Robust peer review is crucial to the quality and reputation of scholarly journals. The Journal of Proteome Data and Methods is extremely grateful to its reviewers for contributing their time, effort and expertise to this important process. This Guide to Reviewers provides advice for reviewers on preparing and submitting their reviews.

About the journal

The Journal of Proteome Data and Methods is an Open Access data journal published by Japanese Proteomics Society. The journal welcomes the submission of Data Descriptor, Protocol, Data Processing Note, and Review (which are invite-only). The official language is English, and single-blind peer review is employed. Articles are published online-only as they become available. Our main target audience is researchers who use and reuse proteomics data and need to keep abreast of the latest experimental methods, but we invite all those with an interest in proteomics and data-science to join us. The journal adheres to the principles and guidelines of the Committee on Publication Ethics (COPE).

Criteria of Acceptance

The Journal of Proteome Data and Methods is a data journal and also publishes articles on experimental and computational protocols. As such, the journal publishes articles that demonstrate detailed, robust presentation of datasets or protocols – regardless of their potential and/or perceived importance or impact. Reviewers provide evaluations of the consistency between data and metadata, and if sufficient descriptions are provided that enable the reproduction of the data and analyses. Review articles are evaluated by for interest, scientific importance and completeness.

Conflict of interest

A robust peer review process relies on reviewer feedback that is both fair and objective. If there are actual, perceived or potential circumstances that could influence a reviewer’s ability to act impartially, a conflict of interest exists.

The Editor will try to avoid conflicts of interest when inviting reviewers to assess a manuscript. However, it can often be difficult or impossible to identify potential bias. If you have been invited to review a manuscript, please consider if your ability to judge it fairly and objectively might be influenced by situations such as:

A conflict of interest may not be apparent until after you have accepted the invitation to review and have begun your assessment of the manuscript. If, at any time during the review process, you believe you may have a conflict of interest with a manuscript you are reviewing, please contact the Editorial Office immediately.


The Journal of Proteome Data and Methods aims to provide authors with efficient peer review and rapid editorial decisions. We ask reviewers to complete their reviews within two weeks. Please let the Editorial Office know as soon as possible if you expect your review to be delayed. This helps us to keep authors informed and to make alternative arrangements if necessary.


Unpublished manuscripts

Reviewers should treat all manuscripts confidentially throughout the peer review process. The Journal of Proteome Data and Methods asks reviewers to follow these guidelines at all times:

The Journal of Proteome Data and Methods recognizes that invited reviewers may wish to provide training to PhD students or post-doctoral staff by involving them in the review process. To ensure that their involvement does not violate the confidentiality of the review process, the invited reviewer must inform the PhD students and/or post-docs of these guidelines and let the Editor know their full names and positions. The invited reviewer is ultimately responsible for the quality and accuracy of the review.

Reviewer identity

The Journal of Proteome Data and Methods maintains the confidentiality of reviewers’ identities at all times. A reviewer’s name will be disclosed by journal staff only if the reviewer specifically asks for such disclosure.

Writing your review

A good review is concise yet comprehensive. It serves two main purposes: to provide the Editor with enough information to determine whether the manuscript should be published in the journal; and to give authors feedback on their manuscript and, if necessary, advice on how to improve it.

Review are separated into three parts in ScholarOne: multiple-choice question, comments to the author(s), and comments to the Editor.

Multiple-choice questions

This question concern your overall impressions of the manuscript, such as your recommendation on its suitability for publication. The answers to the question are shared only with the Editor, not the author(s).

Comments to the author(s)

Ideally, your review should include:

When preparing your comments, consider the following aspects of the manuscript:

The following questions may help you to assess each part of the manuscript:

When writing critical comments, make sure they are constructive and are aimed at the research, not the researchers. If you make assertions of fact, provide supporting evidence.

You should avoid making a recommendation for publication or otherwise in your comments to the author(s), as the Editor’s decision may be based on conflicting reviews.

Comments to the Editor

Helpful comments to the Editor include:

Comments to the Editor are kept confidential and are not shared with the author(s).

Submitting your review

Submit your review to the Journal of Proteome Data and Methods using the link provided in the Editor’s invitation email or by logging in to your account on the journal’s manuscript submission and peer review website. If you encounter any difficulties, please contact the Editorial Office.

Next steps

Please keep a copy of your review. If you recommended revision, the Editor may invite you to comment on the manuscript when it has been revised.

When the Editor makes a final decision on the manuscript, you will receive a copy of the decision letter along with all reviewers’ comments to the authors. Reviewers’ identities remain confidential unless a reviewer has signed their review.

Contact details

Journal of Proteome Data and Methods Editorial Office:

  1. About the journal
  2. Criteria of Acceptance
  3. Conflict of interest
  4. Timing
  5. Confidentiality
  6. Submitting your review
  7. Next steps
  8. Contact details