How to Write the Methods Section of a Research Paper

Writing a research paper is both an art and a skill, and knowing how to write the methods section of a research paper is the first crucial step in mastering scientific writing. If, like the majority of early career researchers, you believe that the methods section is the simplest to write and needs little in the way of careful consideration or thought, this article will help you understand it is not¹.

We have all probably asked our supervisors, coworkers, or search engines “how to write a methods section of a research paper” at some point in our scientific careers, so you are not alone if that’s how you ended up here.  Even for seasoned researchers, selecting what to include in the methods section from a wealth of experimental information can occasionally be a source of distress and perplexity.  

Additionally, journal specifications, in some cases, may make it more of a requirement rather than a choice to provide a selective yet descriptive account of the experimental procedure. Hence, knowing these nuances of how to write the methods section of a research paper is critical to its success. The methods section of the research paper is not supposed to be a detailed heavy, dull section that some researchers tend to write; rather, it should be the central component of the study that justifies the validity and reliability of the research.

Are you still unsure of how the methods section of a research paper forms the basis of every investigation? Consider the last article you read but ignore the methods section and concentrate on the other parts of the paper. Now think whether you could repeat the study and be sure of the credibility of the findings despite knowing the literature review and even having the data in front of you. You have the answer!  

Having established the importance of the methods section, the next question is how to write the methods section of a research paper that unifies the overall study. The purpose of the methods section, which was earlier called as Materials and Methods, is to describe how the authors went about answering the “research question” at hand. Here, the objective is to tell a coherent story that gives a detailed account of how the study was conducted, the rationale behind specific experimental procedures, the experimental setup, objects (variables) involved, the research protocol employed, tools utilized to measure, calculations and measurements, and the analysis of the collected data².

In this article, we will take a deep dive into this topic and provide a detailed overview of how to write the methods section of a research paper. For the sake of clarity, we have separated the subject into various sections with corresponding subheadings. 

What is the methods section of a research paper? 

The methods section is a fundamental section of any paper since it typically discusses the ‘what’, ‘how’, ‘which’, and ‘why’ of the study, which is necessary to arrive at the final conclusions. In a research article, the introduction, which serves to set the foundation for comprehending the background and results is usually followed by the methods section, which precedes the result and discussion sections. The methods section must explicitly state what was done, how it was done, which equipment, tools and techniques were utilized, how were the measurements/calculations taken, and why specific research protocols, software, and analytical methods were employed. 

Why is the methods section important? 

The primary goal of the methods section is to provide pertinent details about the experimental approach so that the reader may put the results in perspective and, if necessary, replicate the findings³.  This section offers readers the chance to evaluate the reliability and validity of any study. In short, it also serves as the study’s blueprint, assisting researchers who might be unsure about any other portion in establishing the study’s context and validity. The methods plays a rather crucial role in determining the fate of the article; an incomplete and unreliable methods section can frequently result in early rejections and may lead to numerous rounds of modifications during the publication process. This means that the reviewers also often use methods section to assess the reliability and validity of the research protocol and the data analysis employed to address the research topic. In other words, the purpose of the methods section is to demonstrate the research acumen and subject-matter expertise of the author(s) in their field. 

Structure of methods section of a research paper 

Similar to the research paper, the methods section also follows a defined structure; this may be dictated by the guidelines of a specific journal or can be presented in a chronological or thematic manner based on the study type. When writing the methods section, authors should keep in mind that they are telling a story about how the research was conducted. They should only report relevant information to avoid confusing the reader and include details that would aid in connecting various aspects of the entire research activity together. It is generally advisable to present experiments in the order in which they were conducted. This facilitates the logical flow of the research and allows readers to follow the progression of the study design.  

It is also essential to clearly state the rationale behind each experiment and how the findings of earlier experiments informed the design or interpretation of later experiments. This allows the readers to understand the overall purpose of the study design and the significance of each experiment within that context. However, depending on the particular research question and method, it may make sense to present information in a different order; therefore, authors must select the best structure and strategy for their individual studies.  

In cases where there is a lot of information, divide the sections into subheadings to cover the pertinent details. If the journal guidelines pose restrictions on the word limit, additional important information can be supplied in the supplementary files. A simple rule of thumb for sectioning the method section is to begin by explaining the methodological approach (what was done), describing the data collection methods (how it was done), providing the analysis method (how the data was analyzed), and explaining the rationale for choosing the methodological strategy. This is described in detail in the upcoming sections.   

