Peer Review and Publication

This section explains the editorial processes at Nature Protocols, which can be outlined in the following steps:

  1. The author submits a manuscript and it receives a tracking number.
  2. An editor is assigned to the manuscript.
  3. The editorial team decides whether to send the manuscript out to review. If the decision is not to send the manuscript for review, the editor contacts the author with the decision.
  4. The editor assigns potential reviewers to the manuscript and the author is notified.
  5. Reviewers agree to review the manuscript.
  6. Reviewers submit their reports to the editor.
  7. The editorial team discusses the reports and the editor makes the final decision. This process may involve further consultation with the reviewers and editor-mediated communications between the reviewers.
  8. The editor contacts the author with the decision.
  9. If the decision is negative, the author can choose to upload their protocol to Protocol Exchange (www.nature.com/protocolexchange/) instead. Protocol Exchange is an open-access online repository for protocols, which is completely free to use (no article-processing fee). All uploaded protocols are made freely available, assigned a DOI for citation purposes, and published under a CC-BY licence. Protocols can be linked to any publications in which they are used. You can also establish a dedicated page to collect all the Protocols used in your lab. By uploading your Protocols to Protocol Exchange, you are enabling researchers to more readily reproduce or adapt your methodology, as well as increasing the visibility of your research. Protocol Exchange acts as a preprint server for protocols and sharing your protocol does not preclude publication in Nature Protocols should you wish to resubmit at a later date. 

On this page: First editorial decision | Peer review | Decision after review and revision | Acceptance and publication | Appeals

First editorial decision

When a new submission is received, it is assigned to a primary editor, who consults with the other editors and decides whether it should be sent for peer review based on our editorial criteria. Like other journals in the Nature family, Nature Protocols has no external editorial board, although we send some presubmission enquiries for informal peer review to help ensure authors are only asked to prepare full versions of protocols that are suitable for publication in Nature Protocols. The primary purpose of getting experts in the field to informally review a presubmission enquiry is to establish whether a full version of the proposed protocol would be of sufficient interest to our readers.

Peer review

All submitted manuscripts are read by the editorial staff. To save authors and referees time, we only send articles that meet our editorial criteria for formal peer review. Referee selection is critical to the review process, and we base our choice on many factors, including expertise, reputation, specific recommendations and our own previous experience of a referee’s characteristics. For instance, we avoid using referees who are chronically slow, careless, too harsh or too lenient. Author suggestions for referees are often helpful, although they are not always followed. We ask referees to consider both the technical merits of the work and its interest to a broad readership. By policy, referees are not identified to the authors, except at the request of the referee.

Decision after review and revision

When all the referee reports are received, the editors then make one of the following decisions based on the reviewers’ advice:

  • Accept, with or without editorial revisions
  • Invite the authors to revise their manuscript to address specific concerns before a final decision is reached
  • Reject, but indicate to the authors that resubmission may be appropriate in the future, typically if parts of the protocol have not been sufficiently validated by prior publication of appropriate primary papers.
  • Reject outright, typically on grounds of inaccuracies or lack of usefulness.

Editorial decisions are not a matter of counting votes or numerical rank assessments, and we do not always follow the majority recommendation. We try to evaluate the strength of the arguments raised by each referee and by the authors, and we may also consider other information not available to either party. Our primary responsibilities are to our readers and to the scientific community at large, and in deciding how best to serve them, we must weigh the claims of each paper against the many others also under consideration.

In cases where the referees have requested well-defined changes to the manuscript that do not appear to require extensive further experiments, editors may request a revised manuscript that addresses the referees' concerns. The revised version is normally sent back to some or all of the original referees for re-review. The decision letter will specify a deadline, and revisions that are returned within this period will retain their original submission date. An invited revision should be submitted via the revision link to the online submission system provided in the decision letter, not as a new manuscript. The revised manuscript should be accompanied by a cover letter that includes a point-by-point response to referees' comments and an explanation of how the manuscript has been changed.

Acceptance and publication

If the authors have successfully addressed all the comments of the reviewers and the editors, the editors will deem the paper acceptable for publication and authors will be invited to make minor changes and submit a final version. For the final revision, authors should use the revision link to the online submission system provided in the decision letter to upload a final version of the text with all the requested format changes. Electronic files of the final figures, at high resolution, should be sent separately.

Once all editorial issues are resolved, the paper is formally accepted. The received date is the date on which the editors received the original (or if previously rejected, the resubmitted) manuscript. The accepted date is when the editor sends the acceptance letter. Authors have a chance to review the final text and display items in a typeset proof. Only essential changes (e.g. factual incorrectness, typing errors, layout problems) should be made at this stage. Authors are welcome to discuss proposed changes with the editors, but Nature Protocols reserves the right to make the final decision about matters of style and figure size.

A high priority of Nature Protocols is that all papers be accessible to non-specialists. Manuscripts are often subject to substantial editing to achieve this goal. All articles undergo editing by our in-house editors, taking into account structure, flow, clarity, language and scientific correctness, to ensure that the article meets our high publication standards. The degree of editing varies from article to article. All suggested changes are subject to approval by the authors before formal acceptance. After acceptance, a copy editor may make further changes so that the text and figures are readable and clear to those outside the field, and so that papers conform to our style. Nature Protocols uses British English spelling.

Advance online publication

Nature Protocols provides Advance Online Publication (AOP) of research articles, which benefits authors with an earlier publication date and allows our readers access to accepted papers before they appear in print. Note that papers published online are definitive and may be altered only through the publication of a print corrigendum or erratum, so authors should make every effort to ensure that the page proofs are correct. All AOP articles are given a unique digital object identifier (DOI) number, which can be used to cite the paper before print publication. Follow this link for details about advance online publication.

Cover and other artwork

Authors of accepted papers are encouraged to submit images for consideration as a cover. Cover images are normally linked to a specific paper in that issue, but we may also be able to use other images elsewhere in the journal, such as on the table of contents. Illustrations are selected for their scientific interest and aesthetic appeal. Please send prints or electronic files (rather than slides) in the first instance. Please also include a clear and concise legend explaining the image.

Appeals

Even in cases where editors did not invite resubmission, some authors ask the editors to reconsider a rejection decision. These are considered appeals, which, by policy, must take second place to the normal workload. Decisions are reversed on appeal only if the editors are convinced that the original decision was a factual mistake. Further consideration may be merited if a referee made substantial errors of fact or showed evidence of bias, but only if a reversal of that referee's opinion would have changed the original decision. If an appeal merits further consideration, the editors may send the authors' response or the revised paper to one or more referees, or they may ask one referee to comment on the concerns raised by another referee. On occasion, particularly if the editors feel that additional technical expertise is needed to make a decision, they may obtain advice from additional referees.