in “Cleaning Stainless Steel
Parts” on page 95.

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 6 Maintenance
Cleaning Ion Source Components

Reassembling the Ion Source Lens Assembly

Ensure that the lenses are clean and dry before you reassemble the lens assembly.

Y To reassemble the ion source lens assembly

1. Wearing clean, lint- and powder- free gloves, reassemble the L4 lens assembly.
a. Insert lens L4 into the lens holder. See Figure 47.
b. Install the lens clip by pinching the ends with your fingers or a pair of tweezers. Seat
the lens clip in the lens holder.
2. Reassemble the L1, L2, L3 lens assembly. See Figure 46.
a. Reinstall the lenses and spacers in the lens holder in the order and orientation shown
in Figure 46.
b. Reinstall the lens clip by pinching the ends with your fingers or a pair of tweezers and
seating it in the lens holder.
c. Insert the lens alignment tool (in the TSQ Quantum GC Accessory Kit) into the lens
assembly and align the lenses
3. Insert the L4 lens assembly into the L1, L2, L3 lens assembly. Align the lead pins.
See Figure 45.

Reinstalling the Ion Source Lens Assembly

Y To reinstall the ion source lens assembly onto the ion source

1. Wearing clean, lint- and powder- free gloves, insert the lens assembly into the ion source.
See Figure 45.
2. Use the retainer clip and threaded standoff to secure the lens assembly to the ion source.
See Figure 44.
IMPORTANT For accurate temperature readings of the heater block, fully screw the
threaded standoff into the ion source to ensure contact between the temperature
sensor with the heater block.

Reinstalling the Ion Source

Y To reinstall the ion source into the vacuum manifold

1. Wearing clean, lint- and powder- free gloves, place the ion source onto the magnet yoke.
2. Position the ion source in the vacuum manifold and ensure the following:
• The transfer line is seated in the sample inlet aperture in the ion source.

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6 Maintenance
Replacing the Ion Source Filament

• The two thumbscrews are aligned with the screw holes in the Q0 quadrupole mount.
See Figure 43.
3. Secure the ion source to the Q0 quadrupole mount by alternately tightening each
thumbscrew one-half turn at a time. Make sure there is no play in the ion source.
4. Reconnect the connectors to the lead pins on the EI/CI Source PCB, lens L1, L2, L3
assembly (the orientation is not important), and lens L4 assembly. See Figure 43.
5. Reinsert the capillary column into the ion source.
a. Using the I/R tool, remove the ion volume. See “Removing the Ion Volume” on
page 69.
b. Push the column in until you can see it through the inlet valve.
c. Pull the column back just far enough that you cannot see it.
d. Tighten the transfer line nut and transfer line union.
e. Using the I/R tool, install the ion volume. See “Installing the Ion Volume” on
page 76.
6. Close and secure the cover to the ion source vacuum manifold.

Replacing the Ion Source Filament

The number of ions produced in the ion source is approximately proportional to the filament
emission current. If ion production is lacking, you might have to replace the filament. If the
measured emission current is substantially less than the value that the emission current is set
to, or if the measured emission current decreases over time, then the filament has failed or is
failing and requires replacement.

See Figure 42 on page 82 and Figure 48 on page page 91 for the location of the ion source
components.
Tools Needed
• Filament (P/N 120320-0030)
• Gloves, cleanroom grade (P/N 23827-0008 and 23827-0009)
• Lint-free cloth

Frequency
If filament fails

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 6 Maintenance
Replacing the Ion Source Filament

Y To replace the ion source filament

1. Prepare a clean work area by covering the area with lint-free cloth.
2. Shut down and vent the TSQ Quantum GC. See “Shutting Down the System
Completely” on page 49.

CAUTION Shock Hazard. Unplug the TSQ Quantum GC before proceeding.

3. Wearing clean, lint- and powder- free gloves, remove the ion source from the magnet
yoke.
Figure 48. Disassembling the ion source to replace the filament

Filament
retainer clip

Filament

Centering ring

Ion source block and

EI/CI Source PCB

Lens assembly
retainer clip

Threaded standoff
Heater ring and
lens assembly

4. Unscrew the threaded standoff and remove the retainer clip that secures the heater ring
and lens assembly to the ion source block. See Figure 48.
5. Pull the heater ring and lens assembly out of the ion source block.

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Disassembling and Reassembling the Ion Source Completely

6. Remove the retainer clip that secures the filament and centering ring to the ion source
block.
7. Remove the filament and centering ring from the ion source block.
Note Now is a good time to clean the ion source block. Use the procedure described
in “Cleaning Stainless Steel Parts” on page 95 to clean the ion source block.

8. Inspect and install a new filament (P/N 120320-0030, in the TSQ Quantum GC Accessory
Kit).
a. Verify that the filament wire is centered in the electron lens hole.
b. Insert the filament into the centering ring.
c. Seat the filament on the EI/CI Source PCB.
d. Secure the filament with the retainer clip.
9. Press the heater ring and lens assembly onto the ion source block.
10. Use the retainer clip and threaded standoff to secure the lens assembly to the ion source.
See Figure 48.
IMPORTANT For accurate temperature readings of the heater block, fully screw the
threaded standoff into the ion source to ensure contact between the temperature
sensor with the heater block.

11. Reinstall the ion source onto the magnet yoke.

12. Reinstall the ion source into the vacuum manifold. See “Reinstalling the Ion Source” on
page 89.
13. Restart the system. See “Starting Up the System after a Complete Shutdown” on page 51.

Disassembling and Reassembling the Ion Source Completely

Disassemble the ion source completely to clean the ion source block or replace the EI/CI
Source PCB.

See Figure 49 for the location of the ion source components.

Tools Needed
• Gloves, cleanroom grade (P/N 23827-0008 and 23827-0009)
• Lint-free cloth

Frequency
As needed

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Disassembling and Reassembling the Ion Source Completely

Y To disassemble the ion source completely

1. Prepare a clean work area by covering the area with lint-free cloth.
2. Shut down and vent the TSQ Quantum GC. See“Shutting Down the System
Completely” on page 49.

CAUTION Shock Hazard. Unplug the TSQ Quantum GC before proceeding.

3. Wearing clean, lint- and powder- free gloves, remove the ion source. See “Removing the
Ion Source” on page 84.
4. Remove the ion source from the magnet yoke.
Figure 49. Disassembling the ion source

Filament
retainer clip

Filament

Centering ring

Ion source block

Base studs EI/CI Source PCB Lens assembly Heater ring Lens assembly
retainer clip

5. Remove the ion source lens assembly from the ion source. See “Removing the Ion Source
Lens Assembly” on page 86.
6. Pull the heater ring off the ion source block.
7. Unscrew and remove the three base studs.

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Disassembling and Reassembling the Ion Source Completely

CAUTION Shock Hazard. Do not pull the EI/CI Source PCB out of the ion source
block. This might damage the EI/CI Source PCB.

8. Remove the EI/CI Source PCB.

a. Place the ion source on a clean surface with the cartridge heaters down and the EI/CI
Source PCB up.
b. Press down on the ion source block to separate it from the EI/CI Source PCB.
9. Remove the retainer clip that secures the filament and centering ring to the ion source
block.
10. Remove the filament and centering ring from the ion source block.
11. Clean the ion source block and lenses. See “Cleaning Stainless Steel Parts” on page 95.
Clean non-stainless steel parts as described in “Cleaning Non-Stainless Steel or Hybrid
Part” on page 97.

Y To reassemble the ion source

1. Reinstall the EI/CI Source PCB and filament.

a. Align and insert the cartridge heaters and temperature sensor on the EI/CI Source
PCB with the corresponding holes in the ion source block.
IMPORTANT Ensure that the temperature sensor is seated snugly.

b. Reinstall the three base studs.

c. Align the filament leads with the EI/CI Source PCB connectors and gently press the
leads into the connectors. Normally, there is a small gap (about 0.016 in.) between
the filament and the connectors. The gap allows the ceramic centering ring to
properly position and align the electron lens hole with the ion volume.
2. Press the heater ring and lens assembly onto the ion source block.
3. Use the retainer clip and threaded standoff to secure the lens assembly to the ion source.
See Figure 49.
IMPORTANT For accurate temperature readings of the heater block, fully screw the
threaded standoff into the ion source to ensure contact between the temperature
sensor with the heater block.

4. Reinstall the ion source into the vacuum manifold. See “Reinstalling the Ion Source” on
page 89.
5. Restart the system. See “Starting Up the System after a Complete Shutdown” on page 51.

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Disassembling and Reassembling the Ion Source Completely

Cleaning Stainless Steel Parts

Tools Needed
• Acetone, reagent grade (or other suitable polar solvent)
• Aluminum oxide abrasive, number 600 (P/N 32000-60340)
• Applicators, cotton-tipped (P/N 00301-01-00015)
• Beaker, 450 mL
• Clean, dry gas
• De-ionized water
• Detergent (Alconox, Micro, or equivalent)
• Dremel rotary tool or equivalent (recommended)
• Foil, aluminum
• Forceps (P/N 76360-0400)
• Gloves, cleanroom grade (P/N 23827-0008 and 23827-0009)
• Glycerol, reagent grade
• Lint-free cloth
• Protective eyewear
• Tap water
• Toothbrush, soft
• Ultrasonic cleaner

Frequency
As needed to clean these stainless steel parts:
• Ion volumes
• Ion source block
• Ion source lenses

CAUTION Material and Eye Hazard. Wear impermeable laboratory gloves and eye
protection when performing cleaning procedures.

Y To clean stainless-steel parts

1. Remove contamination from all the surfaces you are cleaning.

a. Use a slurry of number 600 aluminum oxide in glycerol and a cleaning brush or
cotton-tipped applicator. Contamination appears as dark or discolored areas, but
often is not visible. The heaviest contamination is usually found around the
apertures, such as the electron entrance hole on an ion volume.
b. Clean each part thoroughly, even if no contamination is visible.
c. To clean the inside corners, use the wooden end of an applicator cut at an angle.
d. Use a Dremel® tool with the polishing swab at its lowest speed to increase cleaning
efficiency, as well as decrease the time required to clean the items. To prevent

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Disassembling and Reassembling the Ion Source Completely

personal injury, be sure to keep the Dremel tool away from possible hazards, such as
standing water or flammable solvents.
2. Rinse the parts with clean water. Use a clean applicator or toothbrush to remove the
aluminum oxide slurry. Do not let the slurry dry on the metal; dried aluminum oxide is
difficult to remove.
3. Sonicate the parts in a warm detergent solution.
a. Using forceps, place the parts in a beaker containing warm detergent solution.
b. Place the beaker and contents in an ultrasonic bath for five minutes.
c. Rinse the parts with tap water to remove the detergent.
4. Sonicate the parts in deionized water.
a. Using forceps, place the parts in a beaker containing deionized water.
b. Place the beaker and contents in an ultrasonic bath for five minutes.
c. If the water is cloudy after sonicating, pour off the water, add fresh water, and place
the beaker and its contents in an ultrasonic bath again for five minutes. Repeat until
the water is clear.
5. Sonicate the parts in acetone.
a. Using forceps, place the parts in a beaker containing acetone.
b. Using forceps, transfer the parts to a beaker containing fresh acetone.
c. Place the beaker and contents in an ultrasonic bath again for five minutes.
6. Blow-dry the parts immediately. Use clean, dry gas to blow the acetone off the parts.
7. Using forceps, place the parts in a beaker, cover the beaker with aluminum foil, and put
the beaker in the oven.
8. Dry the parts in an oven set at 100 oC for 30 minutes.
9. Allow the parts to cool before putting them back together.