How to write the methods section of a research paper 

Contrary to widespread assumption, the methods section of a research paper should be prepared once the study is complete to prevent missing any key parameter. Hence, please make sure that all relevant experiments are done before you start writing a methods section. The next step for authors is to look up any applicable academic style manuals or journal-specific standards to ensure that the methods section is formatted correctly. The methods section of a research paper typically constitutes materials and methods; while writing this section, authors usually arrange the information under each category.

The materials category describes the samples, materials, treatments, and instruments, while experimental design, sample preparation, data collection, and data analysis are a part of the method category. According to the nature of the study, authors should include additional subsections within the methods section, such as ethical considerations like the declaration of Helsinki (for studies involving human subjects), demographic information of the participants, and any other crucial information that can affect the output of the study. Simply put, the methods section has two major components: content and format. Here is an easy checklist for you to consider if you are struggling with how to write the methods section of a research paper.  

Content: 

• Explain the research design, subjects, and sample details 
• Include information on inclusion and exclusion criteria 
• Mention ethical or any other permission required for the study 
• Include information about materials, experimental setup, tools, and software 
• Add details of data collection and analysis methods 
• Incorporate how research biases were avoided or confounding variables were controlled 
• Evaluate and justify the experimental procedure selected to address the research question 

Format: 

• Provide precise and clear details of each experiment 
• Flowcharts, infographics, or tables can be used to present complex information    
• Use past tense to show that the experiments have been done  
• Follow academic style guides (such as APA or MLA) to structure the content 
• Citations should be included as per standard protocols in the field 

Now that you know how to write the methods section of a research paper, let’s address another challenge researchers face while writing the methods section—what to include in the methods section.  How much information is too much is not always obvious when it comes to trying to include data in the methods section of a paper. In the next section, we examine this issue and explore potential solutions.  

What to include in the methods section of a research paper 

The technical nature of the methods section occasionally makes it harder to present the information clearly and concisely while staying within the study context. Many young researchers tend to veer off subject significantly, and they frequently commit the sin of becoming bogged down in itty bitty details, making the text harder to read and impairing its overall flow. However, the best way to write the methods section is to start with crucial components of the experiments. If you have trouble deciding which elements are essential, think about leaving out those that would make it more challenging to comprehend the context or replicate the results. The top-down approach helps to ensure all relevant information is incorporated and vital information is not lost in technicalities. Next, remember to add details that are significant to assess the validity and reliability of the study. Here is a simple checklist for you to follow (bonus tip: you can also make a checklist for your own study to avoid missing any critical information while writing the methods section). 

• Structuring the methods section: Authors should diligently follow journal guidelines and adhere to the specific author instructions provided when writing the methods section. Journals typically have specific guidelines for formatting the methods section; for example, Frontiers in Plant Sciences advises arranging the materials and methods section by subheading and citing relevant literature. There are several standardized checklists available for different study types in the biomedical field, including CONSORT (Consolidated Standards of Reporting Trials) for randomized clinical trials, PRISMA (Preferred Reporting Items for Systematic reviews and Meta-Analysis) for systematic reviews and meta-analysis, and STROBE (STrengthening the Reporting of OBservational studies in Epidemiology) for cohort, case-control, cross-sectional studies. Before starting the methods section, check the checklist available in your field that can function as a guide.    

• Organizing different sections to tell a story: Once you are sure of the format required for structuring the methods section, the next is to present the sections in a logical manner; as mentioned earlier, the sections can be organized according to the chronology or themes. In the chronological arrangement, you should discuss the methods in accordance with how the experiments were carried out. An example of the method section of a research paper of an animal study should first ideally include information about the species, weight, sex, strain, and age. Next, the number of animals, their initial conditions, and their living and housing conditions should also be mentioned. Second, how the groups are assigned and the intervention (drug treatment, stress, or other) given to each group, and finally, the details of tools and techniques used to measure, collect, and analyze the data. Experiments involving animal or human subjects should additionally state an ethics approval statement. It is best to arrange the section using the thematic approach when discussing distinct experiments not following a sequential order. 

• Define and explain the objects and procedure: Experimental procedure should clearly be stated in the methods section. Samples, necessary preparations (samples, treatment, and drug), and methods for manipulation need to be included. All variables (control, dependent, independent, and confounding) must be clearly defined, particularly if the confounding variables can affect the outcome of the study. 

