What to Include in Materials and Methods

By Dr. Zubair Khalid, DVM, MS, PhD · 2026-08-27

Quick Answer

• List every biological material, chemical reagent, equipment item, and software tool that another researcher would need to repeat your work, including exact names and catalog numbers.
• Specify the source, lot number, concentration, and preparation details for each material so the method is reproducible without contacting you.
• A materials list cannot substitute for a complete methods narrative, and institutional policies or journal guidelines may impose additional reporting requirements beyond the items described here.

At a Glance

Why Materials and Methods Matter for Reproducibility

The materials and methods section is the part of a research paper that allows another laboratory to repeat your experiment and obtain comparable results. Without a complete list of what you used and how you used it, the rest of your paper cannot be independently verified. The National Library of Medicine hosts research methods resources that emphasize the importance of detailed methodological reporting for the advancement of biomedical science. When you omit a critical detail, such as the specific cell line passage number or the buffer pH, another researcher may spend weeks troubleshooting a problem that your original notes could have prevented.

The Committee on Publication Ethics Core Practices identify data integrity and reproducibility as central expectations for published research. Journals and funding agencies increasingly require authors to demonstrate that their work can be replicated. A thorough materials and methods section is the primary mechanism for meeting that expectation. When reviewers cannot determine what you actually did, they cannot assess whether your conclusions are justified.

The materials and methods section also serves a practical purpose for you as the author. When you write out every detail while the experiment is fresh in your memory, you create a permanent record that protects you from later questions about your work. This record becomes especially valuable if a collaborator asks for clarification, a journal requests additional information, or a reader contacts you about reproducing your findings.

Core Principles for Listing Materials

Identify What Another Researcher Needs

The central question for every item in your materials list is whether someone else needs this information to repeat your work. If the answer is yes, include it. If the answer is no, consider whether the detail is still relevant for interpretation. A common error is listing only the most obvious items, such as the primary antibody or the cell line, while omitting the buffer components, the plasticware, or the software settings that are equally essential.

Think about the entire workflow from start to finish. For each step in your protocol, ask what materials are involved. This includes items that may seem trivial, such as the type of pipette tips or the brand of microcentrifuge tubes. Some plastics bind proteins or nucleic acids differently, and this can affect your results. A researcher who cannot identify the exact product may unknowingly introduce variability into their replication attempt.

Use Exact Names and Identifiers

Generic descriptions are not sufficient for reproducibility. Write the full chemical name instead of an abbreviation, and include the supplier and catalog number for every commercial product. For biological materials, include the strain designation, the source repository, and any relevant stock numbers. For equipment, include the manufacturer and model number so a reader can identify the instrument specifications.

The EQUATOR Network provides reporting guidelines that help authors decide which details are essential for different study types. These guidelines are developed by methodologists and editors who have analyzed where papers commonly fail to provide adequate information. Consulting the relevant guideline for your study design before you write can prevent omissions that would otherwise trigger revision requests.

Distinguish Essential from Optional Details

Not every detail belongs in the materials and methods section. Standard laboratory procedures that are widely known, such as how to run an agarose gel or how to perform a basic Western blot, can be described briefly with a citation to a standard protocol. The level of detail should match the novelty and complexity of your work. A new technique requires extensive description, while a routine step can be summarized.

The key is to provide enough information for replication without burying the reader in irrelevant minutiae. If a detail does not affect the outcome, it may not need to be listed. However, when in doubt, include the information. The cost of an extra sentence is small compared with the cost of an irreproducible result.

Biological Materials

Cell Lines and Primary Cells

For cell lines, provide the exact name, the species of origin, the tissue type, and the source. Include the catalog number if the line was purchased from a repository such as ATCC or the European Collection of Authenticated Cell Cultures. State whether the cells were authenticated and tested for mycoplasma contamination, because these quality-control steps affect the reliability of your results.

