Supplementary Materials: What to Include and How

A supplement is not overflow storage. Editors and reviewers read it, it is often published as supplied, and anything a reader needs to judge your findings belongs in the article.

Guide · 11 min read · Directive Publications Editorial Team

What supplementary materials are for

Supplementary materials are files published online alongside an article rather than inside it: extra tables and figures, extended methods, questionnaires, protocols, videos, and sometimes data. Journals call them different things (supplementary information, supporting information, online supplement, data supplement), but the purpose is the same. They let you give interested readers more detail without lengthening the article that everyone reads.

The ICMJE recommendations on preparing a manuscript describe the idea plainly: extra materials and technical details can go in an appendix or the electronic version "where they will be accessible but will not interrupt the flow of the text." The same recommendations add two conditions that matter more than authors often realise. Supplementary electronic-only material should be submitted and sent for peer review at the same time as the main manuscript, and the text should tell readers that the additional information exists and where to find it.

So a supplement is part of your submission, not a place to put things after the fact. Editors and reviewers can open it, and readers can cite it.

Integral or additional: the test that decides placement

The most useful framework comes from the NISO and NFAIS Recommended Practices for Online Supplemental Journal Article Materials (NISO RP-15-2013). It separates supplementary content into two kinds:

• Integral content is essential for the full understanding of the work but sits outside the article for technical, business or logistical reasons. Examples it gives include methods needed to evaluate a study, detailed results needed to understand the outcomes, and tables or figures that provide data required to verify the work.
• Additional content expands the article but is not essential to understanding it. Examples include expanded methods sections, extended bibliographies, additional supporting data or results, and copies of instruments or surveys.

The same document says that deciding which category material falls into is the journal's call, and it treats integral content as a category it expected to disappear as technology allowed better integration into the article.

For you as an author, this gives a practical test. Ask of each item: would a careful reader need this to judge whether my main finding holds? If yes, it is integral, and the safest place for it is the article itself. If it adds depth, robustness or transparency but the argument stands without it, it is additional content and a good candidate for the supplement.

The common failure is the reverse. Authors move the primary outcome table, the key sensitivity analysis or the description of how the exposure was measured into the supplement to meet a word limit, and the article no longer supports its own conclusion. Reviewers notice, and so do readers who never open the supplement. If you are struggling with space, our guide to writing a methods section others can reproduce covers what has to stay in the main text.

What typically belongs in an online supplement

What a journal accepts varies, so treat this as a starting list to check against the instructions for authors.

The PRISMA 2020 explanation paper itself recommends placing detailed methods or additional results, such as those for less critical outcomes, in supplementary files. That is a good summary of the whole principle: detail and secondary material go out, the core stays in.

What to keep out of the supplement

• Results your conclusions depend on. Move them back into the article.
• Material that has already been published. JAMA states that online-only material should be original and not previously published. If you reuse a published figure or table, you need the same permissions as you would in the main text.
• Identifiable patient information. A supplement is published just like the article. Case details, images and spreadsheets in it need the same de-identification and consent as anything in the main text.
• Unedited dumps. Raw output files, every exploratory analysis or a whole thesis chapter make the supplement harder to review and rarely help readers. JAMA states that the amount of online-only material should be limited and justified.

Supplement or data repository?

Research data, code and large files often have a better home than the journal supplement. A supplement is attached to one article on one publisher's platform. A dedicated repository can give the dataset its own persistent identifier, metadata and citation, and some funders and journals expect data to be shared that way.

The PLOS guidance on supporting information encourages authors to deposit research data in a suitable repository where appropriate, and recommends that supporting information files be under 10 MB for ease of reader access. NISO RP-15-2013 recommends persistent identifiers, preferably DOIs, for supplemental content and says an author's own website should never be the sole place supplemental materials are posted, because no personal website can be considered stable.

A workable split looks like this:

• Repository: datasets, analysis code, large image sets, anything others may want to reuse or cite separately. Cite it in the reference list or data availability statement with its identifier.
• Supplement: documents and tables that explain this paper, such as extra results, protocols, instruments and the search strategy.
• Neither: material that is identifiable, confidential or that you have no right to share. Describe how access can be requested instead.

