Clinical Chemistry 56:6

897–901 (2010) Clinical Chemistry

Guide to Scientific Writing

Who, What, When, Where, How, and Why:

The Ingredients in the Recipe for a Successful
Methods Section
Thomas M. Annesley*

In a prior article on abstracts I discussed the need, when ondary consideration after clarity and adequate detail.
writing a paper, to tell the story by answering ques- As long as you help readers reach the goals listed above,
tions. If I extended that concept by asking what ques- your Methods section should be as long as necessary to
tion(s) the Methods section of a paper answers, the first describe the important experiments in your study.
response that comes to my mind is “How did I perform The importance of each question in Table 1 and
the study?” Yet “how” is just one of the main ingredi- the amount of detail required can vary depending on
ents in the recipe for a successful Methods section. An the type of study and the target audience. For example,
informative Methods section also starts with 1 part if you are comparing 2 analytical methods for quanti-
what, 1 part when, 1 part where, 1 part who, and 1 part fying serum human chorionic gonadotropin and need
why. As with any recipe, the proportions of each can be to identify specimens from healthy individuals, preg-
modified to taste, depending on the study type and nant women, or patients with renal failure or cancer,
journal format, but each must be added lest someone you might rely on the existing medical record and the
notice that something seems to be missing from the prior judgment of several clinicians. Detailing where
final product. the diagnosis was made (e.g., clinic vs hospital) or who
The Methods section is also called the Materials made the diagnosis (e.g., attending physician vs resi-
and Methods, Patients and Methods, Study Design, or dent) becomes less important to the reader than detail-
Experimental section. The goals of this section are to ing what protocols were followed to compare the as-
allow readers to (a) understand how and why the ex- says, where the analyses were performed, and what
periments were performed, (b) better understand the instruments were used.
remainder of the paper and how the results and con- By comparison, if you are doing a clinical study for
clusions derived from the experiments, (c) be able to which a diagnosis, histopathology interpretation, or re-
reproduce the study with an expectation of success, and sponse to treatment is the major outcome, then who
(d) acknowledge that the results and conclusions are made the diagnosis or what diagnostic criteria were
valid based on the strength of the methods and study used become key details compared with who in the
design. Making sure to include the important details central laboratory tested the patient’s blood or what
about who, what, when, where, how, and why in the was the analytical principle behind the commercial
study can help achieve these goals. I have listed in Table method used. In the second example you still want to
1 some example questions that, depending on the state that the testing was performed in the central lab-
study, might be important to answer for the reader. In oratory on a specified analyzer, but no additional de-
the remainder of this article I discuss other important tails are needed.
ingredients that can help you develop a winning recipe Errors of omission (insufficient detail) are com-
for your Methods sections. mon in Methods sections. Experimental conditions
and details sometimes become self-obvious to authors
Length and Detail and may be unintentionally left out. One way to avoid
leaving out important detail is to treat the first draft as
Although the Methods section should not read like a if it were a standard operating procedure used for train-
procedure manual or cookbook, it is the one part of a ing individuals about the analyses, diagnostic criteria,
research paper for which length (word count) is a sec- drug preparation, or even surgery used in the research
study. If you consider what details would cause the ex-
periment to fail if left out, you may decide that some
details (e.g., wearing latex gloves, the brand of pipette,
University of Michigan Health System, Ann Arbor, MI. where reagents are stored in the laboratory, type of su-
* Address correspondence to the author at: University of Michigan Health System, tures) are relevant only to your facility and do not need
Room UH2G332, 1500 East Medical Center Drive, Ann Arbor, MI 48109-5054.
E-mail annesley@[Link]. to be included in the final paper. But you may discover
Previously published online at DOI: 10.1373/clinchem.2010.146589 that you forgot to include something as simple, yet crit-

