Online manuscript review

We strongly recommend referees submit their comments via our online submission system by following the link provided in the editor's email. For help with the system please click here or contact us.

About Nature Protocols

Nature Protocols is a forum for the publication of protocols. Although it comes from the same publisher as Nature and Nature Methods, Nature Protocols is editorially independent. As with the other Nature titles, there is no external editorial board, and all editorial decisions are the responsibility of the full-time editorial staff, we thus value the opinion of the expert reviewers we select. More information about Nature Protocols, including aims and scope of the journal, can be found here. For any additional queries about Nature Protocols, we encourage referees to contact us.

Criteria for publication

Nature Protocols is a forum for the publication of proven protocols. Thus the protocols we publish must have been used by the authors of published research papers to undertake the research published therein; and we do not publish primary research. Nevertheless, we appreciate that protocols are constantly evolving, thus if the methodology has been improved on since the original publication, we invite our authors to give us the latest version of the protocol, as this will be most useful to our readers. We are interested in reviewers' views on both the technical merits of the work and its interest to a broad readership. Over time we seek to publish all protocols currently used, and are keen to publish the best possible version of each.

The review process

All submitted manuscripts are read by the editorial staff. To save authors and referees time, only those papers that seem most likely to meet our editorial criteria are sent for formal review. Those papers judged by the editors to not be in protocol style, or of insufficient general interest, are rejected promptly without external review (although these decisions may be based on informal advice from experts in the field).

Manuscripts judged to be of potential interest to our readership are sent for formal review, typically to two or three reviewers. The editors then make a decision based on the reviewers' advice, from among several possibilities:

• 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.

Referees are welcome to recommend a particular course of action, but they should bear in mind that other referees may have different views, and the editors may have to make a decision based on conflicting advice. The most useful reports, therefore, provide the editors with the information on which a decision should be based. Setting out the arguments for and against publication is often as helpful as a direct recommendation one way or the other.

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 we make our decisions accordingly.

We may go back to referees for further advice, particularly in cases where referees disagree with each other, or where the authors believe they have been misunderstood on points of fact. We therefore ask that referees should be willing to provide follow-up advice as requested. We are very aware, however, that referees are normally reluctant to be drawn into prolonged disputes, so we try to keep consultation to the minimum we judge necessary to provide a fair hearing for the authors.

Editors will not send resubmitted papers to the referees if it seems that the authors have not made a serious attempt to address the referees' criticisms.

We take referees' criticisms very seriously, and in particular, we are very reluctant to disregard technical criticisms. In cases where one referee alone opposes publication, we may consult with the other referees as to whether s/he is applying an unduly critical standard. We occasionally bring in additional referees to resolve disputes, but we prefer to avoid doing so unless there is a specific issue on which we feel a need for further advice.

Selecting referees

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.

We normally check with potential referees before sending them manuscripts to review. Referees should bear in mind that these messages contain confidential information, which should be treated as such.

Writing the review

The primary purpose of the review is to provide the editors with the information needed to reach a decision, plus to make suggestions as to how the manuscript can be improved, should this be deemed appropriate. As far as possible, a negative review should explain to the authors the weaknesses of their manuscript, so that rejected authors can understand the basis for the decision. Confidential comments to the editor are welcome, but it is helpful if the main points are stated in the comments for transmission to the authors. It can be difficult to justify an editorial decision if contradictory messages are transmitted to the Editors and Authors.

We ask referees to comment on whether the above criteria for publication have been met, plus to answer the following questions:

• Are the title and abstract/summary appropriate for this protocol?
• Do the applications of the protocol described in the introduction seem reasonable?
• Are there any other potential applications for the protocol the author could discuss?
• Are all the materials and equipment needed listed? Basic materials or equipment that a lab using the type of protocol would have already does not need to be listed, e.g. pipette.
• Do you think the steps listed in the procedure would lead to the described outcome?
• Are the steps listed in the procedure clearly explained?
• Are any important steps missing from the procedure?
• Are appropriate controls suggested?
• Are all the critical steps highlighted?
• Is the time-line realistic?
• Is the troubleshooting guide, if included, thorough? If it is not included would it be a useful inclusion?
• Is there any additional information that it might be useful to include?
• Are the anticipated results reasonable, and if so, are they useful to readers?
• Are any important references missing?
• Are the references included useful?
• Could a competent PhD/graduate student in this discipline successfully implement the protocol with minimum guidance?
• Could the protocol be improved by additional figures or tables, such as diagrams of equipment set up, schematics of protocol stages, etc.

Wherever possible, when considering the above questions, it would be helpful if referees could supply guidance as to how the protocol could be improved to address any issues the referee highlights. Please note that we do not expect reviewers to perform the procedure described, as we appreciate this is not practical in the time frame required for prompt publication.

Confidentiality

We ask referees to treat the review process as strictly confidential, and not to discuss the manuscript with anyone not directly involved in the review. It is acceptable to consult with laboratory colleagues, but please identify them to the editors. Consulting with experts from outside the referee's own laboratory may be acceptable, but please check with the editors before doing so, to avoid involving anyone who may have been excluded by the authors.

Timing

Nature Protocols is committed to rapid editorial decisions and publication, and we believe that an efficient editorial process is a valuable service both to our authors and to the scientific community as a whole. We therefore ask referees to respond promptly (normally within ten days of receiving a manuscript, although this may be either longer or shorter by prior arrangement). If referees anticipate a longer delay, we ask them to let us know so that we can keep the authors informed and, where necessary, find alternative referees.

Anonymity

We do not release referees' identities to authors or to other referees, except when referees specifically ask to be identified. Unless they feel strongly, however, we prefer that referees should remain anonymous throughout the review process and beyond. Before revealing their identities, referees should consider the possibility that they may be asked to comment on the criticisms of other referees; identified referees may find it more difficult to be objective in such circumstances.

We ask referees not to identify themselves to authors without the editor's knowledge. If they wish to reveal their identities, this should be done via the editor.

We deplore any attempt by authors to confront referees or determine their identities. Our own policy is to neither confirm nor deny any speculation about referees' identities, and we encourage referees to consider adopting a similar policy.

Editing referee reports

As a matter of policy, we do not suppress referees' reports; any comments that were intended for the authors are transmitted, regardless of what we may think of the content. On rare occasions, we may edit a report to remove offensive language or comments that reveal confidential information about other matters. We ask referees to avoid saying anything that may cause needless offense; conversely, authors should recognize that criticisms are not necessarily unfair simply because they are expressed in robust language. In the event that we disagree with a referee's comment, for example, should it contravene house editorial style, we will insert a comment to that effect, clearly from the Editor, within the referee report, or indicate this in a covering letter to the author.

Competing interests

Our normal policy is to avoid referees whom the authors have excluded, for whatever reason. We also usually try to avoid referees who have recent or ongoing collaborations with the authors directly related to the procedure described, who have commented on drafts of the manuscript, who we know to have a history of dispute with the authors, or who have a financial interest in the outcome. It is not possible for the editors to know of all possible biases, however, so we ask referees to draw our attention to anything that might affect their review, and to decline to review in cases where they feel unable to be objective.

We recognize, however, that competing interests are not always clear-cut, and the above circumstances need not automatically undermine the validity of a report. Indeed, the people best qualified to evaluate a paper are often those closest to the field, and a skeptical attitude toward a particular claim does not mean that a referee cannot be persuaded by new evidence. We try to take these factors into account when weighing referees' reports.

Feedback

We appreciate that many researchers will not have reviewed a protocol previously; we thus welcome feedback on the review process and welcome suggestions for improvement to it.