Nature Methods Formatting Requirements: Complete Author Guide

Nature Methods abstracts must be unreferenced, and the word limit depends on the article type.

• Word limit: up to 150 words for Articles, Analyses, Resources and Registered Reports; up to 70 words for Brief Communications

• Citations: Not allowed in the abstract

• Abbreviations: Define at first use

The abstract should state the problem with existing methods, describe the new approach at a high level, and present the key performance metrics. For a methods paper, specific performance numbers are expected. Write "Our approach achieves 94% accuracy on the benchmark dataset, a 12-percentage-point improvement over the current standard" rather than "Our approach substantially outperforms existing methods."

Don't describe the biological application in detail in the abstract unless the method was developed specifically for that application. The abstract should sell the method, not the biology.

A detail that matters: Nature Methods abstracts frequently include a sentence about code/data availability (e.g., "The software is available at github.com..."). This isn't formally required in the abstract, but editors favor it because it signals openness.

Nature Methods allows Articles up to 6 display items (figures and/or tables) in the main text.

Figure specifications (applied once a paper is accepted in principle):

Extended Data: Up to 10 Extended Data display items are allowed. They are online-only display items and are not copy-edited or styled by Nature Methods. They don't count toward the 6-item display limit. For methods papers, Extended Data commonly contains additional benchmarking results, parameter sensitivity analyses, and comparison metrics against alternative methods.

Supplementary Information: Beyond Extended Data, you can include Supplementary Information files (Supplementary Figures, Tables, Notes, Videos, Software). These are peer-reviewed but hosted as separate downloadable files. For complex tables larger than an A4 PDF page, the journal recommends combining them on separate tabs within one Excel workbook.

For Nature Methods specifically, method comparison figures are expected to be fair and transparent. If you're benchmarking your method against alternatives, show results on the same datasets with the same evaluation metrics. Reviewers will check this carefully.

Schematic diagrams: Almost every Nature Methods Article includes a method overview schematic as Figure 1. This diagram should show the workflow or algorithmic pipeline clearly. Use consistent visual language. Don't mix different diagramming styles within a single figure.

Nature Methods uses the standard Nature citation style.

In-text citations: Numbered sequentially as references first appear in the text. References that are uncited or cited out of sequence may delay production.

Reference list format:

1. Smith, A. B., Johnson, C. D. & Williams, E. F. Title of article. Nat. Methods 22, 123-130 (2025).

Key formatting details:

• Author names: Last name, comma, then initials with periods (as in the journal's own example, "Eigler, D. M.")

• Use "&" before the last author

• Page range in the format start-end

• Year in parentheses at the end

• Research objects such as datasets, protocols and code that have been assigned a DOI are included in the reference list; unpublished meeting abstracts and papers in preparation are not

Nature Methods recommends up to 50 references for Articles as a guideline, and up to 100 for Reviews (exceptions are possible in special cases). The higher count reflects the need to cite prior methods, benchmarking datasets, and validation studies.

Include tables at the end of your text document, and place any Methods-only references with the Methods at the end of the paper.

Nature Methods uses a tiered supplementary system.

Extended Data (Tier 1): Up to 10 figures or tables, published online only. Use this for essential supporting data that strengthens the main findings but doesn't fit in the 6 display item limit. For methods papers, this typically includes additional benchmarks, robustness analyses, and cross-validation results.

Supplementary Information (Tier 2): Files that readers can download. This includes Supplementary Figures, Supplementary Tables (often as Excel), Supplementary Notes (for mathematical derivations or extended protocol descriptions), and Supplementary Videos. These are also peer-reviewed.

Source Data (Tier 3): Raw, unprocessed data underlying each figure. Nature Methods encourages Source Data for your figures whenever possible, and full-length, unprocessed gels and blots must be provided as source data for any relevant figures. This supports the journal's commitment to reproducibility.

Code and software: Nature Portfolio policy requires a Code availability statement for studies that use custom code or algorithms central to the conclusions, and requires that the code be shared with editors and reviewers during peer review. Nature Portfolio considers it best practice to release custom code in a DOI-minting repository such as Zenodo or Code Ocean upon publication, and the editors can decline a paper if important code is unavailable. The README in the repository should include installation instructions, example usage, and expected outputs. Reviewers may test your code.

Reporting Summary: Life sciences manuscripts sent for peer review must include a completed Nature Portfolio reporting summary, which is made available to editors and reviewers and published with accepted manuscripts. The form is linked from the Nature Methods editorial policies page.

Nature Methods doesn't require a formal cover page in the same way clinical journals do. However, the manuscript file must begin with specific elements.