For primary cells, describe the donor species, strain, age, sex, and tissue of origin. Include the isolation method and any purification steps. If the cells were cultured, specify the passage number and the culture conditions. Primary cells are more variable than immortalized lines, so the source details are especially important for reproducibility.

Animal Models

For animal studies, specify the species, strain, sex, age, weight, and source of the animals. Include the genetic background and any modifications, such as knockout or transgenic constructs. State the housing conditions, including temperature, light cycle, and diet, because these environmental factors can influence physiological outcomes.

The National Institutes of Health provides guidance for researchers who receive federal funding, and this guidance includes expectations for rigorous experimental design. When you describe your animal model precisely, you enable other researchers to determine whether your findings are likely to generalize to their own experimental conditions.

Microbial Strains and Vectors

For bacteria, yeast, or other microorganisms, provide the species, strain designation, and source. Include any genetic modifications and the selection markers used. For plasmids or viral vectors, specify the backbone, the insert, the promoter, and the resistance cassette. Provide the source of the vector and any relevant accession numbers.

If you constructed a new vector, describe the cloning strategy in enough detail that another researcher could reproduce the construction. Include the primers used, the restriction sites, and the sequencing verification. The sequence data should be deposited in a public database so that others can access it.

Chemical Reagents and Buffers

Reagent Specifications

For every chemical reagent, provide the full chemical name, the purity grade, and the supplier. Include the catalog number and, when relevant, the lot number. The purity grade matters because analytical grade reagents may behave differently from technical grade products. The supplier matters because manufacturing processes can introduce impurities that affect experimental outcomes.

For solutions that you prepared yourself, state the concentration of each component and the solvent. Include the pH if the buffer is pH-sensitive. Describe the preparation method if it is unusual, such as heating or sonication. For commercially prepared solutions, provide the product name and catalog number.

Antibodies and Proteins

For antibodies, provide the target antigen, the host species, the clonality, and the conjugate if applicable. Include the supplier, catalog number, and lot number. State the dilution used and the incubation conditions. The same antibody from different lots can vary in performance, so the lot number is important for troubleshooting.

For recombinant proteins or enzymes, provide the source, the expression system, and the purity. Include the specific activity if the product is characterized by activity instead of mass. State the storage conditions and any reconstitution steps.

Kits and Commercial Assays

For commercial kits, provide the manufacturer, the kit name, and the catalog number. State the kit lot number and the expiration date. Describe any modifications you made to the manufacturer protocol, because deviations can affect the results. If you used the kit exactly as instructed, state that clearly.

The National Library of Medicine resources include guidance on reporting for studies that use commercial assays. When you identify the exact kit and lot, you allow other researchers to determine whether their results can be compared with yours.

Equipment and Instrumentation

Essential Instrument Details

For each piece of equipment, provide the instrument type, the manufacturer, and the model number. Include the key settings or parameters that affect the measurement. For example, for a centrifuge, state the rotor type, the speed, the temperature, and the duration. For a spectrophotometer, state the wavelength and the path length.

The level of detail should reflect the importance of the instrument to your results. A standard microcentrifuge can be described briefly, while a specialized instrument such as a confocal microscope or a flow cytometer requires more detail about the configuration and the acquisition settings.

Calibration and Maintenance

State whether the instrument was calibrated and when the calibration was performed. Include any quality-control checks that were run before data collection. For instruments that require regular maintenance, such as pH meters or balances, describe the maintenance schedule if it is relevant to the results.

The National Institutes of Health data management and sharing policy emphasizes the importance of documenting the conditions under which data are collected. Instrument calibration records are part of that documentation. When you report calibration information, you help reviewers assess the reliability of your measurements.

Software and Analysis Tools

For software, provide the program name, the version number, and the manufacturer or developer. Include the operating system if the software behavior depends on it. Describe the analysis parameters and any custom scripts or code that you used. If you wrote custom code, state where the code is available and how to access it.

The ORCID for Researchers resource describes how persistent identifiers for researchers support the connection between individuals and their work. Similarly, persistent identifiers for software and datasets, such as DOIs, help readers locate the exact tools you used. When you provide version numbers and access information, you enable others to run the same analysis.