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Cleaning Non-Stainless Steel or Hybrid Part

Tools Needed
• Acetone, reagent grade (or other suitable polar solvent)
• Aluminum oxide abrasive, number 600 (P/N 32000-60340)
• Applicators, cotton-tipped (P/N 00301-01-00015)
• Beaker, 450 mL
• Clean, dry gas
• De-ionized water
• Detergent (Alconox, Micro, or equivalent)
• Dremel rotary tool or equivalent (recommended)
• Forceps (P/N 76360-0400)
• Gloves, cleanroom grade (P/N 23827-0008 and 23827-0009)
• Glycerol, reagent grade
• Lint-free cloth
• Protective eyewear
• Tap water
• Toothbrush, soft

Frequency
As needed to clean non-stainless steel parts (such as aluminum,
ceramic, or gold-plated), or to clean hybrid parts that are partially
made of stainless steel:
• Lens holder and spacers
• Filament spacer
• Heater ring

CAUTION Material and Eye Hazard. Wear impermeable laboratory gloves and eye
protection when performing cleaning procedures.

Y To clean non-stainless steel or hybrid parts

1. Remove contamination from stainless steel surfaces. It is only necessary to clean a surface
that comes in contact with the ion beam.
a. Use a slurry of number 600 aluminum oxide in glycerol and a cleaning brush or
cotton-tipped applicator. Contamination appears as dark or discolored areas, but
often is not visible.
b. Clean each part thoroughly, even if no contamination is visible.
c. To clean the inside corners, use the wooden end of an applicator cut at an angle.

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Maintaining the Forepump

d. Use a Dremel tool with the polishing swab at its lowest speed to increase cleaning
efficiency, as well as decrease the time required to clean the items. To prevent
personal injury, be sure to keep the tool away from possible hazards, such as standing
water or flammable solvents.
2. Rinse the parts with clean water. Use a clean applicator or toothbrush to remove the
aluminum oxide slurry. Do not let the slurry dry on the metal; dried aluminum oxide is
difficult to remove.
3. Scrub all of the parts with a warm detergent solution.
a. Scrub the parts with a toothbrush or clean applicator. Do not soak or sonicate the
parts in detergent.
b. Using forceps, rinse the parts thoroughly with tap water to remove the detergent.

CAUTION Do not leave aluminum parts, such as the heater ring, in the detergent.
Basic solutions, like detergent, discolor aluminum.

4. Rinse the parts in deionized water. Using forceps, dip the parts in a beaker of deionized
water. Change the water if it becomes cloudy. Do not soak or sonicate the parts.
5. Rinse the parts with acetone. Using forceps, dip the parts in a beaker of acetone. Change
the acetone if it becomes cloudy. Do not soak or sonicate the parts.
6. Blow-dry the parts immediately. Use clean, dry gas to blow the acetone off the parts.

Maintaining the Forepump

The forepump is located under the TSQ Quantum GC work table. Inspecting, adding,
purging, and changing the oil are all that is required to maintain the forepump.

Forepump oil is a translucent, light amber color, which you must check often. During normal
operation, oil must always be visible in the oil level sight glass between the MIN and MAX
marks. If the oil level is below the MIN mark, add oil. If the oil is cloudy or discolored, purge
the oil to decontaminate dissolved solvents. If the pump oil is still discolored, change it. You
should change the pump oil every 3,000 hours (about four months) of operation. Refer to the
manufacturer’s documentation for procedures for purging, adding, and changing the
forepump oil.

CAUTION If you use ammonia as a chemical ionization reagent gas, change the oil every
month. Ammonia is highly basic and quickly damages seals in the forepump. Purging the
oil with the Gas Ballast Control helps remove dissolved ammonia from the oil.

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 6 Maintenance
Adding Calibration Compound

Adding Calibration Compound

Tools Needed
• Calibration compound (P/N 50010-02500)
• Syringe (P/N 36502019)
• 9/16-in., open-ended wrench

Frequency
Yearly or as needed

The calibration compound is a liquid whose mass spectrum of ions is used to tune and
calibrate the TSQ Quantum GC. The TSQ Quantum GC uses FC-43 as its calibration
compound. Although you cannot visually determine when a calibration compound needs to
be added to the TSQ Quantum GC, Xcalibur Automatic Tune produces an error message
indicating that “the intensity of calibration gas ions is too low.” This message indicates that
calibration compound must be added. However, there are many factors other than a decrease
in the calibration compound that can cause a shortage of calibration gas ions. As a rule, add
calibration compound to the TSQ Quantum GC once a year.

Y To add calibration compound

1. Shut down and vent the TSQ Quantum GC. See “Shutting Down the System
Completely” on page 49.
2. Lower the GC oven and transfer line temperatures to 30 °C and allow them to cool
before continuing.

CAUTION The transfer line is hot. Allow it to cool to room temperature before
moving the GC.

3. Move the GC far enough from the mass spectrometer to access the calibration compound
vial compartment. See the location of the calibration compound vial compartment in
Figure 50.
4. Remove the cover to the calibration compound vial compartment.
5. Remove the calibration compound vial from the calibration gas flow module.
See Figure 51.
a. Use a 9/16-in. wrench to remove the nut from the calibration compound vial.
b. Slide the vial away from the calibration valve fitting with the ferrule and nut
attached.

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6 Maintenance
Adding Calibration Compound

c. Remove the ferrule and nut.

CAUTION Having more than 0.1 mL of the calibration compound can damage
the calibration gas flow module. Be sure that there is less than 0.1 mL of the
calibration compound in the vial.

6. Add the calibration compound.

a. Draw up no more than 0.1 mL of calibration compound into a clean syringe.
b. Insert the syringe in the calibration compound vial until it comes in contact with the
white frit at the bottom of the vial.
c. Inject no more than 0.1 mL of calibration compound into the white frit. The frit
absorbs the calibration compound, so if the calibration compound is pooled
(calibrant covers the top of the frit), then you have too much in the vial. Immediatey
pour out the excess calibrant according to local environmental regulations.
7. Remove the syringe from the calibration compound vial.

Figure 50. Location of the calibration compound vial compartment

Calibration
compound vial
compartment

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 6 Maintenance
Adding Calibration Compound

Figure 51. Calibration compound vial

Ferrule

Nut

Calibration
compound vial

8. Inspect the 1/4-in. ferrule for damage. Replace it if necessary (P/N 95001-20310).
9. Reinstall the calibration compound vial (P/N 96000-40013) into the module.
a. Hold the vial vertically and place the nut on the neck of the vial.
b. Place the 1/4-in. ferrule over the neck of the vial and into the nut.
c. Connect the vial to the calibration valve fitting with the nut and ferrule.
10. Reinstall the cover to the calibration compound vial compartment.
11. Position the GC next to the mass spectrometer.
12. Restart your system. See “Starting Up the System after a Complete Shutdown” on
page 51.

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6 Maintenance
Replacing the Ball Valve Seal

Replacing the Ball Valve Seal

Tools Needed
• Ball valve seal kit (P/N 119265-0003))

Frequency
If the ball valve seal leaks air after you insert the direct insertion
probe or I/R tool into the inlet valve and tighten the inlet valve
knob

The ball valve seal in the inlet valve can become worn over time. Replace the ball valve seal if
it leaks air after you insert the direct insertion probe or I/R tool and tighten the inlet valve
knob. The ball valve seal kit (P/N 119265-0003) is included in the TSQ Quantum GC
Accessory Kit.

The ball valve seal consists of a Teflon® spool and two O-rings. See Figure 52.
Figure 52. Components of the ball valve seal and inlet valve

Inlet valve
housing

Inlet valve
insert

Inlet valve
knob

Ball valve seal

components

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 6 Maintenance
Replacing the Ball Valve Seal

Use the ball valve seal extraction tool (part of the ball valve seal kit, P/N 119265-0003) to
remove the ball valve seal. See Figure 53.

Y To remove the ball valve seal

1. Loosen the inlet valve knob counter-clockwise until you can remove it.
2. Remove the inlet valve knob, plug, and insert.
3. Insert the not-engaged ball valve seal extraction tool into the inlet valve housing.
4. Engage the ball valve seal by pushing the plunger of the ball valve seal extraction tool
forward.
5. Remove the seal and tool.
6. Pull the plunger back to disengage the seal.
Figure 53. Ball valve seal extraction tool and ball valve seal, not engaged (left) and engaged (right)

Y To install the ball valve seal

1. Obtain the ball valve seal kit (P/N 119265-0003) from the Accessory Kit.
2. Assemble the ball valve seal by installing the two O-rings onto the Teflon spool.
3. Insert the ball valve seal into the ball valve manifold with your finger.
4. Install the inlet valve knob and insert.
5. Install the inlet valve plug and tighten the inlet valve knob clockwise.

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6 Maintenance
Removing and Installing a GC Capillary Column

Removing and Installing a GC Capillary Column

Removing a GC Column

Tools Needed
• Gloves, cleanroom grade (P/N 23827-0008 and 23827-0009)
• Wrench, open-ended, 5/16-in.
• Wrench, open-ended, 7/16-in.
• Wrench, open-ended, 6 mm

Frequency
As needed for maintenance or column replacement

Y To remove a GC capillary column

1. Shut down the TSQ Quantum GC and gas chromatograph.

a. Shut down and vent the TSQ Quantum GC. See “Shutting Down the System
Completely” on page 49.
b. Lower the oven, injector, and transfer line temperatures to 30 °C and allow them to
cool before continuing.

CAUTION The oven, injector, and transfer line are hot. Allow them to cool to
room temperature before touching them.

c. Once the oven, injector, and transfer line are cool, turn off the gas chromatograph.
2. Remove the column from the transfer line. See Figure 54.
a. Unscrew the transfer line nut.
b. Remove the column from the transfer line.

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 6 Maintenance
Removing and Installing a GC Capillary Column

Figure 54. GC injector and transfer line unions

3. Remove the column from the injector. See Figure 54.

a. Unscrew the injector nut.
b. Remove the column from the injector.