• Match the order of the methods section with the order of results: Though not mandatory, organizing the manuscript in a logical and coherent manner can improve the readability and clarity of the paper. This can be done by following a consistent structure throughout the manuscript; readers can easily navigate through the different sections and understand the methods and results in relation to each other. Using experiment names as headings for both the methods and results sections can also make it simpler for readers to locate specific information and corroborate it if needed.  

• Relevant information must always be included: The methods section should have information on all experiments conducted and their details clearly mentioned. Ask the journal whether there is a way to offer more information in the supplemental files or external repositories if your target journal has strict word limitations. For example, Nature communications encourages authors to deposit their step-by-step protocols in an open-resource depository, Protocol Exchange which allows the protocols to be linked with the manuscript upon publication. Providing access to detailed protocols also helps to increase the transparency and reproducibility of the research. 

• It’s all in the details: The methods section should meticulously list all the materials, tools, instruments, and software used for different experiments. Specify the testing equipment on which data was obtained, together with its manufacturer’s information, location, city, and state or any other stimuli used to manipulate the variables. Provide specifics on the research process you employed; if it was a standard protocol, cite previous studies that also used the protocol.  Include any protocol modifications that were made, as well as any other factors that were taken into account when planning the study or gathering data. Any new or modified techniques should be explained by the authors. Typically, readers evaluate the reliability and validity of the procedures using the cited literature, and a widely accepted checklist helps to support the credibility of the methodology. Note: Authors should include a statement on sample size estimation (if applicable), which is often missed. It enables the reader to determine how many subjects will be required to detect the expected change in the outcome variables within a given confidence interval. 

• Write for the audience: While explaining the details in the methods section, authors should be mindful of their target audience, as some of the rationale or assumptions on which specific procedures are based might not always be obvious to the audience, particularly for a general audience. Therefore, when in doubt, the objective of a procedure should be specified either in relation to the research question or to the entire protocol. 

• Data interpretation and analysis: Information on data processing, statistical testing, levels of significance, and analysis tools and software should be added. Mention if the recommendations and expertise of an experienced statistician were followed. Also, evaluate and justify the preferred statistical method used in the study and its significance. 

What NOT to include in the methods section of a research paper 

To address “how to write the methods section of a research paper”, authors should not only pay careful attention to what to include but also what not to include in the methods section of a research paper. Here is a list of do not’s when writing the methods section: 

• Do not elaborate on specifics of standard methods/procedures: You should refrain from adding unnecessary details of experiments and practices that are well established and cited previously.  Instead, simply cite relevant literature or mention if the manufacturer’s protocol was followed. 

• Do not add unnecessary details: Do not include minute details of the experimental procedure and materials/instruments used that are not significant for the outcome of the experiment. For example, there is no need to mention the brand name of the water bath used for incubation.   

• Do not discuss the results: The methods section is not to discuss the results or refer to the tables and figures; save it for the results and discussion section. Also, focus on the methods selected to conduct the study and avoid diverting to other methods or commenting on their pros or cons. 

• Do not make the section bulky: For extensive methods and protocols, provide the essential details and share the rest of the information in the supplemental files. The writing should be clear yet concise to maintain the flow of the section. 

We hope that by this point, you understand how crucial it is to write a thoughtful and precise methods section and the ins and outs of how to write the methods section of a research paper. To restate, the entire purpose of the methods section is to enable others to reproduce the results or verify the research. We sincerely hope that this post has cleared up any confusion and given you a fresh perspective on the methods section.

As a parting gift, we’re leaving you with a handy checklist that will help you understand how to write the methods section of a research paper. Feel free to download this checklist and use or share this with those who you think may benefit from it. 

References 

1. Bhattacharya, D. How to write the Methods section of a research paper. Editage Insights, 2018. https://www.editage.com/insights/how-to-write-the-methods-section-of-a-research-paper (2018).
2. Kallet, R. H. How to Write the Methods Section of a Research Paper. Respiratory Care 49, 1229–1232 (2004). https://pubmed.ncbi.nlm.nih.gov/15447808/
3. Grindstaff, T. L. & Saliba, S. A. AVOIDING MANUSCRIPT MISTAKES. Int J Sports Phys Ther 7, 518–524 (2012). https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3474299/

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