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:
- having a personal relationship with any author
- having worked or published with any of the authors in the past 3 years
- having a financial interest in the work or the outcome of the manuscript
- working on the same topic or in direct competition with any of the authors
- having seen or advised on drafts of the manuscript.
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.
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:
- Do not disclose your role in reviewing the manuscript.
- Do not discuss the manuscript with anyone who is not directly involved in the peer review process.
- Do not use any information from an unpublished manuscript in your own research or publications.
- Do not cite any unpublished manuscripts or their contents.
- Do not reveal your identity to the authors during the peer review process without first obtaining the Editor’s approval.
- Check with the Editor before consulting colleagues (either within or outside your own research group) about the manuscript, to ensure that you do not inadvertently violate confidentiality or impartiality.
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.
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.
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:
- a short summary of the manuscript, including comments about samples and methods
- a general overview of the manuscript’s strengths and weaknesses
- statement whether all items in the metadata checklist are satisfied
- numbered comments that address specific criticisms about the manuscript.
When preparing your comments, consider the following aspects of the manuscript:
- Relevance: Does the work fit the journal’s scope and readership?
- Reproducibility: Do authors show sufficient information to reproduce their experiments or data?
- Written quality: Is the manuscript clearly presented?
The following questions may help you to assess each part of the manuscript:
- Does the Title accurately reflect the manuscript’s datasets or protocols?
- Does the Abstract adequately describe the background or context of the work, the objectives of the research project and the methods used?
- Does the Introduction provide adequate background and context for the work?
- Have the authors clearly presented the need for the data and protocols and their novelty?
- Data descriptions (for Data Descriptor manuscripts)
- Have the authors described the sample metadata in enough detail? Please refer to metadata checklist.
- Have the authors clearly explained the relationship between samples and data files?
- Have the authors clearly explained the correspondence between samples and labels such as SILAC and TMT?
- Materials and Methods (for Protocol and Data Processing Note)
- Have the authors described the methods in enough detail to allow others to replicate them?
- In the case of human/animal experimentation, have the authors adhered to established codes of practice and ethics?
- Did the authors use appropriate methods?
- Results (for Protocol and Data Processing Note)
- Have the authors explained their results clearly and adequately?
- Discussion (for Protocol and Data Processing Note)
- Is the Discussion supported by the results?
- Have the authors considered any alternative explanations for their results?
- Have the authors made unsupported claims or inappropriate speculations?
- Are all cited references relevant and necessary? Has any relevant literature been omitted?
- Have the authors cited the data described in the manuscript adequately?
- Is each table and figure necessary? Are any potentially useful ones missing?
- Are the tables and figures complete and interpretable?
- Is the manuscript clearly written?
- Have the authors adhered to established codes of publication ethics?
- Are there any errors in fact, methodology, or analyses?
- Has the manuscript been published previously, in part or in whole, in any language?
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:
- a summary of your comments to the author(s), to help the Editor quickly assess your review
- your recommendation regarding publication in the journal. Setting out clear arguments for or against publication is more helpful than simply stating your recommendation to accept or reject the manuscript.
- if it is not suitable for publication, any advice on how the manuscript could be improved to encourage resubmission in the future.
- any concerns you may have about potential ethical violations in either the research or the manuscript.
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.
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.
Journal of Proteome Data and Methods Editorial Office: firstname.lastname@example.org