897
Clinical Chemistry
Guide to Scientific Writing

to provide a detailed description that this test is a

Table 1. Who, what, when, where, how, and nonparametric alternative to the 2-sample t-test for
why questions to consider when writing the assessing whether 2 independent samples of obser-
Methods section. vations come from the same distribution. Readers
can access information about this statistical test
Who elsewhere.
Who maintained the records? Who reviewed the data? Who
collected the specimens? Who enrolled the study Style and Format
participants? Who supplied the reagents? Who made the
primary diagnosis? Who did the statistical analyses? Who
reviewed the protocol for ethics approval? Who provided the The Methods section should be divided into subsec-
funding? tions with associated subheadings. The use of subhead-
What ings helps organize the material in the reader’s mind.
What reagents, methods, and instruments were used? What When the materials used in the study are described, 3
type of study was it? What were the inclusion and exclusion formats are appropriate—as a listing under the sub-
criteria for enrolling study participants? What protocol was heading of reagents and supplies, as part of the descrip-
followed? What treatments were given? What endpoints were
measured? What data transformation was performed? What tion of an individual experiment, or both. Generic re-
statistical software package was used? What was the cutoff agents, such as solvents, chemicals, and buffers, that are
for statistical significance? What control studies were used throughout the study or in multiple places in the
performed? What validation experiments were performed?
study protocol can be listed in a subheading labeled as
When Materials. However, if a reagent is specific to an indi-
When were specimens collected? When were the analyses vidual experiment or method, such as a PCR experi-
performed? When was the study initiated? When was the
study terminated? When were the diagnoses made?
ment, then the reagents, enzymes, etc. used solely for
the PCR should be listed in the paragraph detailing the
Where
PCR experiment, thereby helping the reader associate
Where were the records kept? Where were the specimens the importance of specific reagents with specific exper-
analyzed? Where were the study participants enrolled? Where
was the study performed? iments. Be sure to include the source or vendor for all
How
chemicals, reagents, animals, and instruments used in
the study. Some journals also request that the location
How were samples collected, processed, and stored? How many
replicates were performed? How was the data reported? How of the vendor be included the first time that the mate-
were the study participants selected? How were patients rial is mentioned.
recruited? How was the sample size determined? How were The Methods section should be written in the past
study participants assigned to groups? How was response
measured? How were endpoints measured? How were control
tense because you are describing experiments and pro-
and disease groups defined? tocols that you did in the past:
Why • The experiment was performed at room temperature.
Why was a species chosen (mice vs rats)? Why was a selected • We quantified the drug by immunoassay.
analytical method chosen? Why was a selected experiment
performed? Why were experiments done in a certain order?
• Assay correlation was determined by Spearman rank
correlation.
• We performed a 2-way ANOVA.
ical, as the pH of a buffer, the need to perform sample • Study participants were recruited from the blood donor
preparation in glass vs plastic, or an antibiotic drip dur- service.
ing the surgery. • Human embryonic kidney cells were cultured in Dul-
Of course, errors of commission (irrelevant detail) becco’s modified Eagle’s medium.
can detract from the Methods section as well, and you • Tissue release of C-reactive protein was monitored after
must make sure to avoid adding information that can blood flow restriction.
be cited and found elsewhere. For example, if you used The 2 exceptions to the use of the past tense are the
a previously published method without modification, presentation of summarized data and the introduction
it is sufficient to reference the method and its principle of figures and tables within the Methods section:
(e.g., “We used the LC-MS/MS method of Anderson
for quantifying testosterone.”). However, if you mod- • Our protocol is summarized in Figure 1.
ified the published method in any way, then it is imper- • Figure 1 illustrates the steps in the procedure.
ative that you include details of any modifications • The data are summarized as median and interquartile
that were made (and why). Or if in a clinical study range.
you compared continuous secondary endpoints with • The results from these analyses are presented as relative
use of the Wilcoxon rank-sum test, there is no need risk ratios with 95% CIs.

