How to Write the Methods Section of your Research Paper

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In this article freelance medical writer for Kolabtree Laura Moro-Martin, MSc, PhD, provides tips to write the methods section of a research paper, along with common errors to avoid.  

Goals of the methods section

The Methods section of a research article reports what you did and what you used to perform your research. It describes the tools and processes that enabled you to meet the objectives stated in the Introduction. The Methods section, depending on the field and the journal, can also be called Materials and Methods, Procedures, Methodology, Experiments, or other similar terms. Being a descriptive section where no analysis or interpretation is required, writing the Methods can help you to beat the ‘blank page syndrome’ that many of us suffer when starting to write a new paper. It is better to write the Methods section–at least a first version of it–while performing or immediately upon completion of the experiment. But do not get the wrong idea! Although the Methods could be one of the easiest sections to write, it often happens that some details are missed or that experimental procedures that seem very clear for you are not that obvious for the reader.

Therefore, the main goals of the Methods section are to present the experimental design, to allow the reader to interpret your results, and to give enough detail to replicate your work.

Structure of the methods section

Regarding the structure, this section starts with general information applying to the entire manuscript (for example, study population, sample collection, sample site, animal models, etc.) and then goes on to specific experimental details. The Methods section should include:

  • the organism(s) studied (plant, animal, human, etc.), their pre-experiment handling and care whenever relevant, and the study location and time if they are important factors;
  • in the case of field studies, a description of the study site, including the precise location and significant physical or biological features;
  • the experimental or sampling design, including the study population, controls, treatments applied, variables of study, sample collection and data management, etc.
  • the protocol for data collection, detailing all experimental procedures;
  • the analysis of data, either qualitative analyses or statistical procedures.

Advice on how to write the Methods section

Writing the Methods section may seem a tedious task. Yes, even as a reader, you may associate methods with ‘boredom’ because of its highly technical nature. However, a well-written methodology section enhances your chances of publication and strengthens the conclusions of your work, so it is worth investing time in meticulous writing. Take into account that this section is closely scrutinized by the journal editors and peer reviewers. The key for a great Methods section is to include all the relevant information without providing excessive or unnecessary detail. Be detailed but concise. Here you have a few more tips:

– Since the Methods section is meant to convey how the research was conducted, you should follow the accepted conventions of your field for writing.

– It is equally important to follow precisely the ‘Instructions for Authors’ of your target journal or other specific guidelines depending on your field or study type. For example, in the case of a randomized clinical trial, you will need to follow the CONSORT (Consolidated Standards of Reporting Trials) guideline or, when writing a systematic review, the PRISMA (Preferred Reporting Items for Systematic reviews and Meta-Analyses) guideline.

  • You can adequately structure the Methods section by using paragraphs and subheadings to identify different subsections that generally indicate a different experiment. The subheading can correspond to the specific objective or the name of each experiment. Then, you can start the paragraph providing a short rationale behind that particular experiment.
  • Be consistent in the notation and terminology, and specify unconventional terms or definitions that you are using.
  • Include citations for previously published methods, and describe any modification that you introduced.
  • As a general rule, any essential materials, quantities, procedures, and equipment that could influence the results should be specified. When the equipment or software used is integral to a procedure, the manufacturer should be mentioned, including location details at the first mention. For example, it is not necessary to mention the manufacturer of a light microscope to count cells or the provider of the sodium chloride used to prepare a saline solution, but you will have to mention the model and manufacturer of an electron microscope and any experimental grade compounds or pharmaceuticals that you used.
  • Human or animal studies should include an ethics statement mentioning the body that approved the experimental protocol. In the case of clinical research, you need to indicate that you obtained informed consent from all the study participants.
  • You need to describe the obstacles faced while performing the experimental part and how you overcame them to help validate your results. This is often described in the ‘Study limitations’ in the Discussion section. Similarly, the reasons why you used a particular method or how that method is superior to others should go in the Discussion section.

Methods and Results should match

The Methods section should follow the order of the results generated through those experimental procedures. You need to explain the methodology that you applied to obtain all the experimental observations. Creating a flowchart figure describing the different steps, in particular in the case of complex study designs or experimental procedures, can be of help for the reader.