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6 Maintenance
Removing and Installing a GC Capillary Column

Installing a GC Column
Tools Needed
• Capillary column
• Gloves, cleanroom grade (P/N 23827-0008 and 23827-0009)
• Injector ferrule, for 0.25 mm column (P/N 290 134 88)
• Leak detector, hand-held electronic (GL Sciences, Inc., model LD-228, or
equivalent)
• Lint-free tissue
• Magnifying glass
• Methanol or other suitable solvent
• Scoring wafer (or sapphire scribe) to cut capillary column
• Transfer line ferrule, 0.4 mm ID (P/N A0101-18100)
• Wrench, open-ended, 5/16-in.
• Wrench, two, open-ended, 7/16-in.
• Wrench, open-ended, 6 mm

Frequency
As needed

Refer to the manuals supplied with your GC for additional setup information.

Y To install a GC capillary column

CAUTION Burn Hazard. The injector, oven, and transfer line might be hot. Allow them
to cool to room temperature before touching them.

1. Connect the column to the injector as shown in Figure 54.

Note Wear clean, lint- and powder-free gloves when you handle the column and
injector ferrule.

a. Unwind about half a turn of the column.

b. Wipe about 100 mm (4 in.) of the column with a tissue soaked in methanol.
c. Insert the column through the injector nut and ferrule (open end up).
d. Wipe the column again with a tissue soaked in methanol.

Note To help you measure the proper distance between the nut and the end of
the column, slide a septum on the column before the injector nut.

e. Score and then break the column about 2.5 cm (1 in.) from the end with a scoring
wafer. With the magnifying glass, check for an even, flat cut. Repeat if necessary.

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 6 Maintenance
Removing and Installing a GC Capillary Column

f. Insert the column into the injector so that the end of the column is the proper
distance from the back of the injector nut. Proper distances are as follows: splitless =
64 mm, split = 40 mm, PTV = 30 mm.
g. Tighten the injector nut by hand, and then turn it an additional quarter turn with
the wrench.
h. Score and break the column outlet about 2.5 cm (1 in.) from the end with a scoring
wafer.
i. Turn on the gas chromatograph.
2. Set up the gas chromatograph.
a. Set the oven and injector temperatures to 30 °C.
b. Set the injector flow to 1.0 mL/min.
c. Turn off vacuum compensation (under the Right or Left Carrier menu).
d. Dip the column outlet in a small vial of methanol. Bubbles indicate there is flow
through the column.
e. Allow the column to purge for at least 10 minutes.
3. Perform a column characterization.
a. Raise the oven and injector temperatures to 50 °C and allow them to stabilize.
b. Run a column evaluation according to the procedures in the GC documentation.
c. Expect a K factor of about 0.7 to 0.9 for a 15 m, 0.25 mm ID column (1.3 to 2.0 for
a 30 m, 0.25 mm ID column). If the column does not report a K factor within this
range or within 0.1 units of the previously stored value, check for a leak or broken
column using the leak detector. The K factor is a measured resistance for the column.
A K factor that is too low might indicate a leak in the system, while a K factor that is
too high might indicate a blockage.
d. Raise the oven temperature to 150 °C and allow it to stabilize.
4. Perform a column leak check.
a. Run an automated leak check according to the procedures in the GC documentation.
b. If the report indicates a leak, look for leaks and use the leak detector to fix leaks at all
the fittings in the GC.
c. Repeat column evaluation and leak check procedures until no leaks can be found.

CAUTION Do not raise the oven temperature until you are sure the system is
leak-free. At temperatures above 100 °C, oxygen exposure will destroy the
column.

5. Condition the column. New columns must be conditioned before inserting them into the
TSQ Quantum GC.

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6 Maintenance
Removing and Installing a GC Capillary Column

CAUTION If the column is inserted into the transfer line, the material released from
the column during the conditioning (column bleed) will contaminate the ion source.
You must then clean the ion source.

a. Raise the injector temperature to the desired temperature (normally 250 °C).
b. Run the slow temperature program that is recommended by the manufacturer. For
example, hold the column at 40 °C for 15 minutes; then ramp it to 10 °C per minute
up to 10 °C above the maximum temperature at which you will operate the column
(normally 300 + 10 °C = 310 °C). Hold the column at this temperature for two
hours.

CAUTION Never exceed the manufacturer’s maximum operating temperature.

6. Connect the column to the transfer line.

a. Shut down and vent the TSQ Quantum GC. See“Shutting Down the System
Completely” on page 49.
b. Lower the oven temperature to 30 °C and allow it to cool before continuing.

CAUTION Burn Hazard. The oven and transfer line might be hot. Allow them to
cool to room temperature before touching them. Do not touch the injector when
it is hot.

c. Wearing clean, lint- and powder-free gloves, unwind about one turn of the column
(shown in Figure 54) from the column outlet end.
d. Wipe about 450 mm (18 in.) of the column with a tissue soaked in methanol.
Note Sliding a septum on the column before the transfer line nut helps you
measure the proper distance between the nut and the end of the column. The
column should extend approximately 1 to 2 mm past the end of the transfer line.

e. Insert the column through the transfer line nut and ferrule. Wipe the column again
with a tissue soaked in methanol.
f. Score and break the end of the column with a scoring wafer. With the magnifying
glass, check for an even, flat cut. Repeat if necessary.
g. Insert the column into the transfer line.
i. Open the lid of the ion source vacuum chamber so that you can get a better view
of the column.
ii. Using the I/R tool, remove the ion volume. See “Removing the Ion Volume” on
page 69.
iii. Insert the column into the transfer line and tighten the transfer line nut by hand.

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 6 Maintenance
Removing and Installing a GC Capillary Column

iv. Push the column in until you can see it through the inlet valve.
v. Pull the column back just far enough that you cannot see it.
vi. Tighten the transfer line nut and transfer line union.
vii. Using the I/R tool, replace the ion volume. See “Installing the Ion Volume” on
page 76.

7. Condition the transfer line ferrule. Graphite/vespel ferrules like the transfer line ferrule
require conditioning to ensure a leak-tight seal.
a. Raise the oven temperature to the maximum temperature at which you will operate
the column (normally 300 °C).
b. Wait 10 minutes.
c. Lower the oven temperature to 30 °C and allow it to cool before continuing.

CAUTION The oven might be hot. Allow it to cool to room temperature before
opening it. Do not touch the injector, which will still be hot.

d. Re-tighten the transfer line nut and the transfer line union.
8. Set up the gas chromatograph.
a. Make sure the column does not have any sharp bends and that it does not touch any
metal objects or walls inside the oven.
b. Raise the oven temperature to the initial temperature that you will use (normally
40 °C).
c. Turn on the vacuum compensation (under the Right or Left Carrier menu).

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 7

Diagnostics and Troubleshooting

The TSQ Quantum GC system diagnostics can test many components of the TSQ Quantum
GC mass spectrometer. If there is a problem with the instrument electronics, the diagnostics
can often locate the problem. Replacing a faulty PCB or assembly can usually correct the
problem. After the PCB or assembly is replaced, the diagnostic tests are rerun to verify the
instrument is functioning properly.

Contents
• Running the TSQ Quantum GC System Diagnostics
• Troubleshooting
• Replacing a Fuse
• Replacing PCBs and Power Supplies

Note Three levels of protection are possible:

• No protection—All operators can access all workspaces.
• Automatic protection—Tune Master uses the default password, lctsq, to protect the
secure workspaces.
• Custom password protection—The Key Operator (or Laboratory Administrator or
Manager) can select a password to protect the secure workspaces.

If your TSQ Quantum GC system has been password protected, you must obtain the
password before you can access the secure workspaces (including the System Tune and
Calibration workspace). If the instrument password is lost, you must reinstall the TSQ
Quantum GC software to reset the default password (lctsq).

Running the TSQ Quantum GC System Diagnostics

The TSQ Quantum GC system diagnostics are used to test the major electronic circuits
within the instrument and indicate whether the circuits pass or fail the tests. If there is a
problem with the instrument electronics, the TSQ Quantum GC system diagnostics can
often locate the problem.

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7 Diagnostics and Troubleshooting
Running the TSQ Quantum GC System Diagnostics

The TSQ Quantum GC system diagnostics do not diagnose problems that are not electrical
in nature. For example, they do not diagnose poor sensitivity due to misaligned or dirty
components or to improper tuning. Therefore, it is important that the person running the
diagnostics be familiar with system operation and basic hardware theory as well as the details
of the diagnostics.

Typically, only a Thermo Fisher Scientific Field Service Engineer runs diagnostic tests
because certain tests can overwrite system parameters. However, before calling a Thermo
Fisher Scientific Field Service Engineer to run diagnostics, consider the following:
• Did the system fail when you were running samples?
• Did problems occur after you performed maintenance on the instrument, data system, or
peripherals?
• Did you change the configuration of the system, cables, or peripherals just before the
problem occurred?

If the answer is yes to the first item above, there is the possibility of a hardware failure, and
running the diagnostics is appropriate.

If the answer is yes to either of the last two questions above, the problem is probably
mechanical, not electrical. Reverify that alignment, configurations, and cable connections are
correct before you call the Thermo Fisher Scientific Field Service Engineer. Keep careful notes
documenting the nature of the problem and the corrective steps you have taken. If you are not
successful in correcting the problem, you can e-mail this information to Field Service
engineer. Field Service can then do a preliminary evaluation of the problem before the Field
Service engineer arrives at your site.

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 7 Diagnostics and Troubleshooting
Troubleshooting

Troubleshooting
The following topics discuss possible TSQ Quantum GC problems and solutions.

Communication Issues
Communication issues likely involve links between the data system and the mass
spectrometer, gas chromatograph, or autosampler. This section does not address
communication issues with other devices.

Communication issues can occur during the following:

• Data transfer between the mass spectrometer and the data system
• Mass spectrometer, gas chromatograph, and autosampler current status readbacks
• Instrument control, method downloading, and uploading
• Start, stop, pause, and initialize functions
• Error messages

How does the MS communication work?

The flow of digital information in the TSQ Quantum GC system is bi-directional; the data
system downloads analytical methods to the instrument and activates functions to start, stop,
shut down, start up, and initialize. The TSQ Quantum GC reports its readiness state, current
tasks, various voltages, heated zones, and pressure readings. It also delivers a steady stream of
mass spectral data during acquisition.

Why does the MS have communication issues?

Some communication issues are due to mechanical faults—for instance, a cable might be
unplugged, or a device might be turned off. In other cases, the instrument method could be
incorrect for TSQ Quantum GC operations. Less common communication issues are due to
defective electronic hardware components.

How do I detect communication issues?

You might detect communication issues from an error message delivered by the data system,
or you might notice the failure of the data system to perform some expected task.

Issue: Data system is Possible Causes/Solutions

unable to initiate
communication with • The software is not configured correctly. Select and configure the TSQ Quantum GC
TSQ Quantum GC. from the Instrument Configuration window.
• The Ethernet cable is unplugged. Verify that the Ethernet cable is connected to the
Ethernet port on the TSQ Quantum GC. See Figure 12 on page page 23.

