How to write a methods section
How to write a methods section
Author Resources > Choosing the right journal > Writing a methods section
Writing a methods section is a great opportunity to showcase the clarity and rigor of your research. While it requires a thoughtful balance between readability and the level of detail needed for reproducibility and replicability, it is achievable. With the right approach, you can craft a methods section that is both clear and credible. Follow our guidance to learn how to write one that meets high standards while remaining accessible and informative.
What is the purpose of a methods section?
The methods section of a research paper provides the information needed to judge a study's validity. It therefore requires a clear and precise description of how the experiment was conducted, as well as the rationale for selecting a particular experimental procedure. The methods section should explain how experiments were designed, how the results were analyzed, and what methods were used to answer the research question.
Why do methods matter?
Methods are now viewed as a key element in establishing the credibility of the research being reported, alongside the open availability of data and results. A clear methods section impacts editorial evaluation and readers’ understanding, and is also the backbone of transparency and replicability.
What to include in your methods section
What you include in your methods section depends on your field of expertise and the experiments you are performing. However, the general principle in place at the majority of journals is summarized well by our guidelines for PLOS One:
"The Materials and Methods section should provide enough detail to allow suitably skilled investigators to fully replicate your study."
The methods should enable readers to understand your paper, and replicate your study. However, there is no need to go into the level of detail that a lay-person would require—the focus is on the reader who is also trained in your field, with the appropriate skills and knowledge to attempt a replication.
Writing a thoughtful methods section
When writing a methods section, consider the following:
- Keep in mind future replicability, alongside understanding and readability.
- Follow checklists, and field- and journal-specific guidelines.
- Consider a commitment to rigorous and transparent science a personal responsibility, and not just adhering to journal guidelines.
- Establish whether there are persistent identifiers for any research resources you use that can be specifically cited in your methods section.
- Deposit your laboratory protocols in Protocols.io, establishing a permanent link to them. You can update your protocols later if you improve on them, as can future scientists who follow your protocols.
- Consider visual aids like flow-diagrams, lists, to help with reading other sections of the paper.
Avoid these common pitfalls when writing a methods section:
- Summarize or abbreviate methods without giving full details in a discoverable supplemental section.
- Presume you will always be able to remember how you performed the experiments, or have access to private or institutional notebooks and resources.
- Attempt to hide constraints or non-optimal decisions you had to make–transparency is the key to ensuring the credibility of your research.
How much detail to include in a methods section
While methods sections should reflect the principles of rigorous science, many disciplines have developed standards and tools to support accurate reporting. Always consult the submission guidelines of your target journal to ensure compliance with any field- or journal-specific requirements.
A strong methods section supports reproducibility and helps others understand and replicate your work. Be thorough, even if the journal does not require extensive detail—exceeding minimum standards is never a problem. If word limits apply, include additional searchable details in supplemental materials.
We recommend planning the level of detail in your methods section by imagining that you are writing for your future self, replicating your own work. When you consider that you might be at a different institution, with different account logins, applications, resources, and access levels, you can imagine the level of specificity that you would need to redo the exact experiment. Consider:
- Which details would you need to remember?
- Which cell line, antibody, software, or reagent did you use, and does it have a Research Resource ID (RRID) that you can cite?
- Which version of a questionnaire did you use in your survey?
- Which visual stimulus did you show participants, and is it publicly available?
- What participants did you exclude?
- During your work, what processes did you adjust?
If you were to replicate the work, you would want to know about any adjustments—so would others. Even if a method was not ideal, transparency prevents future issues. It is always better to disclose limitations than risk reproducibility or ethical concerns.
Consider whether a visual representation of your methods could be appropriate or aid in understanding your process. A visual reference readers can easily return to, like a flow-diagram, decision-tree, or checklist, can help readers better understand the complete article, not just the methods section.
Alongside detailing your methods, confirm that your research followed all relevant ethical guidelines. Even if ethics are covered in a separate section, your protocols must align with those standards.
Aim to be thorough
A strong methods section supports reproducibility and helps others understand and replicate your work. Be thorough, even if the journal doesn’t require extensive detail—exceeding minimum standards is never a problem. If word limits apply, include additional searchable details in supplemental materials.
Imagine replicating your own work
We recommend planning the level of detail in your methods section by imagining that you are writing for your future self, replicating your own work. When you consider that you might be at a different institution, with different account logins, applications, resources, and access levels, you can imagine the level of specificity that you would need to redo the exact experiment. Consider:
- Which details would you need to remember?
- Which cell line, antibody, software, or reagent did you use, and does it have a Research Resource ID (RRID) that you can cite?
- Which version of a questionnaire did you use in your survey?
- Which visual stimulus did you show participants, and is it publicly available?
- What participants did you exclude?
- During your work, what processes did you adjust?
Capture any changes to your protocols
If you were to replicate the work, you'd want to know about any adjustments—so would others. Even if a method wasn’t ideal, transparency prevents future issues. It’s always better to disclose limitations than risk reproducibility or ethical concerns.
Visual aids for methods help when reading the whole paper
Consider whether a visual representation of your methods could be appropriate or aid in understanding your process. A visual reference readers can easily return to, like a flow-diagram, decision-tree, or checklist, can help readers better understand the complete article, not just the methods section.
Ethical considerations
Alongside detailing your methods, confirm that your research followed all relevant ethical guidelines. Even if ethics are covered in a separate section, your protocols must align with those standards.
Existing standards, checklists, guidelines, partners
You can read some key initiatives below.
Randomized Controlled Trials – CONSORT
The Consolidated Standards of Reporting Trials (CONSORT) project covers various initiatives intended to prevent inadequate reporting of randomized controlled trials. The primary initiative is an evidence-based minimum set of recommendations for reporting randomized trials known as the CONSORT Statement.
Systematic Reviews and Meta-Analyses – PRISMA
The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) is an evidence-based minimum set of items focusing on the reporting of reviews evaluating randomized trials and other types of research.
Research using Animals – ARRIVE
The Animal Research: Reporting of In Vivo Experiments (ARRIVE) guidelines encourage maximizing the information reported in research using animals thereby minimizing unnecessary studies. (Original study and proposal, and updated guidelines, in PLOS Biology.)
Laboratory Protocols
Protocols.io has developed a platform specifically for sharing and updating laboratory protocols. These protocols are assigned their own DOI and can be linked from methods sections of papers to enhance reproducibility. Contextualize your protocol and improve discovery with an accompanying Lab Protocol article in PLOS One.
Consistent reporting of Materials, Design, and Analysis – the MDAR checklist
A cross-publisher group of editors and experts have developed, tested, and rolled out a checklist to help establish and harmonize reporting standards in the Life Sciences. The checklist helps authors compile their methods, while also helping editors and reviewers check methods. It also establishes a minimum set of requirements for transparent reporting and is adaptable to any discipline within the Life Sciences, by covering a breadth of potentially relevant methodological items and considerations.
Final thoughts
A clear methods section impacts editorial evaluation and readers’ understanding. It also helps build trust in your research through transparency and replicability. Follow our guidance to write a helpful methods section so others can reproduce, support, and build upon your research.
Next: Writing your manuscript
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How to write an abstract for a journal article