898 Clinical Chemistry 56:6 (2010)

 Clinical Chemistry
Guide to Scientific Writing

describe for the reader why the experiment was

Table 2. All passive voice, all active voice, and performed.
combined use of both. The Methods section should present the experi-
mental procedures in chronological order. An excep-
All passive voice: tion can be made to using this format if all of the ex-
Study participants were recruited from the blood donor clinic. periments were performed independently of one
Each participant was asked to fill out a questionnaire, which another, with no clear ordering of their performance.
was then used to classify each individual. Heart rate, blood
pressure, and temperature were evaluated by a nurse for In this situation the experiments can be ordered from
each individual, at which time a 10-mL blood sample was most to least important, helping to ensure that the
obtained from each participant by a phlebotomist for routine most important experiment is brought to the attention
chemistry testing. This information was compiled and used to
create a database of patient characteristics vs laboratory
of, and retained by, the reader.
results. It is important that the details for specific experi-
All active voice: ments be presented chronologically as well. I remem-
ber one set of instructions for an instrument repair that
We recruited study participants from the blood donor clinic. We
asked each participant to fill out a questionnaire, which we stated something like, “Turn the luer lock counter-
then used to classify each individual. A nurse evaluated each clockwise to unlock and remove the valve. But first,
individual for heart rate, blood pressure, and temperature, at bleed the gas to remove the backpressure so the valve
which time a phlebotomist obtained a 10-mL blood sample
from each participant for routine chemistry testing. We
does not fly outward and potentially cause injury.” No
compiled this information and created a database of patient kidding! Similarly, chronology in sentence structure
characteristics vs laboratory results. serves both the author and reader well. Instead of writ-
Combined passive and active voice, irrelevant information ing “the supernatant was transferred to another tube
removed: after centrifugation at 8800g for 10 minutes,” the actual
We recruited study participants from the blood donor clinic. sequence of events should be written as “after centrif-
Each participant was asked to fill out a questionnaire, which ugation at 8800g for 10 minutes, the supernatant was
we then used to classify each individual. Heart rate, blood
pressure, and temperature were evaluated, and a 10-mL transferred to another tube.” Similarly, “we obtained a
blood sample obtained for routine chemistry testing. We 3-mm punch biopsy sample after the patient gave in-
compiled this information and created a database of patient formed consent” is better stated as “after the patient
characteristics vs laboratory results. gave informed consent, we obtained a 3-mm punch
biopsy sample.”
Tables and figures should be included in the Meth-
Resources on writing differ in their preference for ods section only if they will save a large amount of text,
either the passive or the active voice for the Methods and be of clear benefit in helping the reader understand
section. Either style is acceptable if used properly, but a the experiment being described. For example, in a
combination of both provides the reader with some methods paper you may have a large number of assay
variation in presentation of the experiments. Whatever parameters that must be summarized (e.g., gradient
form you choose, be sure to avoid monotony in the conditions, mass transitions, voltage settings, detector
presentation, as shown in Table 2. The first 2 examples settings, and programmed instrument changes). De-
in Table 2 also include potentially irrelevant informa- scribing these one after another in the text may result in
tion such as who measured heart rate and blood pres- a cumbersome paragraph of numbers and terms that
sure, and who obtained the blood samples. Another would be more easily understood if summarized in a
way to avoid monotony when using predominantly the table. In another situation you may be describing a
passive or active voice is to use transition phrases: complex workflow protocol that is better understood
as a schematic diagram. Nevertheless, the circum-
• After mixing for 1 minute, we added 7 mL methylene
stances justifying a table or figure in the Methods sec-
chloride . . .
tion are few in number.
• To evaluate ion suppression, extracts were prepared . . .
The decision of whether to put information in the
• Because the cells did not adhere to polypropylene, fibro-
Methods section vs the Results section can be confus-
blasts were grown . . .
ing. The general rule is that anything known or planned
• Because of its signal-enhancing properties, cinnamic
at the beginning of the study goes in the Methods sec-
acid was added . . .
tion, and anything that was not known or planned goes
• Based on previous reports of calcitrol-induced inhibi-
in the Results section. In some types of studies, how-
tion, we added calcitrol . . .
ever, the initial experiments described in the Methods
In addition to avoiding monotony and improving section may yield data that lead to a change in subse-
the flow of the text, transition phrases can be used to quent experiments or to additional experiments. Be-
start a new paragraph, introduce a new experiment, or cause these later experiments are driven by data ob-