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7 Diagnostics and Troubleshooting
Troubleshooting

• The Ethernet card in the PC is not configured or is faulty. Check the configuration or
replace the Ethernet card if necessary.
• The system is in Service Mode. Return the electronics service switch to operating
position.
• The incorrect Ethernet cable is used for the MS. Use the supplied 10 Base-T Category 5
crossover cable (P/N 76396-0052, in TSQ Quantum GC Accessory Kit).

Note You can extend the length of the Ethernet cable by plugging a standard
Category 5 cable in series with the supplied crossover cable.

Issue: Computer Possible Cause/Solution

intermittently loses
communication with • The Ethernet cable is loose or damaged. Inspect the cable and replace it if necessary.
TSQ Quantum GC.

Issue: Unable to Possible Cause/Solution

download methods to
the TSQ Quantum GC. • The software is not properly configured. Verify the correct settings in Instrument
Configuration.

Issue: Acquisition does Possible Causes/Solutions

not begin as expected.
• The TSQ Quantum GC start mode is not properly configured. Verify that the
instrument is configured properly. Refer to Xcalibur Help for more information.
• The TSQ Quantum GC Instrument Setup file has incorrect settings. Check the start
time in the TSQ Quantum GC Instrument Setup file.
• The forepressure is too high due to solvent peak. Reduce injection volume or extend
filament/multiplier delay time until after solvent peak.
• The remote start cable to the GC is disconnected. Connect the remote start cable.
• The GC did not start. Verify GC instrument method and configuration. Verify the
connection between the autosampler and GC.
• The autosampler did not start. Verify autosampler instrument method and configuration.
Verify that the sample is present.
• The heated zone stipend is not attained. See “Heated Zone Issues” on page 118.

Issue: Acquisition Possible Causes/Solutions

terminates
unexpectedly. • The end run time in the TSQ Quantum GC instrument method is incorrect. Check the
instrument method for the GC and the MS.
• The data system is out of disk space. Check disk space; back up and remove files.

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 7 Diagnostics and Troubleshooting
Troubleshooting

Issue: Unable to Possible Causes/Solutions

initialize the gas
chromatograph. • The GC is not turned on. Turn on the GC.
• The GC is not configured properly in Xcalibur. Check Instrument Configuration.
• The cable between COM1 and GC is disconnected. Verify connection.
• COM1 is not configured properly. Verify COM port configuration.

Issue: Unable to Possible Causes/Solutions

download methods to
the gas chromatograph. • There is a discrepancy between the instrument method and configuration. Verify
consistency between method and instrument configuration.
• COM1 is not configured properly. Verify COM port configuration.

Issue: Unable to Possible Causes/Solutions

initialize the
autosampler. • The autosampler is not turned on. Turn on autosampler.
• The autosampler is not configured properly in Xcalibur. Check Instrument
Configuration.
• The cable between the GC and autosampler is disconnected. Verify connection.
• The autosampler instrument configuration is not set to the correct port. Verify
connection and configuration.

Issue: Unable to Possible Cause/Solution

download methods to
the Autosampler. • There is a discrepancy between instrument method and configuration. Verify consistency
between instrument method and instrument configuration.

Contamination Issues
Chemical noise is always present in any mass spectrometer. As a result, the high sensitivity of
the mass spectrometer can cause new users to confuse background with a contamination
problem. Additionally, the spectra shown in Xcalibur Tune and Real-Time Display are
auto-normalized, which can make the background appear high-level.

Some chemical noise does occur, such as septum bleed after a series of injections, vial sample
bleed (which occurs if more than one injection is made from a sample vial), and siloxane
peaks that appear in the chromatogram at regular intervals from focusing at the head of the
column or in the injector.

Other possible contamination sources include hydrocarbon contamination of the carrier gas,
pump oil, or instrument cleaning solvents.

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7 Diagnostics and Troubleshooting
Troubleshooting

Always wear clean, lint- and powder- free gloves when handling ion source and mass analyzer
components, and ensure that the carrier gas filter, carrier gas lines, and gas regulators are free
of contamination and leaks.

Issue: Excessive Possible Causes/Solutions

chemical background
due to a column bleed • The capillary column has not been properly conditioned. Condition the capillary
(m/z 429, 355, 281). column.
• The capillary column is damaged as a result of exposure to oxygen. Find the source of the
oxygen in the carrier gas or air leak. Recondition or replace the capillary column.

Issue: Excessive Possible Causes/Solutions

injection port septum
bleed (Typical m/z 207, • The septum is worn out or damaged. Replace the septum.
429, 355, 281).
• Small pieces of septum are in the injection port liner. Replace the injection port liner;
condition the capillary column.

Issue: Phthalate Possible Causes/Solutions

background (m/z 149,
167, 279). • Phthalate contamination has occurred due to sample handling or solvent contamination.
• Packaging materials could be the source of phthalates.
• Isolate source of phthalates such as vial lids or plastic solvent containers and remedy.

Issue: Excessive Possible Causes/Solutions

hydrocarbon
contamination (Typical • Carrier gas tubing is contaminated.
ions are m/z 43, 57, 71,
• Isolate source of hydrocarbon contamination and remedy.
85, 99).
• Replace carrier gas tubing.
• Change carrier gas filters.

Issue: Chemical Possible Causes/Solutions

background due to
rhenium oxide (m/z • These series of rhenium oxide ions come from oxidation of the rhenium filament wire
185/187, 201/203, due to the introduction of air into the ion source while the filament is on.
217/219, 233/235,
250/252). • Check for air leaks and remedy. See “High Vacuum Issues” on page 119 for more
information.

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 7 Diagnostics and Troubleshooting
Troubleshooting

Issue: Spectra are

observed due to the
Solvent Spectra
following solvents:
Acetone (m/z 43, 58, 59)
Hexane (m/z 41, 43, 56, 57, 58, 85, 86)
Methanol (m/z 31)
Methylene chloride (m/z 84, 83)
Toluene (m/z 91, 92)
Trichloroethane (m/z 151, 153)
Xylene (m/z 105, 106)

Possible Causes/Solutions

• There is residual solvent from a cleaning procedure or laboratory background

contamination. When you finish performing a cleaning procedure, allow cleaned
components to dry thoroughly. Warm parts in the GC oven to drive off residual solvent.
• The observed compounds have been introduced through sample injection. The ultimate
source is either a sample solvent or the autosampler rinsing solvent. Optimize GC
method to separate solvent peak from the area of interest in the chromatogram.

Filament and Lens Control Issues

The lifetime of a filament depends on its exposure to oxygen and solvent vapors. The filament
assembly protects the filament and increases its lifetime for many months.

Xcalibur diagnostics test the filament for continuity and current regulation. Testing the
filament for continuity before each acquisition ensures that an open filament condition will
stop an autosampler sequence and generate an error message.

Diagnostics test the lenses of the TSQ Quantum GC. A flat line, which represents voltage
readback versus the predicted voltage ramp, indicates a lens or other control fault.
Contamination causes lens performance to deteriorate over time; the amount of time depends
on what type of sample and ionization mode you use.

Be careful to handle the lenses with care, and do not use harsh cleaning techniques. Damaged
lenses cause short circuits, which in turn can cause damage to the lens drivers.

Issue: Diagnostics Possible Cause/Solution

indicate that the
filament is open. • The filament is open. Vent the system and remove the filament. Normal resistance is
1.0 Ω. Replace if open.

Issue: Unstable Possible Cause/Solution

emission current.
• The filament is near the end of its life span. Replace the filament.

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7 Diagnostics and Troubleshooting
Troubleshooting

Issue: Short Possible Causes/Solutions

filament lifetime.
• There is an air leak contributing to short filament lifetime. Check for leaks; repair if any
are found. See “High Vacuum Issues” on page 119 for more information.
• The filament is on during the solvent peak. Increase acquisition delay time until the
solvent peak has passed.
• High emission current is being used. Use lower emission current to extend lifetime.

Issue: Diagnostics Possible Causes/Solutions

indicate a flat lens
response. • The power supply to the lens has a fault. Contact Thermo Fisher Scientific Technical
Support.
• There is a fault with the lens drivers. Contact Thermo Fisher Scientific Technical
Support.

Heated Zone Issues

The ion source and transfer line are heated zones related to the TSQ Quantum GC. The ion
source heater is controlled by the TSQ Quantum GC and the transfer line heater is controlled
by the Aux1 heated zone of the TRACE GC.

A heated zone problem is often the result of downloading an instrument method to the TSQ
Quantum GC that has a different setpoint than the current setting, causing a delay while the
heated zone heats or cools.

Component failures are less common but can occur. These are usually related to open circuits
in heater cartridges or faulty temperature sensors.

This manual does not discuss heated zones in the gas chromatograph.

Issue: Excessive Possible Causes/Solutions

chromatographic peak
tailing. • The ion source, transfer line, or both are not hot enough. Increase the transfer line
temperature. It should be at least as hot as the highest GC oven temperature. Then, try
increasing the ion source temperature.
• The sample analyte is adsorbing in the GC injector. Clean and deactivate the injection
liner. You can also try liners made of different materials.
• The GC oven is not ramped to a high enough temperature. Extend upper oven
temperature.
• The GC column must be replaced or does not have the appropriate stationary phase for
your application. Change the GC column. See “Removing and Installing a GC Capillary
Column” on page 104.

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 7 Diagnostics and Troubleshooting
Troubleshooting

• The GC column does not extend far enough past the end of the transfer line tip. If the
end of the column is inside the tip, an excessive amount of GC effluent will contact the
inside wall of the tip. Follow the procedure described in “Installing a GC Column” on
page 106.

Issue: Source heater Possible Causes/Solutions

will not heat.
• One or more heater cartridges on the EI/CI Source PCB is defective. Replace the EI/CI
Source PCB.
• The ion source temperature sensor (RTD) is defective. Replace the EI/CI Source PCB.

Issue: Source Possible Cause/Solution

heater overheats.
• The ion source temperature sensor (RTD) is defective. Replace the EI/CI Source PCB if
necessary.

Issue: Transfer Possible Causes/Solutions

line will not heat.
• Aux1 zone of the GC is not configured for MS Transfer Line. Configure Aux1 zone of
the GC and set transfer line temperature in the GC Method Editor.
• Transfer line heater elements are defective. Replace the transfer line.
• The transfer line temperature sensor (RTD) is defective. Replace the transfer line.

Issue: Transfer Possible Cause/Solution

line overheats.
• The transfer line temperature sensor is defective. Replace the transfer line.