Required opening elements:

• Title (concise)

• Author names with superscript affiliation numbers

• Affiliations with full institutional addresses

• Corresponding author(s) with email addresses

• ORCID iDs (corresponding authors of accepted papers are asked to link theirs before the final version is submitted; other authors are encouraged to)

Declare any relevant funding in a separate funding statement.

The cover letter is a separate document uploaded through the submission portal. For Nature Methods, the cover letter should clearly state what the method does, what problem it solves, and why it's a significant advance over existing approaches. Editors use the cover letter for triage, so don't waste it on generic praise for the journal.

Nature Methods has several requirements and conventions that go beyond standard Nature Portfolio guidelines.

1. Reproducibility is the editorial priority. Nature Methods editors evaluate manuscripts primarily on whether the method can be reproduced by other labs. Vague methods descriptions are the single most common reason for revision requests. Include exact software versions, parameter settings, hardware specifications (for computational methods), and reagent catalog numbers (for experimental methods).

2. Method validation expectations are high. Showing that your method works on your own data isn't sufficient. Nature Methods expects validation on independent datasets, comparison against established methods using accepted benchmarks, and ideally, independent validation by a collaborating lab. If you can't get independent validation, be explicit about limitations.

3. The "Online Methods" section is where the real paper lives. For methods journals, the Online Methods section is often more important than the main text. Reviewers spend more time on it, and readers rely on it for implementation. Don't treat it as an afterthought. Write it with the same care as the main text.

4. Code review is real. Reviewers will download your code, try to install it, and attempt to run the examples. If your GitHub repository has a broken build, missing dependencies, or unclear documentation, expect a major revision request regardless of the science.

5. Reviewers are chosen to cover the technical aspects. Nature Portfolio journals typically send manuscripts to two or three reviewers, and sometimes more when special advice is needed, for example on statistics or a particular technique. Reviewers are expected to review all data, including extended data and supplementary information.

6. Benchmark datasets must be specified precisely. When comparing methods, state the exact dataset version, download date, preprocessing steps, and train/test splits. "We used the MNIST dataset" isn't sufficient. "We used the MNIST dataset (LeCun et al., yann.lecun.com, downloaded 2025-06-15, 60,000 training / 10,000 test images, no preprocessing)" is what they expect.

Nature Methods submissions require careful attention to both scientific rigor and formatting precision. The emphasis on reproducibility means that even small omissions, like a missing software version or an unclear parameter description, can trigger major revisions.

Nature Methods pre-submission checklist checks your formatting against Nature Methods' specific requirements, including display item counts, reference style, structural organization, and word limits. It catches the formatting issues that are easy to miss when you're focused on the science.

For related journals, see our guides to Nature formatting requirements and other journal submission guides. If you're deciding between Nature Methods and a competing venue, understanding the formatting differences up front saves time regardless of where you submit.

For manuscripts targeting Nature Methods, four patterns generate the most consistent desk-rejection outcomes.

Benchmarking is incomplete or limited to datasets chosen by the authors. Nature Methods editors and reviewers require systematic benchmarking of new computational or experimental methods against existing state-of-the-art alternatives. Submissions where comparison methods are limited to approaches the authors selected, or where benchmarking uses only datasets where the new method is expected to perform well, are returned with requests for expanded independent benchmarks.

Biological application is presented as illustrative rather than as a genuine discovery. Nature Methods distinguishes between methods papers where the biological application demonstrates what the method enables and papers where the biology is merely an example of the tool working. Editors evaluate whether the biological question addressed could not have been answered with existing approaches. Submissions where the application section describes confirmatory biology using the new tool, rather than a biological advance that required the tool, are redirected to more methods-focused venues or asked to revise the framing.

Reporting requirements for computational methods not met. Nature Methods expects methods descriptions detailed enough to enable replication, which for a computational method means reporting the software, parameter choices, training data sources, and computational environment. Nature Portfolio policy requires a Code availability statement for custom code central to the conclusions, and the code must be shared with editors and reviewers during peer review; the editors can decline a paper if important code is unavailable.

Protocol is incomplete for wet-lab methods. For experimental methods, Nature Methods reviewers evaluate whether the protocol is described with sufficient detail for independent replication without contacting the authors. Critical parameters (concentrations, timing, temperature, equipment specifications) that affect method performance must be specified. Manuscripts that describe a new experimental protocol in general terms without providing the critical parameters that distinguish the method from existing approaches are asked to revise the Methods section before review.

A Nature Methods submission readiness check evaluates manuscript structure, benchmarking completeness, and code availability compliance against these desk-rejection patterns before you submit.

For a manuscript-specific signal before you submit, run a Nature Methods submission readiness check.

Or see example reports before you finalize.