Preparing the statistical methods subsection

This is probably one of the parts of the Methods section creating more problems among researchers in the life and medical sciences. The statistical analysis should be thoroughly described at the end of the Methods section, without the need to reiterate them in the Results section. Since the statistical analysis crucially determines the study findings, you will need to explain their rationale in detail.

You need to specify the variables, not only the control, independent, and dependent variables, but also potential extraneous variables that might influence the results of your study. In particular, you need to include the specific tests used for the different types of data, the prerequisites (e.g., distribution normality) that were tested and previous assumptions that you applied, data transformations, potential confounders, significance or confidence interval levels used, any other numerical (e.g., normalizing data) or graphical techniques used to analyse the data, post hoc tests applied, and any study-specific criteria (for example, established thresholds). The specific software used for statistical analyses should be always mentioned. If in doubt, you can consult the biostatistician of your team to receive help to write this subsection.

The style of the Methods section

The Methods section requires a specific type of discourse that is not found in other parts of the article, and it should read as if you were verbally describing the conduct of the experiment. Think that readers will be learning from you, so they should be able not only to understand and accept your procedure but also to repeat it and obtain similar results. Take into account the specific readership of the journal to adapt the technical jargon (you may need to provide explanations for some technicisms).

The Methods section usually requires the use of third person and passive constructions. However, it is also possible (and some times more effective) to use the active voice and the first person to a certain extent (for example, ‘We collected the samples’, but never ‘I collected the samples’). This section is always written in the past tense since the work that you are reporting has been already done.

Learning from others

Selecting a few good articles from your field as models is always a good idea to improve your scientific writing. In particular, you may want to choose a few articles published in your target journal covering topics similar to yours, and that you think are particularly well written. Read them carefully and observe how the Methods section is structured, and the type and amount of information provided. Reading and learning from others is always a good starting point to write your paper.

Put yourself in the readers’ shoes

Before submitting your manuscript, you need to ask yourself a few questions to be sure that your Methods section is complete and understandable. Is there enough information to allow the reproduction of the experiments? Is there unnecessary information that can be eliminated without affecting the interpretation? Have we mentioned all the necessary references, all the controls, and the source of the reagents? Reflect on the answers and decide whether your Methods still need further improvement.

Common errors to avoid while writing the Methods section of your research paper

There are several mistakes that frequently occur when drafting the Methods section of a paper. Here we have collected a few examples:

  • Providing too little (not allowing the correct interpretation of the results or the replication of the experiments) or too much (providing a full account, almost a laboratory notebook) information.
  • Repeating published methods instead of citing them.
  • Failing to provide a context for the methods (it is useful to ‘think out loud’ to guide the reader and justify the choices you made, including sentences of this type: ‘In order to…, we….’; ‘Our aim was to…’; ‘in an attempt to…’; ‘for the purpose of…; ‘to validate …’; etc.) and using visual organizers (such as subheadings).
  • The Results section does not correspond with the Methods section (you need to explain the experimental procedures for all the results that you obtained).
  • Using ambiguous terms to designate parameters or conditions (such as controls, treatments, etc.) that require specific identifiers to be clearly understood (your own designators such as ‘Sample 1’ and ‘Sample 2’ or ‘Treatment A’ and ‘Treatment B’ are meaningless out of context and difficult to follow).
  • Overuse or misuse of the passive voice. For example, since the agent is not indicated in the passive voice, your own work may become confused with the standard procedures that you are describing or with the work from other researchers, making difficult to identify your contribution. You can avoid this by adding words such as ‘In this study’, ‘In our experiments’, ‘Here’, or by moving to the active voice.

In summary, writing a good Methods section will help you to establish the robustness of your study by making the reader able to understand, interpret, and replicate your experiments. Do not underestimate it… and of course, good writing!

Need help to write the methods section of your research paper? Consult freelance scientific editors on Kolabtree or access statistical review services from experts. 

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About Author

Dr. Laura Moro-Martin is an experienced science writer and scientific consultant with a solid background in health and biomedical research. She has more than 10 years of experience in biotechnology and biomedical research, mainly in infectious diseases and cancer. She has a PhD in Medicine and a Master in Science Communication and Journalism. She was awarded a Marie Curie postdoctoral researcher in 2015. She has been a freelance scientific-medical writer or advisor and can consult on projects involving grant writing and project proposals (H2020 and SBIR), digital news, monographic articles, scientific editing, systematic reviews, educational materials (online Master's), and others.

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