High Vacuum Issues

High vacuum problems can manifest themselves in two ways:
• An intermittent vacuum condition (the vacuum pressure in the vacuum manifold
fluxuates intermittently) can cause chromatographic signals to drop out, or, if the
pressures exceed the maximum allowed pressures set in Xcalibur (See Table 3 on page 53),
then the TSQ Quantum GC turns off.
• If the vacuum is consistent enough that it does not exceed the maximum allowed pressure
and avoids the Xcalibur automatic shutdown, non-reproducible false chromatographic
peaks can be generated in the chromatogram.

Typical forepressure readbacks are 30 to 40 mTorr (in EI mode), and typical manifold
pressure (ion gauge readback) is 2 × 10-5 Torr with argon collision gas on, and 2 × 10-6 Torr
with Ar collision gas off.

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7 Diagnostics and Troubleshooting
Troubleshooting

The most reliable way to find vacuum leaks is to spray a gas around the vacuum manifold and
look for the characteristics ions in full-scan EI. Argon produces m/z 40. Alternatively, you can
use compressed electronic dusting spray containing an HFC. For example, Falcon®
Dust-Off®and MicroCare® Micro-Blast™ contain tetrafluoroethane, which produces ions at
m/z 69 and 83.

Issue: Forepump will Possible Causes/Solutions

not turn on.
• The forepump is off. Check the forepump switch.
• The vacuum service switch is in the Off position. Place the vacuum service switch in the
operating position.
• The forepump power cable from the TSQ Quantum GC is not connected. Connect the
power cable.
• The forepump is faulty. Replace the forepump.

Issue: Forepump Possible Causes/Solutions

powers on, but will not
pump down. • The oil level in the forepump is insufficient. Check oil level; add oil if necessary.
• The foreline is leaking. Check the clamps and connectors. Replace the foreline hose if a
hole is found.
• The vacuum manifold cover is leaking.
• The forepump is faulty. Replace the forepump.

Issue: Turbo pump Possible Cause/Solution

shuts off during
operation. • The foreline pressure is too high. Check for leaks in the foreline.

Issue: Unexpected full Possible Causes/Solutions

ventilation occurs.
• A gross leak is present. Check for leaks.
• The system was vented through the inlet valve. Close and plug the inlet valve.
• The GC column broke at the transfer line. Replace the GC column. See “Removing and
Installing a GC Capillary Column” on page 104.
• The foreline was cut. Replace the foreline hose.

Issue: Vacuum is faulty. Possible Solutions

• A gross leak is present. Check for leaks.

• The pressure in the analyzer region of the vacuum manifold, as measured by the ion
gauge, must be below the pressures listed in Table 3 on page 53.

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 7 Diagnostics and Troubleshooting
Troubleshooting

Linearity Issues
Linearity issues occur when a plot of intensity versus concentration of a known compound is
not linear. Poor instrument operating conditions can cause linearity problems. Additionally,
certain compounds do not give a desired linear response due to chromatographic activity.

A well-maintained instrument provides good linear response over a wide range of

concentrations for most compounds. Like any instrument, however, the TSQ Quantum GC
has a saturation point.

Perform routine injector and column maintenance to minimize linearity problems. Usually, a
hardware fault that affects linearity shows different issues than those that might be attributed
to linearity.

Issue: Calibration plots Possible Causes/Solutions

not sufficiently linear.
• High-end standards are too concentrated for the MS. Use the split injection technique to
decrease the amount of sample or lower emission current to reduce MS sensitivity.
• The ion volume and lenses are dirty. Clean ion volume and lenses as described in
“Cleaning Ion Source Components” on page 81.
• The electron multiplier setting is incorrect. Run Auto Tune - Calibration as described in
“Tuning and Calibrating” on page 59.
• The injection port liner or capillary column is dirty. Change the injection port liner and
trim the capillary column.
• The capillary column stationary phase is too thin for high concentration samples. Use a
higher capacity capillary column with a thicker stationary phase, or use a split injection
technique.
• The capillary column is bad. Replace the capillary column. See “Removing and Installing
a GC Capillary Column” on page 104.

Power Supply Issues

Xcalibur diagnostics detect most power supply issues. Power supply problems often involve a
blown fuse, faulty electronic components, or something as simple as a disconnected cable.
Fuses should be replaced by a Thermo Fisher Scientific Field Service Engineer.

Issue: TSQ Quantum Possible Causes/Solutions

GC will not power on.
• The power cord is disconnected. Verify that the power cord is plugged in.
• Voltage is not coming from the electrical outlet. Verify that the electrical outlet is
operational.
• The Power Module is faulty. Contact Thermo Fisher Scientific Technical Support.

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7 Diagnostics and Troubleshooting
Troubleshooting

Issue: The TSQ Possible Causes/Solutions

Quantum GC powers on,
but trips the circuit • The Power Module is faulty. Contact Thermo Fisher Scientific Technical Support.
breaker.
• The forepump causes the circuit breaker to trip. Check forepump; replace it if necessary.

Sensitivity Issues
If you observe a drop in instrument sensitivity, you should determine if the sensitivity drop
was sudden or if it occurred gradually. A sudden loss of sensitivity can be the result of sudden
component failure or an unnoticed change in the analytical method. Simple errors such as a
plugged autosampler syringe or too low sample level in the sample vial can give the
appearance of instrument failure.

Gradual drops in sensitivity are usually the result of ion volume or lens contamination, and
are easily remedied by cleaning the ion volume or lenses.

The electron multiplier influences sensitivity and has a limited lifetime. Eventually the
electron multiplier must be replaced.

Improper GC maintenance is another cause of diminished sensitivity. It is important to

establish a routine maintenance program for the GC. See the TRACE GC Maintenance
Manual for more information on establishing a maintenance program.

Issue: The Possible Causes/Solutions

chromatogram has a
low total ion current • The GC temperature ramp does not continue to a high enough temperature to elute high
signal. boiling point compounds. Multiple injections cause these compounds to accumulate in a
column, reducing sensitivity. Extend upper temperature or the time at upper temperature
in the GC oven ramp.
• The instrument is out of tune, or the tune file is incorrect. Select correct tune file for the
method or run automatic tune as described in “Tuning and Calibrating” on page 59.
• The ion volume is contaminated. Clean the ion volume.
• The ion volume is incorrectly positioned. Position the ion volume properly.
• The magnets above and below the ion source are installed incorrectly. Position both
magnets so the south pole is on top. Electrons will not focus into the ion volume if one
magnet is upside down.
• Dust has collected in the Electron Multiplier or on the conversion dynode. Contact
Thermo Fisher Scientific Technical Support.
• The emission current is set too low. Check the setting listed for the emission current.
Choose Tune > Manual and select the Controls tab.
• The ground connection between the electrometer PCB and anode feedthrough is faulty.
Contact Thermo Fisher Scientific Technical Support.

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 7 Diagnostics and Troubleshooting
Troubleshooting

• There is a problem with the filament or lens control. See “Filament and Lens Control
Issues” on page 117 for more information.
• The EI/CI Source PCB is faulty, allowing emission current to leak to ground. Contact
Thermo Fisher Scientific Technical Support.
• Reagent gas is leaking into the analyzer, suppressing EI signal. Check for presence of CI
Reagent ions in spectrum. Replace CI Gas Flow Module if necessary.

Issue: Poor Possible Causes/Solutions

compound sensitivity.
• The syringe, injection port liner, and column depth in injector are incorrectly matched.
See TRACE GC Operators Manual for the correct combination.
• Sample delivery is insufficient due to a plugged syringe needle. Clean or replace the
syringe.
• The injection port liner is contaminated. Clean or replace the injection port liner.
• Graphite or septa particles contaminate the injection port. Clean the injection port.
• The injector or septum is leaking. Replace septum and perform leak check on the GC.
• The capillary column is at the end of its life span. Replace the capillary column.
• Method development problems are present. Contact Thermo Fisher Scientific Technical
Support.

Issue: Sensitivity is Possible Causes/Solutions

unstable or shows
decrease with repeated • The GC temperature ramp does not continue to a high enough temperature to elute high
injections. boiling point compounds. Multiple injections cause these compounds to accumulate in a
column, reducing sensitivity. Extend the upper temperature or the time at upper
temperature in the GC oven ramp.
• The ion volume or lenses are contaminated. Clean the ion volume and lenses as described
in “Cleaning Ion Source Components” on page 81.
• The ion source temperature is too low and causes the ion source to contaminate too
quickly. Clean ion volume and lenses as described in “Cleaning Ion Source Components”
on page 81 and then raise ion source temperature.
• There is a problem with the filament emission current control. See “Filament and Lens
Control Issues” on page 117 for more information.
• The electron multiplier is faulty. Contact Thermo Fisher Scientific Technical Support.
• The injection port liner or capillary column is contaminated. Replace the injection port
liner and trim the capillary column.

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7 Diagnostics and Troubleshooting
Troubleshooting

Issue: Poor Possible Causes/Solutions

sensitivity in
CI mode. • An EI ion volume is installed. Install a CI ion volume as described in “Changing
Ionization Modes” on page 69.
• The small hole in the CI ion volume is plugged. Use a dental pick or old syringe needle to
clear it.
• The filament is not aligned. Remove the ion volume and check if the ion burn is centered
around the small electron entrance hole. Be sure the filament is properly inserted into the
connector. Carefully bend the filament wire to better align it with the ion volume.
• The ion volume is not inserted properly. While running the instrument, you can push on
the ion volume with the I/R Tool. Be sure to monitor the pressure to ensure that you get
a good seal around the I/R Tool. Otherwise, you may damage the filament. An increase in
signal calibration gas as you push on the ion volume usually indicates that the filament is
not aligned properly.

Stability Issues
Stability helps provide consistent instrument precision and the reproducibility of accurate
results. Good operating conditions for the mass spectrometer, gas chromatograph, and
autosampler contribute to instrument stability.

Sample preparation, spiking errors, sample injection errors, and lack of routine maintenance
on the instruments can cause false stability issues.

When hardware faults affect instrument stability, investigate simple solutions first, such as
cleaning the ion volume and lenses, or checking for air leaks. Usually, a hardware fault that
affects stability shows different issues than those which might be attributed to stability.

Issue: The signal Possible Causes/Solutions

response is unstable or
drops out unexpectedly. • There is a problem with the filament or lens control. See “Filament and Lens Control
Issues” on page 117 for more information.
• There is an air leak. Check for leaks. See “High Vacuum Issues” on page 119 for more
information.
• There is a high vacuum problem. See “High Vacuum Issues” on page 119 for more
information.
• There is a contamination problem. See “Contamination Issues” on page 115 for more
information.
• Dust has collected in the electron multiplier or on the conversion dynode. Contact
Thermo Fisher Scientific Technical Support.

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 7 Diagnostics and Troubleshooting
Troubleshooting

Tuning Issues
You can suspect a tuning problem when Xcalibur Auto Tune - Calibration fails. Auto Tune -
Calibration performs several functions, and issues or error messages indicate different
problems. Diagnostics can usually uncover a tuning problem.