Software and Data Analysis Tools

Statistical Software

For statistical analysis, specify the software package and version. State the specific tests used and the assumptions checked. Include the threshold for statistical significance and whether corrections were applied for multiple comparisons. If you used a specialized statistical method, provide a citation to the method and describe the implementation.

The EQUATOR Network reporting guidelines often include specific requirements for statistical reporting. These requirements help readers understand how the analysis was performed and whether the conclusions are justified. When you describe your statistical approach precisely, you allow others to evaluate the appropriateness of your methods.

Image Analysis and Data Processing

For image analysis, provide the software name, version, and the specific analysis pipeline. Describe the settings for background subtraction, thresholding, and quantification. State whether any images were excluded and the criteria for exclusion. Image processing can substantially affect the results, so the details matter.

For data processing, describe any normalization, transformation, or filtering steps. State the software used and the parameters applied. If you used a pipeline that combines multiple tools, describe the sequence of steps and the version of each tool.

Code and Reproducible Workflows

If you used custom code for analysis, provide the code repository location and the version. Describe the computational environment, including the operating system and the software dependencies. The National Institutes of Health data management and sharing policy encourages researchers to share the code and software needed to reproduce their analyses.

When you share your code, include documentation that explains how to run it and what inputs it requires. Provide example data if possible so that others can verify that the code works. The goal is to allow another researcher to reproduce your analysis from the raw data.

How to Write the Materials and Methods Section

Organize by Experimental Procedure

Organize the materials and methods section by experimental procedure instead of by material type. This structure helps the reader follow the logic of your study. For each procedure, describe the materials used and the steps performed. This approach is more readable than a list of all materials followed by a list of all methods.

Start with a brief overview of the experimental design, then describe each procedure in the order it was performed. Use subheadings to separate distinct experiments or analyses. The EQUATOR Network provides reporting guidelines that can help you determine the appropriate structure for your study type.

Write in the Past Tense

Write the materials and methods section in the past tense because you are describing what you did. Use the passive voice when the actor is not important, such as "the cells were incubated for 24 hours." Use the active voice when the actor matters, such as "we collected blood samples from the tail vein."

The writing should be clear and direct. Avoid unnecessary jargon and define any abbreviations at first use. The goal is to communicate your methods to a reader who may not be familiar with your specific techniques.

Include Statistical Methods

Describe the statistical methods in enough detail that a reader could reproduce the analysis. State the software used, the specific tests performed, and the criteria for significance. Include information about sample size determination and any data exclusions. The National Library of Medicine resources include guidance on statistical reporting for biomedical research.

If you used a complex statistical model, describe the model structure and the assumptions. State how you handled missing data and outliers. The goal is to provide enough information for a reviewer to assess whether the analysis was appropriate.

Common Failure Patterns in Materials and Methods

Omitting Critical Details

The most common failure is omitting details that are essential for replication. This often happens because the author assumes the reader will know the standard procedure or because the author does not realize the importance of a specific detail. For example, failing to state the cell passage number or the antibody lot number can make replication impossible.

To avoid this failure, review your protocol step by step and ask whether each detail is necessary. Consider asking a colleague to read your methods section and identify anything they would need to know to repeat the work. A fresh perspective can reveal omissions that you have overlooked.

Using Vague Descriptions

Vague descriptions such as "the cells were treated with the drug" or "the samples were analyzed by PCR" do not provide enough information for replication. Specify the drug, the concentration, the duration of treatment, and the vehicle control. Specify the PCR primers, the annealing temperature, and the number of cycles.

The EQUATOR Network guidelines emphasize the importance of precise reporting. When you use vague language, you force the reader to guess at your methods, which undermines the reproducibility of your work.

Listing Materials Without Methods

A list of materials without the corresponding methods is not sufficient. The reader needs to know how each material was used. For example, listing a specific antibody without stating the dilution, the incubation time, and the detection method does not allow replication. The materials and methods section must integrate the materials with the procedures.