If you deposit data or code, our guide to citing data, software and code explains how to reference them so they count as citable outputs.

How to prepare supplementary files, step by step

1. Read the journal's supplement rules first

Before you build anything, find the section of the instructions for authors that covers supplementary material. Look for the labelling convention, accepted file formats, size limits, whether everything goes in one file or several, how references are handled, and whether the files will be edited. Journals differ on all of these. JAMA asks for online-only material as a single document with consecutively numbered pages; PLOS accepts separate files of almost any type.

2. Sort every item into article, supplement or repository

Apply the integral-or-additional test from earlier to each table, figure and section you are considering moving. Do this before you trim for word count, not after, so that the decision is about what readers need rather than what fits.

3. Label and number every item in the journal's style

Use the journal's own convention exactly. JAMA prefixes online-only elements with "e" (eTable 1, eFigure 1, eMethods). PLOS requires an "S" and a number (S1 Table, S2 Fig) and asks that file names match the captions, so the file for S2 Fig is named S2_fig. Number items in the order they are first cited, and give each a short descriptive title.

4. Cite each item in the main text

Point to every supplementary item at the place where a reader would want it, not only in a list at the end. NISO recommends in-text citation and links at the relevant point because it gives readers context and immediate access. If an item is never cited, ask whether it needs to be published at all. PLOS also asks that supporting information captions be listed at the end of the manuscript file.

5. Make each file understandable on its own

Readers often reach supplementary files directly, without the article open beside them. Start each file with the article title, the authors and a list of what it contains; JAMA asks that the first page of the online-only document list the number and title of each element. Give every table and figure a full caption, define abbreviations again, and state units. The standards in our guide to tables and figures in medical papers apply here as much as in the article.

6. Check references, privacy and consistency

Handle references as the journal requires. JAMA asks for a separate reference section in the online-only document that includes every reference cited there, even those also cited in the main manuscript; other journals fold supplement references into the main list. Then check for identifiers: names, dates, record numbers, faces in images, and hidden content such as tracked changes, comments, hidden spreadsheet tabs and file metadata. Finally, confirm that every number in the supplement matches the main text, the abstract and the tables.

7. Submit the supplement with the manuscript, and keep it current

Upload the supplementary files with the first submission so reviewers can see them, as ICMJE recommends. When you revise, update the supplement as carefully as the article. A revised main table with an unrevised eTable is a common, avoidable inconsistency, and reviewers who checked the first version may check again.

Assume it will be published exactly as you send it

This is the point that should change how senior authors supervise supplements. Many journals do not copyedit or typeset supplementary files. PLOS states that supporting information files are published exactly as provided and are not copyedited. JAMA states that online-only material will not be edited or formatted, so authors are responsible for the accuracy and presentation of all such material. NISO RP-15-2013 recommends that unedited content be labelled as supplied by the author.

That has three consequences:

• Errors stay in the record. A wrong axis label or a transposed column in a supplement is published with your name on it, and fixing it later may require a formal correction.
• Reviewers judge it. JAMA puts online-only material through peer review with the manuscript, as ICMJE recommends, so a careless supplement weakens confidence in the whole paper.
• Formatting is your job. Fonts, page breaks, legible figures and readable file formats are not something production will tidy up. A PDF is usually the most predictable format for documents; check whether the journal also wants editable source files.

On a multi-author paper, assign one person to own the supplement, and include it in the final read-through that every author signs off. It is easy for a junior colleague to assemble it late, after the senior authors have stopped reading.

Before you upload: a supplement checklist

1. Nothing a reader needs to judge the main finding is only in the supplement
2. Labels follow the journal's convention and match captions and file names
3. Every item is cited in the main text, and every citation points to an existing item
4. Each file opens with the article title and a list of contents
5. Captions, units and abbreviations make each table and figure stand alone
6. References handled as the journal requires
7. No identifying details, tracked changes, comments or hidden spreadsheet tabs
8. Numbers match the main text, abstract and tables after the final revision
9. Datasets and code deposited in a repository and cited with their identifiers
10. File sizes and formats within the journal's limits
11. Every author has seen the final supplement

Directive Publications sets out its requirements for manuscripts in its author guidelines. Check them, or the instructions of whichever journal you are targeting, before you assemble the files.