Issue: “Cannot find Possible Causes/Solutions

Calibration Gas” error
message received. • There is a mechanical problem with the ion source or lenses. Verify that an EI ion volume
is installed. Verify correct orientation and cleanliness of ion volume. Verify cleanliness
and correct operation of lenses.
• Tune file settings are out of usable range. Restore default tune settings and calibration
settings. Run Auto Tune - Calibration. See “Tuning and Calibrating” on page 59.
• The calibration gas vial is empty. Add 100 µL (max) of calibration compound to
calibration gas vial. See “Adding Calibration Compound” on page 99.

Issue: The electron Possible Causes/Solutions

multiplier gain
calibration fails. • The electron multiplier has not been given sufficient time to outgas since venting. Allow
more time to pump out.
• The GC column flow is too high. Lower it to1 mL/min.
• The multiplier is near the end of its lifetime. Multipliers typically last about 2 to 3 years
before they are too noisy for the gain to be set accurately. Contact Thermo Fisher
Scientific Technical Support.
• The multiplier power supply is faulty. Contact Thermo Fisher Scientific Technical
Support.
• The filament is the source of too much background noise. See “Filament and Lens
Control Issues” on page 117 for more information.
• Chemical background in the manifold is elevated. Remedy leaks or sources of water
contamination in carrier gas. See “High Vacuum Issues” on page 119 for more
information.
• The difference between the electron energy and the setpoint is greater than 5 V. Contact
Thermo Fisher Scientific Technical Support for assistance.

Issue: Poor Possible Causes/Solutions

high mass
response. • Poor high m/z ion intensity because the ion source temperature is too high. Reduce the
ion source temperature to reduce the amount of thermal decomposition and
fragmentation of your analyte.
• Poor high m/z ion intensity because of bad ion source lens settings. Run Auto Tune -
Calibration. See “Tuning and Calibrating” on page 59.

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7 Diagnostics and Troubleshooting
Troubleshooting

• Helium pressure in the ion source is too high or low. Set flow to 1.0 mL per minute for
most applications.
• There is a vacuum leak. Find and repair any leaks. Be sure to check the transfer line fitting
in the GC oven. See “High Vacuum Issues” on page 119 for more information.
• An excess amount of low m/z ions, such as hydrocarbons or column bleed. Remedy the
source of these low m/z ions.
• The ion volume or lenses are contaminated. Clean the ion volume or lenses. See
“Cleaning Ion Source Components” on page 81.
• m/z 131 is not base peak because the multiplier gain is too low. The multiplier gain
calibration may set the multiplier voltage too low for a noisy multiplier. Electron
multipliers older than 2 to 3 years are often noisy. Contact Thermo Fisher Scientific
Technical Support.
• There is poor high m/z intensity and poor resolution of low m/z ions because the
conversion dynode is faulty. Contact Thermo Fisher Scientific Technical Support.
• The injection RF is not calibrated. Run Auto Tune - Calibration as described in “Tuning
and Calibrating” on page 59.
• There is a problem with the filament or lens control. See “Filament and Lens Control
Issues” on page 117 for more information.
• Reagent gas is leaking into the analyzer, suppressing EI signal. Check for the presence of
CI Reagent ions in spectrum. Replace the CI Reagent Gas Flow Module if necessary.

Issue: Weak signal. Possible Causes/Solutions

• The ion volume or ion source lenses are dirty. Clean the contaminated components as
described in “Cleaning Ion Source Components” on page 81.
• The multiplier is set too low. Run multiplier gain calibration in Auto Tune - Calibration
as described in “Tuning and Calibrating” on page 59. An electron multiplier older than
2–3 years may be too noisy for the multiplier gain calibration to accurately set the voltage.
The electron multiplier might need to be replaced. Contact Thermo Fisher Scientific
Technical Support.
• The wrong type of ion volume is installed. EI and CI require different ion volumes. They
may not be used interchangeably. Change the ion volume as described in “Changing
Ionization Modes” on page 69.
• The ion volume is absent or incorrectly positioned. Verify that the ion volume is
positioned correctly.
• There is a filament or lens control problem. See “Filament and Lens Control Issues” on
page 117 for more information.
• The electron multiplier is faulty. Contact Thermo Fisher Scientific Technical Support.

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 7 Diagnostics and Troubleshooting
Replacing a Fuse

Replacing a Fuse
CAUTION Fuses protect the various circuits by opening the circuits whenever overcurrent
occurs. On the TSQ Quantum GC mass spectrometer, a failed fuse indicates a failed
board or electronic module that must be replaced by a Thermo Fisher Scientific Field
Service Engineer.

Replacing PCBs and Power Supplies

CAUTION The TSQ Quantum GC mass spectrometer electronic assemblies are

close-packed to minimize the size of the system. Due to the complexity of removing and
reinstalling the TSQ Quantum GC mass spectrometer electronic assemblies, only a
Thermo Fisher Scientific Field Service Engineer can replace electronic assemblies.

Thermo Scientific TSQ Quantum GC User Guide 127

 8

Using the Direct Sample Probe

With the direct sample probes (direct insertion probe and direct exposure probe) you can
introduce compounds directly into the ion source without GC column separation. This
chapter covers, step-by-step, a direct insertion probe (DIP) experiment using
perfluorotetracosane (CF3(CF2)22CF3, molecular weight 1238.18, melting point 190 ºC).
You can perform a similar experiment using your compound.
P

Contents
• Creating an Instrument Method
• Creating a Sequence

• Preparing the Probe and Inlet Valve

• Preparing the Mass Spectrometer

• Running the Sequence

• Examining the Raw Data in Qual Browser

• Removing the Probe

Creating an Instrument Method

An instrument method contains the settings that the TSQ Quantum GC uses during an
experiment. Use the Instrument Setup view to create the instrument method.

Y To create an instrument method

1. On the Xcalibur Home Page, click the Instrument Setup icon to open the Instrument
Setup view. Click the Scan Editor tab.
2. On the Scan Editor page, create a one segment, one scan event instrument method. In
this example, the segment is 8 minutes long (see Figure 55).
3. Specify the mass spectrometer settings, for this example, full-scan scan type, Q1MS scan
mode, and positive polarity.

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8 Using the Direct Sample Probe
Creating an Instrument Method

Figure 55. Scan Editor page of Instrument Setup

4. Click the EI/CI tab to display the EI/CI page (see Figure 56).

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 8 Using the Direct Sample Probe
Creating an Instrument Method

Figure 56. EI/CI page of Instrument Setup

5. Enter or select the following settings:

• Number of States: 1

• State at Start of Run: On

• Calibration Gas Setting: Off

• Use DIP/DEP Probe:

This example is an EI experiment with a 200 µA emission current.

6. Save the instrument method.

a. Choose File > Save As to open the Save As dialog box.

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8 Using the Direct Sample Probe
Creating a Sequence

b. Save the instrument method as a .meth file. In this example we name the instrument
method Dip [Link].

Creating a Sequence
A sequence contains sample information—one sample per row. In this example the sequence
has one sample.
Note If the sequence has more than one sample, Xcalibur prompts you to reload the
probe after each sample.

Y To create a sequence

1. On the Xcalibur Home Page, click the Sequence Setup icon to open the Sequence Setup
view (see Figure 57).

2. Enter the name and path of the instrument method. In this example, it is
C:\Xcalibur\methods\DIP test.

3. Enter a file name and path for the raw file that contains the acquired data. In this
example, it is C:\Xcalibur\Data\data01.
Figure 57. Sequence Setup view, showing one sample in the sequence

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 8 Using the Direct Sample Probe
Preparing the Probe and Inlet Valve

Preparing the Probe and Inlet Valve

Y To prepare the probe and inlet valve

1. Connect the direct sample probe controller to the mass spectrometer by contact closure
with the probe start cable (P/N 70111-63627, in TSQ Quantum GC Accessory Kit).

2. Create a probe method on the controller. Refer to the probe manual. This example uses
the following DIP settings:

• Initial temperature: 50 ºC

• Initial time: 5 s
• Ramp rate: 100 ºC/min

• Final temperature: 200 ºC

• Ramp hold time: 200 s

3. Load sample on the probe.

4. Install the guide bar.

a. With the guide ball track facing left, insert the guide bar into the entry housing. See
Figure 15 on page 26.
b. Push the guide bar in as far as it goes. Rotate it 90° clockwise to lock the guide bar in
the entry housing.
5. Prepare the inlet valve.
a. Make sure the inlet valve is closed with the inlet valve lever down, as shown in
Figure 15 on page 26.
b. Loosen the inlet valve knob counter-clockwise, and remove the inlet valve plug.

Preparing the Mass Spectrometer

Y To prepare the TSQ Quantum GC for the experiment

1. Choose Start > All Programs > Xcalibur > Quantum Tune to open the Tune Master
window if it is not already open. See Figure 58.

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8 Using the Direct Sample Probe
Preparing the Mass Spectrometer

Figure 58. Quantum Tune Master view

2. Ensure that the TSQ Quantum is the only instrument in use and that there are no start
instruments.

a. On the Xcalibur Home Page, click the Sequence Setup icon to open Sequence
Setup, if it is not already open.
b. In Sequence Setup, choose Actions > Run Sequence. The Run Sequence dialog box
opens (see Figure 59).

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 8 Using the Direct Sample Probe
Preparing the Mass Spectrometer

Figure 59. Run Sequence dialog box, showing instruments in use

c. Click Change Instruments to open the Change Instruments In Use dialog box.
Figure 60. Change Instruments In Use dialog box, showing TSQ Quantum in use and no
start instruments

d. Click any Yes in the In Use column to clear all instruments other than the TSQ
Quantum.

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8 Using the Direct Sample Probe
Running the Sequence

e. Ensure that the TSQ Quantum GC has a Yes in the In Use column. Click the area if
necessary.
f. Click any Yes in the Start Instrument column to clear all start instruments.

3. Click OK to save your settings and close the Change Instruments In Use dialog box.

Running the Sequence

You acquire data by running the sequence. Xcalibur saves the acquired data in a raw file.
Note You must have Quantum Tune Master or QuickQuan running so that
Xcalibur can display instrument methods.

Y To run the sequence

1. In the Run Sequence dialog box (see Figure 59 on page 135), click OK to start the
acquisition. Xcalibur displays the Insert Probe message.
Figure 61. Insert Probe message

2. Inset the probe into the inlet valve.

a. Insert the guide ball on the DIP probe into the guide ball hole on the guide bar.
b. Slide the probe forward into the inlet valve until the guide ball is at the guide bar’s
first stop. See Figure 62.
c. Tighten the inlet valve knob clockwise to ensure a leak-tight seal.