Failing to Cite Sources

If you used a published protocol or a commercial kit, cite the source. This allows the reader to access the original description and determine whether your modifications are significant. The National Library of Medicine resources provide guidance on citing methods and protocols.

When you cite a protocol, describe any modifications you made. If you used a kit exactly as instructed, state that. The reader needs to know whether your results can be compared with other studies that used the same kit.

Records and Documentation Practices

Maintain a Laboratory Notebook

The materials and methods section should be written from your laboratory notebook, not from memory. A well-maintained notebook includes the exact product names, catalog numbers, lot numbers, and preparation details for every experiment. When you record this information at the time of the experiment, you avoid the problem of trying to recall details weeks or months later.

The National Institutes of Health data management and sharing policy emphasizes the importance of documenting the research process. Your laboratory notebook is the primary record of your methods. When you write your paper, you can refer to your notebook to ensure that every detail is accurate.

Track Lot Numbers and Expiration Dates

Lot numbers and expiration dates are important for troubleshooting. If a reagent fails to perform as expected, the lot number allows you to identify whether the problem is specific to that batch. Record the lot number and expiration date for every commercial product that could affect your results.

When you write your materials and methods section, include the lot numbers for critical reagents such as antibodies, enzymes, and kits. This information allows other researchers to determine whether their results can be compared with yours.

Document Equipment Settings

Record the settings for every piece of equipment used in your experiments. This includes the centrifuge speed and temperature, the PCR cycling conditions, and the microscope acquisition settings. When you write your methods, include these settings so that others can replicate your conditions.

The National Library of Medicine resources include guidance on reporting equipment and instrumentation. When you document your equipment settings, you enable others to determine whether their instruments are comparable to yours.

Quality Controls and Validation

Include Positive and Negative Controls

Describe the positive and negative controls used in your experiments. Positive controls demonstrate that your assay can detect the expected result, while negative controls demonstrate that your assay does not produce false positives. The materials and methods section should describe the controls and the expected outcomes.

The Committee on Publication Ethics Core Practices emphasize the importance of rigorous experimental design. Controls are a fundamental component of rigorous design. When you describe your controls, you allow reviewers to assess the validity of your results.

Describe Validation Experiments

If you developed a new assay or modified an existing one, describe the validation experiments. This includes tests of specificity, sensitivity, and reproducibility. State the criteria for accepting or rejecting results based on the validation data.

The EQUATOR Network provides reporting guidelines that include recommendations for validation studies. When you describe your validation experiments, you allow others to assess the reliability of your assay.

Report Quality-Control Failures

If any experiments failed quality control and were excluded from the analysis, describe the exclusion criteria and the number of excluded samples. This transparency allows reviewers to assess whether the exclusions could have biased the results. The National Institutes of Health data management and sharing policy encourages transparency in reporting.

Limitations and Professional Escalation

Acknowledge Methodological Limitations

Every method has limitations, and the materials and methods section should acknowledge them. For example, a cell line may not fully represent the in vivo condition, or an antibody may cross-react with related proteins. Acknowledging limitations demonstrates that you understand the scope of your conclusions.

The EQUATOR Network guidelines emphasize the importance of transparent reporting. When you acknowledge limitations, you help readers interpret your results appropriately.

Seek Guidance for Complex Methods

If you are unsure whether your materials and methods section is complete, seek guidance from a mentor, a colleague, or a statistician. The National Library of Medicine resources include guidance on research methods that can help you identify gaps in your reporting.

For complex methods, such as advanced statistical analyses or specialized imaging techniques, consider consulting an expert. The expert can help you identify the details that are essential for replication.

Escalate When Results Cannot Be Reproduced

If another researcher cannot reproduce your results, treat this as a serious issue that requires investigation. Review your materials and methods section to identify any missing details. Check your laboratory notebook for information that was not included in the paper.