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Clinical Chemistry
Guide to Scientific Writing

tained during the course of the study, the description of it.” This statement has evolved into the modern phrase,
these experiments may make more sense if included in “method to one’s madness,” meaning a rational plan
the Results section along with the corresponding that is hidden by a mysterious action, or a strange plan
results: that manages to yield results. This strategy may have
worked for Polonius, but will not work in a scientific
When we evaluated the data, we noted an apparent
paper. Poorly described experiments will trump the
bimodal distribution related to sex. Because the original
patient data set included 13 women and 47 men, we in- credibility of your results. If readers cannot understand
creased the number of samples obtained from women to how and why the experiments were performed, they
45 to confirm whether there was indeed a sex difference. will be hesitant to acknowledge the results and conclu-
Statistical analysis of the expanded data set (45 women sions as valid. So make your Methods section work for
and 47 men) confirmed a bimodal distribution [median you, not against you.
(interquartile range) of 36 (14) mg/L for women and 61
(23) mg/L for men]. Resources and Additional Reading

Lastly, make sure that the Methods section is con- Foote MA. Materials and methods: a recipe for success.
sistent with all of the other sections in the final version Chest 2008;133:291–3.
of your paper. Is there an important method or exper- Iles RL. Guidebook to better medical writing. Olatha,
iment that is missing in the Abstract? Is there a method KS: Iles Publications; 2003.
or experiment listed in the Abstract that is missing in Katz MJ. From research to manuscript. New York:
the Methods section? Are there corresponding results Springer; 2009.
in the Results section to match each method or exper- Lang TA. How to write, publish, and present in the
iment included in the Methods section? Is there an ex- health sciences. Philadelphia: ACP Press; 2010.
planation, either in the Methods section or the Discus- Van Damme H, Michel L, Ceelen W, Malaise J. Twelve
sion, as to why each experiment was performed? As steps to writing an effective materials and methods sec-
stated at the beginning of this article, you don’t want a tion. Acat Chir Belg 2007;107:102.
missing ingredient or the wrong ingredient to affect Zeiger M. Essentials of writing biomedical research pa-
your final product. pers. New York: McGraw Hill; 2000.
Learning Exercise

Answer the following questions about the Methods

Author Contributions: All authors confirmed they have contributed to
section:
the intellectual content of this paper and have met the following 3 re-
1. What are the questions that are answered in a Meth- quirements: (a) significant contributions to the conception and design,
acquisition of data, or analysis and interpretation of data; (b) drafting
ods section?
or revising the article for intellectual content; and (c) final approval of
2. Should the Methods section be written in the past, the published article.
present, or future tense?
3. How does sentence structure differ between the pas- Authors’ Disclosures of Potential Conflicts of Interest: Upon
manuscript submission, all authors completed the Disclosures of Poten-
sive and active voice? tial Conflict of Interest form. Potential conflicts of interest:
4. In what ways are transition phrases helpful?
5. In what order are subsections organized in the text? Employment or Leadership: T.M. Annesley, AACC.
Consultant or Advisory Role: None declared.
6. Are figures and tables allowed in the Methods Stock Ownership: None declared.
section? Honoraria: None declared.
Research Funding: None declared.
Final Thoughts Expert Testimony: None declared.
Role of Sponsor: The funding organizations played no role in the
In Act II of William Shakespeare’s Hamlet, Polonius design of study, choice of enrolled patients, review and interpretation
states, “Though this be madness, yet there is method in of data, or preparation or approval of manuscript.

900 Clinical Chemistry 56:6 (2010)

 Clinical Chemistry
Guide to Scientific Writing

Answers to Learning Exercise

1. Who, what, when, where, how, and why.
2. Past tense, except for presenting summarized data and the introduction of figures and tables.
3. Active voice—the subject of the sentence performs the action (acts upon something). Example: Harold
delivered the flowers.
Passive voice—the subject of the sentence receives the action (is acted upon). Example: The flowers
were delivered by Harold.
4. Help the flow of the text, introduce a new experiment, or describe why an experiment was performed.
5. Chronological order or order of importance.
6. Yes, if they save a large amount of text and help the reader understand the experiment being described.

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