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 8 Using the Direct Sample Probe
Running the Sequence

Figure 62. Probe at the first stop on guide bar

3. Click OK. The forepump evacuates the inlet valve.

4. When the Safe to Open Valve message to appears, click OK.

Figure 63. Safe to Open Valve message

5. Pull the inlet valve lever up to open the inlet valve.

6. Slide the probe into the vacuum manifold until the tip of the probe is fully inserted into
the ion volume holder. See Figure 64.

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8 Using the Direct Sample Probe
Running the Sequence

Figure 64. Probe inserted into the inlet valve

7. When you receive the Acquisition Ready message, click OK. The Quantum GC is now
waiting for contact closure.
Figure 65. Acquisition Ready message
.

8. In Sequence Setup, choose View > Real Time Plot View to display the mass spectrum
and chromatogram.

9. Start the probe method from the probe controller to initiate data acquisition. See
Figure 66 and Figure 67.

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 8 Using the Direct Sample Probe
Running the Sequence

Figure 66. Perfluorotetracosane mass spectrum at 0.56 minute retention time

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8 Using the Direct Sample Probe
Examining the Raw Data in Qual Browser

Figure 67. Perfluorotetracosane chromatogram

Examining the Raw Data in Qual Browser

You can use Qual Browser to display the mass spectrum at various times in the
chromatogram.

Y To examine the raw data

1. On the Xcalibur Home Page, click the Qual Browser icon to open the Qual Browser
window.

2. Click on the chromatogram to display the mass spectrum at that retention time. See
Figure 68.

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 8 Using the Direct Sample Probe
Removing the Probe

Figure 68. Raw file displayed in Qual Browser

Removing the Probe

Y To remove the probe

1. Withdraw the probe until the guide ball on the probe reaches the first stop on the guide
bar (Figure 62).
2. Close the inlet valve by pushing the lever down.

CAUTION Close the inlet valve first. Otherwise, the system vents to the atmosphere.
Do not withdraw the probe beyond the point where the guide ball reaches the first
stop in the guide bar.

3. Loosen the inlet valve knob by turning it counter-clockwise.

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8 Using the Direct Sample Probe
Removing the Probe

4. Continue withdrawing the probe completely from the inlet valve by sliding it through the
guide ball track in the guide bar.

5. Store the probe in its case.

6. Remove the guide bar by rotating it 90° counter-clockwise and sliding it out of the entry
housing.

7. Replace the inlet valve plug and tighten the inlet valve knob clockwise to form a seal. The
inlet valve plug prevents air from entering the vacuum manifold in case the inlet valve is
accidentally opened. You can also remove the inlet valve lever by pulling it free.

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 9

Replaceable Parts and Consumables

This chapter contains TSQ Quantum GC part numbers for replaceable parts and
consumables. To ensure proper results in servicing the Quantum GC system, order only the
parts listed or their equivalent. Contact Thermo Fisher Scientific San Jose and have your TSQ
Quantum GC serial number ready.

These kits with replaceable parts and consumables are available for the TSQ Quantum GC:

Contents
• Accessory Kit
• Chemicals Kit

Accessory Kit
Table 7. TSQ Quantum GC Accessory Kit (P/N 70111-62077) (Sheet 1 of 2)
Description Function Part Number
Fitting, ferrule, SWG, 1/8-in., brass, set 00101-08-00009
Fitting, connection, 1/4 to 1/8-in. 00101-01709
Fitting, connection, 1/4 to 1/8-in. 00101-01712
Fitting, ferrule, SWG, front, 3/8-in., 00101-11500
brass
Ferrule, 0.4mm ID × 1/16 00101-18100
Restek® capillary-grade hydrocarbon For removing hydrocarbons from the GC 00106-99-00001
trap carrier gas
Restek high-capacity oxygen trap For removing oxygen from the GC carrier 00106-99-00002
gas
Cotton swabs For applying cleaning paste to stainless 00301-01-00015
steel parts
Tubing, 1/8-in., copper, pre-cleaned Gas lines 00301-22701
Ball valve seal kit (replacement) For replacing the ball valve seal in the inlet 119265-0003
valve
Lens alignment tool For aligning ion source lenses 1, 2, and 3 120271-0001

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9 Replaceable Parts and Consumables
Chemicals Kit

Table 7. TSQ Quantum GC Accessory Kit (P/N 70111-62077) (Sheet 2 of 2)

Description Function Part Number
Filament assembly For replacing a failed filament in the ion 120320-0030
source
Nitrile gloves medium For handling clean parts that are under 23827-0008
vacuum
Nitrile gloves large For handling clean parts that are under 23827-0009
vacuum
Syringe, 10 uL, 80mm For adding calibration compound 36502019
Tee union, 1/8-in. 00101-01-00012
Cable, start, probe Contact closure cable between the direct 70111-63627
sample probe and the mass spectrometer
Cable, start, GC Contact closure cable between the GC and 70111-63626
the mass spectrometer
Forceps, 10-in., stainless steel For handling ion volumes and clean 76360-0400
components
Cable, 10 base-T, crossover, 15-ft, 76396-0052
shielded

Chemicals Kit
Table 8. TSQ Quantum GC Chemicals Kit (P/N 70111-62078)
Description Function Part Number
Perfluorotributylamine (FC-43) Tuning and calibration compound 50010-02500
Aluminum Oxide Cleaning stainless steel parts 32000-60340
Benzohexane Performance testing 120150-TEST
Octafluoronaphthalene Performance testing 120150-TEST

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 I

Index
A mass spectrum, displaying 60
observed peaks 60
Accessory Kit 143
on, off 60
aluminum oxide 144
spectrum, positive EI mode 61
analyzer assembly, lenses, voltages applied to 35
calibration compound vial
analyzer chamber, location (figure) 39 location (figure) 100
Analyzer Control PCB, discussion 44 removing and reinstalling 100
analyzer region, vacuum manifold, description 38 calibration gas valve, description 42
analyzer region, vacuum manifold, location 38 capillary column
anode, electron multiplier, description 36 conditioning 107
Auto Tune - Calibration 62 installing 106
autosampler removing 104
configuration 16 removing ion source (Caution) 84
photo 2 cathode, electron multiplier, description 35
power outlet 22 Cautions
startup 51, 54 emergency shutdown 21, 47
TriPlus 16 forepump and line power 41
troubleshooting communication problems 115 I/R tool removal, withdrawing 75
AutoSIM scan type 13 Ion Source PCB removal 94
removing ion source and capillary column 84
B replacing fuses 127
replacing PCBs and power supplies 127
ball valve centroid scan, defined 13
extraction tool (figure) 103
chemical ionization (CI)
extraction tool, using 103
discussed 3
seal, replacing 103
gas valve, description 42
ball valve seal kit 143 ion volume 25
benzohexane 144 methane 3
removing ion volume 69
C Chemicals Kit 144
cables 144 circuit breaker 21, 22
calibrating cleaning
and H-SRM (note) 59 aluminum parts 97
discussed 59 ceramic parts 97
frequency (note) 59 frequency 79
running 62 ion volumes 83
System Tune and Calibration workspace 60 lenses L1, L2, L3, L4 83
tune and calibration report 64 list (table) 79
calibration compound stainless steel parts 95
adding 99
flow control, description 42

Thermo Scientific TSQ Quantum GC User Guide 145

Index: D

collision cell direct sample probe

figure 30 and inlet valve 133
location (figure) 39 direct exposure probe (DEP) 18
collision energy (Q2 offset voltage) 34 direct insertion probe (DIP) 18
collision gas inserting into inlet valve (figure) 137
description 32 mass spectrometer, preparing 133
collision gas valve, description 41 photo 18
collision-induced dissociation using 129
discussion 32 dynode 35
column bleed contamination 115
Communication LED E
description 20 EI/CI on Source PCB
figure 20 location (figure) 24, 84, 92
mass spectrometer reset 55 reinstalling 94
mass spectrometer startup 53 removal 94
computer, features 44 removal (Caution) 94
consumables 143 electron ionization (EI)
contamination discussed 3
column bleed 115 ion volume 25
septum bleed 115 removing ion volume 69
solvent ions 117 electron multiplier
troubleshooting 115 anode, description 36
Convectron gauge, description 41 description 35
conversion dynode figure 36
description 35 electronic assemblies
figure 36 description 42
ion detection system 43
D Power Entry Module, description 42
RF voltage generation, description 43
data-dependent scan mode, discussed 11
electronics service switch
data system
description 22
description 44
location (figure) 22, 23
GC interface 45
mass spectrometer components On/Off status 57
instrument interface 45
embedded computer
LAN interface 45
description 43
personal computer 44
resetting 54
primary Ethernet adapter 45
resetting 55 emergency shutdown
Caution 21
shutdown 51
front panel System Power Off button 21
data types, discussed 13
procedure 47
detector system 35 System Power Off button 47
diagnostics
Ethernet 45
password protection 111
Ethernet Link OK LED 23
running 111
DIP, example procedure
1 creating an instrument method 129 F
2 creating a sequence 132 FC-43
3 preparing the probe and inlet valve 133 adding 99
4 preparing the mass spectrometer 133 mass spectrum, displaying 60
5 running the sequence 136 observed peaks 60
6 examining the data 140 on, off 60
perfluorotetracosane 129 part number 144

146 TSQ Quantum GC User Guide Thermo Scientific

 Index: G

spectrum, positive EI mode 61 startup 51, 52

ferrules 143 troubleshooting communication problems 115
filament guide bar
description 25 figure 26, 70
location (figure) 24, 91 intalling 69
on, off 60
part number 90 H
problems, troubleshooting 117
replaceable parts 144 hydrocarbon trap 143
replacing 90
fittings 143 I
forepump inlet gasses hardware
description 40 calibration compound 42
maintenance 98 CI gas valve 42
power cord (Caution) 41 collision gas valve 41
power outlet (figure) 23 description 37
front panel LEDs functional block diagram 38
Communication 20 inlet valve
description 20 and direct sample probe 133
figure 20 Caution 75
Power 20 components (figure) 71
Scan 21 description 26
System 21 figure 26
Vacuum 20 guide bar 26
front panel System Power Off button Insert Probe message 71
figure 21 insertion/removal (I/R) tool, inserting 72
full scan type 11 ion volumes, installing 76
functional description lever, removing 78
autosampler 16 plug orientation 78
data system 44 procedure 70
direct sample probes 18 safe to insert probe message 73
gas chromatograph (GC) 17 Insert Probe message (figure) 71
inlet valve 26 insertion/removal (I/R) tool
ion optics 27 figure 26, 70
mass analyzer 28 inserting 72
mass spectrometer 19 ion volumes, removing and installing 75
Q0 quadrupole 27 lock position 74
transfer line 18 unlock position 70
TSQ Quantum GC 15 withdrawal (Caution) 75
fuses, mass spectrometer, replacing 127 Instrument Configuration window, opening 16, 17
instrument method, creating 129
G ion detection system
conversion dynode 35
gas chromatograph (GC)
description 35
capillary column, installing 106
electron multiplier 35
capillary column, removing 104
electron multiplier gain 36
column installation 106
electronic assemblies 43
communication with data system 45
configuring 17 ion gauge
functional description 17 description 41
leak check 107 location (figure) 39
photo 2 ion optics
power outlet 22 description 27