The Committee on Publication Ethics Core Practices address the handling of allegations of irreproducibility. If you receive a query about your methods, respond promptly and provide the requested information. If you identify an error in your methods, correct it through the appropriate channels.

Safety and Regulatory Context

Follow Institutional Safety Requirements

The materials and methods section should reflect compliance with institutional safety requirements. This includes the use of appropriate personal protective equipment, the handling of hazardous materials, and the disposal of waste. While the methods section does not need to describe every safety procedure, it should mention any special safety considerations.

The National Institutes of Health provides guidance for researchers who receive federal funding, and this guidance includes expectations for safe research practices. When you describe your methods, you should be prepared to provide documentation of your safety compliance if requested.

Comply with Animal and Human Subject Regulations

If your research involved animals or human subjects, describe the approval obtained from the relevant oversight committee. Include the approval number and the date of approval. The Committee on Publication Ethics Core Practices require that research involving animals or humans be conducted in accordance with ethical standards.

The materials and methods section should state that informed consent was obtained for human subjects or that animal protocols were approved by the institutional animal care and use committee. This information is essential for publication and for the ethical conduct of research.

Report Conflicts of Interest

If any materials or equipment were provided by a manufacturer or if you have a financial relationship with a supplier, disclose this in the materials and methods section or in the conflicts of interest statement. The Committee on Publication Ethics Core Practices require transparency about conflicts of interest.

The disclosure should include the nature of the relationship and the potential for bias. When you disclose conflicts, you allow readers to assess whether the relationship could have influenced your results.

Frequently Asked Questions

What is the difference between materials and methods?

Materials are the physical items used in the experiment, such as reagents, equipment, and biological samples. Methods are the procedures performed with those materials. The materials and methods section combines both, describing what was used and how it was used.

How much detail should I include for standard laboratory procedures?

Standard procedures that are widely known can be described briefly with a citation to a published protocol. The level of detail should match the novelty of the procedure. A new technique requires extensive description, while a routine step can be summarized.

Should I include catalog numbers for every reagent?

Catalog numbers are essential for commercial products because they uniquely identify the product. Include the catalog number for every reagent, antibody, kit, and other commercial product. This information allows another researcher to purchase the exact same product.

How do I describe software used for data analysis?

Provide the software name, the version number, and the manufacturer or developer. Describe the analysis parameters and any custom scripts. If you wrote custom code, state where the code is available and how to access it.

What should I do if I cannot remember a specific detail?

Check your laboratory notebook for the information. If the detail is not recorded, you may need to repeat the experiment or acknowledge the omission. The materials and methods section should be written from your records, not from memory.

How do I cite a protocol from another publication?

Cite the original publication and describe any modifications you made. If you used a commercial kit, cite the manufacturer protocol and state whether you followed it exactly or made changes.

Should I include the lot number for antibodies?

Lot numbers are important for antibodies because different lots can vary in performance. Include the lot number for antibodies and other critical reagents. This information allows other researchers to determine whether their results can be compared with yours.

What if my materials and methods section is too long?

The length should match the complexity of your study. Some journals have word limits for the materials and methods section, so check the journal guidelines. If you need to shorten the section, focus on the details that are essential for replication and move less critical information to supplementary materials.

Using the Evidence

Related Articles

• Reference Methods in Research: How to Cite and Describe Protocols
• Writing the Methods Section of a Scientific Paper: A Reproducibility-Focused Guide
• Statistical Methods
• Statistical Analysis Methods
• Flow Cytometry Gating Reproducibility

References and Further Reading

• Research Methods Resources. National Library of Medicine.
• EQUATOR Network. EQUATOR Network.
• Core Practices. Committee on Publication Ethics.
• NIH Grants and Funding. National Institutes of Health.
• ORCID for Researchers. ORCID.
• Data Management and Sharing Policy. National Institutes of Health.
• NCBI Literature Resources. National Center for Biotechnology Information.
• PubMed. National Library of Medicine.

This article is educational and does not replace institutional policy, professional advice, or applicable safety and regulatory requirements.