Thermo Scientific TSQ Quantum GC User Guide 147

Index: L

ion polarity modes,discussed 5 Power LED, mass spectrometer startup 53

ion source Pump On, location (figure) 23
cleaning 90 Scan LED 21
cleaning components 81 System LED 21
cross sectional view (figure) 28 System LED, mass spectrometer reset 55
description 23 System LED, mass spectrometer startup 53
disassembling completely 92 Vacuum LED 20, 20
electrical connections 84 Vent Valve Closed 22, 22
exploded view (figure) 82 Vent Valve Closed (figure) 23
figure 24 lens alignment tool 143
filament, replacing 90 lens L1, L2, L3, and L4
ion source lenses, reinstalling 89 location (figure) 24
Ion Source PCB, location (figure) 93 lenses
lens assembly, disassembling 87 analyzer assembly, voltages applied to 35
lens assembly, exploded view 88 ion source lenses exploded view 88
lens assembly, removing 86 ion source lenses, reassembling 89
lenses, cleaning 83 ion source lenses, reinstalling 89
lenses, reassembling 89 L1, L2, L3 exploded view 88
location (figure) 84 L1, L2, L3, L4 location (figure) 24
reinstalling 89 L1, L2, L3, L4, cleaning 83
removing 84 L21, L22, L23, figure 30
ion source block L31, L32, L33, figure 30
location (figure) 24 linearity problems, troubleshooting 121
ion source chamber
location (figure) 39
ion transmission device
M
defined 5 main power circuit breaker
rod assembly 6 description 21, 22
ion volumes location (figure) 22
attaching and removing from I/R tool 75 maintenance
cleaning 83 ball valve seal, replacing 102
description 25 forepump 98
figure 25 frequency 79
installing 76 GC column installation 106
location (figure) 77 ion source filament, replacing 90
removing 69 ion source lenses, cleaning 83
ionization modes ion volumes, cleaning 83
changing 69 keys to success (note) 79
chemical ionization (CI) 3 procedures (table) 79
discussed 3 mass analysis
electron ionization (EI) 3 collision-induced dissociation 32
discussion 30, 32
RF and dc fields (figure) 30
L mass analyzer
leak check, GC 107 defined 6
LEDs description 28
Communication LED 20 quadrupole rod assembly, functional description 29
Communication LED, mass spectrometer reset 55 mass range 13
Communication LED, mass spectrometer startup 53 mass spectrometer
Ethernet Link OK 22, 23 and direct sample probe 133
Forepump On 22 calibrating 67
Power LED 20 CI gas valve 42
Power LED, mass spectrometer reset 55 circuit breaker, location (figure) 23

148 TSQ Quantum GC User Guide Thermo Scientific

 Index: N

collision gas valve 41 O

diagnostics 111
octafluoronaphthalene 144
electronic assemblies 42
Off condition, mass spectrometer components
electronics service switch, location (figure) 23
On/Off status 57
emergency shutdown 47
front panel LEDs 20 offset voltage, quadrupole 33
functional description 19 oxygen trap 143
fuses, replacing 127
inlet gasses hardware 37 P
inlet valve (figure) 26
Parent scan mode
ion detection system 35
discussed 8
ion detection system electronic assemblies 43
illustration (figure) 8
ion gauge 41
password protection
ion optics 27
diagnostics 111
ion source 24
tuning and calibrating 67
LEDs and system startup 55
maintenance procedures (table) 79 perfluorotetracosane 140
mass analyzer 28 personal computer, features 44
Off condition 57 phthalate contamination 115
On/Off status of components 57 power cord, forepump (Caution) 41
Power Entry Module, description 42 Power Entry Module, description 42
power outlet 22 Power LED
Q0 quadrupole 27 description 20
resetting 54 figure 20
RF voltage generation electronic assemblies 43 mass spectrometer reset 55
right-side power panel 50 mass spectrometer startup 53
shutdown 49 power supply problems, troubleshooting 121
Standby mode 48, 57 pressure, maximim allowed (table) 53
startup 51 probe button 71
tuning 67
procedures
turbomolecular pump 40
adding calibration compound 99
vacuum manifold 38
changing ionization modes 69
vacuum service switch, location (figure) 23
cleaning ion source components 81
vacuum system 37
cleaning ion source lenses 83
vent valve 41
cleaning ion volumes 83
mass spectrometer circuit breaker cleaning stainless steel parts 95
location (figure) 23 complete system shutdown 49
mechanical pump 40 conditioning capillary columns 107
MS main power circuit breaker disassembling ion source lens assembly 87
mass spectrometer components On/Off status 57 displaying FC-43 spectrum 60
MS/MS scan modes dissassembling ion source completely 92
Neutral Loss 9 emergency shutdown 47
Parent 8 GC leak checking 107
Product 6 installing capillary column 106
installing the ion volume 76
N maintaining forepump 98
operating the inlet valve 69
Neutral Loss scan mode placing system in standby 48
discussed 9 reassembly ion source lenses 89
example (figure) 10 reinstalling ion source 89
illustration (figure) 10 reinstalling ion source lenses 89
reinstalling Ion Source PCB 94
removing capillary column 104

Thermo Scientific TSQ Quantum GC User Guide 149

Index: Q

removing ion source 84 RF/dc voltages applied to mass analyzer, discussion 29

removing ion source lens assembly 86 RF voltage generation, discussion 43
removing the ion volume 69 right-side power panel
replacing filament 90 description 50
replacing ion source filament 90 figure 23, 50
resetting mass spectrometer 54 rod assemblies
saving tune and calibration report 66 description 30
starting mass spectrometer 52 ion transmission 6
system startup 51 mass analysis 6
tuning and calibrating 62 mass analyzer(s), quadrupole 29, 32
Product scan mode Q1, Q2, and Q3 (note) 7
discussed 6 roughing pump 40
illustration (figure) 7
profile scan, defined 13
pumps
S
forepump 40 safe to open vValve message
turbomolecular pump 40 direct sample probe 137
safety precautions vi
scan data types
Q centroid scan 13
Q0 quadrupole profile scan 13
cross sectional view (figure) 28 Scan LED
description 27 description 21
figure 27 figure 20
location (figure) 39
scan modes
Q1 quadrupole data dependent 11
figure 29 discussed 5
scan modes 5 mass spectrometer 5
Q1MS and Q3MS scan modes 6 Neutral Loss 9
Q2 rod assembly Neutral Loss, example (figure) 10
figure 30 Neutral Loss, illustrated (figure) 10
scan modes 5 Parent 8
Q3 quadrupole Parent, illustrated (figure) 8
figure 29 Product 6
scan modes 5 Product, illustrated (figure) 7
quadrupole mass analyzer Q1MS and Q3MS 6
functional description 29, 32 summary (table) 6
quadrupole offset voltage 33 scan types
quadrupoles AutoSIM 13
mass analysis 29, 32 discussed 11
Q0, description 27 full scan 11
Q1 and Q3 29 selected ion monitoring (SIM) 12
RF and dc fields 30 selected reaction monitoring (SRM) 12
RF and dc fields (figure) 30, 31 selected ion monitoring (SIM) scan type 12
Qual Browser selected reaction monitoring (SRM) scan type 12
direct sample probe data 140 sensitivity problems, troubleshooting 122
reviewing data 140 septum bleed contamination 115
sequence 132
R creating 132
direct sample probe, running 136
rear power panel
Sequence Setup view 132
location (figure) 48
replaceable parts 143

150 TSQ Quantum GC User Guide Thermo Scientific

 Index: T

shutdown figure 19
data system 51 functional description 18
emergency procedure 47 location (figure) 84
emergency, front panel system power off button 21 union (figure) 105
mass spectrometer 49 TriPlus autosampler
non-emergency 49 cofiguration 16
side cover plate (vacuum manifold), description 40 photo 2
solvent ions masses 117 troubleshooting
solvents autosampler communication 115
purity requirements vii communication 113
spectrometer 13 contamination 115
stability problems, troubleshooting 124 filament and lens control 117
stainless steel, cleaning 95 gas chromatograph communication 115
heated zones 118
Standby mode
high vacuum 119
mass spectrometer components On/Off status 57
linearity 121
placing system in 48
power supplies 121
startup 51
sensitivity 122
autosampler 54
stability 124
gas chromatograph (GC) 52
tuning 125
operating conditions, setting 54
TSQ Quantum GC
System Control PCB, description 43
autosampler 16
System LED calibrating 59
figure 20 data system 44
mass spectrometer reset 55 data types 13
mass spectrometer startup 53 diagnostics 111
system power off button front panel LEDs 20
emergency shutdown 21 functional block diagram (figure) 15
location (figure) 48 functional description 15
system reset button gas chromatograph 17
description 22 ion polarity modes 5
location (figure) 22 LEDs and system startup 55
mass spectrometer reset 55 mass range 13
system shutdown mass spectrometer 19
emergency procedure 47 operating conditions, setting 54
System Tune and Calibration workspace overview 1
displaying 60 photo 2
figure 61, 63 scan modes 5
scan types 11
T shutdown 51
Standby condition 48, 49
tables startup 51
Accessory Kit 143 tuning 59
Chemicals Kit 144 tune and calibration report
mass spectrometer components on/off status 57 figure 65
mass spectrometer maintenance procedures 79 saving 64
maximum allowed pressures 53
tuning
summary of scan modes 6
discussed 59
TRACE GC Ultra gas chromatograph
frequency (note) 59
configuration 17
password protection 67
photo 2
running 62
transfer line System Tune and Calibration workspace 60
capillary column, removing 105 tune and calibration report 64
cross sectional view (figure) 28

Thermo Scientific TSQ Quantum GC User Guide 151

Index: V

tuning problems, troubleshooting 125

turbomolecular pump, description 40

V
Vacuum LED
and analyzer region pressure 20
description 20
figure 20
vacuum manifold
description 38
feedthroughs 39
location (figure) 39
side cover plate, description 40
vacuum pumps
forepump 40
turbomolecular pump 40
vacuum service switch
description 22
location (figure) 23
On/Off status of mass spectrometer components 57
vacuum system
collision gas valve 41
Convectron gauge 41
description 37
forepump 40
functional block diagram (figure) 38
ion gauge 41
maximum allowed pressures 53
powering off 22
problems, troubleshooting 119
turbomolecular pump 40
Vacuum LED 20
vacuum service switch 22
vent valve 41
vent valve
description 41
LED 22
Vent Valve Closed LED 22
voltages
conversion dynode 35
Q0 offset 27
quadrupole RF and DC 30

152 TSQ Quantum GC User Guide Thermo Scientific