For Reviewers
What the Journal of Proteomics and Genomics Research asks of a reviewer: how to weigh an invitation, what to assess, how to write the report, and the obligations that hold from the moment you accept.
- ISSN 2326-0793
- Crossref DOI prefix 10.14302
- Open access · CC BY 4.0
The invitation
Deciding whether to take it
An invitation carries the title and abstract so that the decision can be made before the full manuscript is opened. Three things settle it: whether the subject is one you can judge, whether any interest of yours bears on it, and whether you can give it the time it needs.
Accept
Accept where the methods and the subject fall within your own field, where you hold no interest in the work or its authors, and where the reading and the report can be fitted into the period agreed with the editorial office.
Timing is settled for the manuscript in hand when the invitation is accepted. Where more time turns out to be needed, telling the office early lets the authors be kept informed.
Decline
Declining promptly is the most useful answer where the work sits outside your field, or where a financial, institutional or personal interest touches it. Reviewers are asked to declare any interest that would affect their assessment, and to decline the invitation where one exists.
Suggesting a colleague who could judge the work is welcome, and helps the editor more than a late decline.
A manuscript reaches an invitation only after editorial screening. All submissions undergo initial editorial screening. Manuscripts that meet the journal’s scope and minimum requirements proceed to independent peer review.
The assessment
What a review of this journal’s work covers
The editor is deciding on scope, scientific quality, methodological rigor, ethical compliance, reporting quality, and relevance to the journal. A report is most useful when it speaks to those directly, and gives the evidence behind each judgment.
- Subject fit. The journal gives standing to proteomics on its own, to genomics on its own, and to work integrating the two across biological systems. The question is whether the proteomic or genomic contribution is central to the study rather than incidental to it. The Aims and Scope sets out the domains and the boundary.
- Design and methods. Whether the design can answer the question asked, whether sample preparation, instrumentation, sequencing depth, search parameters or variant calling are reported in enough detail to be repeated, and whether the controls support the comparisons drawn.
- Analysis and statistics. Whether the statistical treatment suits the data, whether multiple testing is handled where the study tests many features at once, and whether effect sizes and uncertainty are reported alongside significance.
- Data, code and reporting. Every empirical research manuscript must include a data-availability statement. Whether identifiers, accession numbers and repository links are given, and whether the analysis could be reproduced from what is described.
- Interpretation. Whether the conclusions stay within what the results show, and whether the limitations a reader would notice are acknowledged in the text.
- Ethics and declarations. Whether approvals, consent and declarations are present where the work requires them. Interventional clinical trials must be registered in an accepted public trial registry at or before the first participant provides consent for enrollment. The registry name, registration number, and registration date must be reported in the manuscript.
The report
Writing something the authors can act on
A report that opens with a short account of what the study did, in the reviewer’s own words, tells the editor at once whether the manuscript is being read as the authors intended. Major concerns follow, each tied to the section, figure or table it concerns, and minor points after them.
Specificity is what makes a report usable: a page or figure reference, the reason the point matters to the conclusions, and where possible what would resolve it. Comments framed around the work rather than the authors serve the same purpose and are easier to act on.
Where a citation would strengthen the manuscript, name it and give the reason the argument needs it. Reviewers suggesting their own work tell the editor so, and the editor weighs the suggestion accordingly.
Confidential remarks for the editor are separate from the comments sent to the authors. Both are read; only the latter reaches the authors.
The recommendation
Choosing a recommendation
The recommendation is advice to the editor rather than the outcome. Reviewers advise; the decision stays with the editor, who weighs the reports alongside the journal’s criteria.
| Recommendation | What it means here |
|---|---|
| Accept | The methods and the data support the conclusions as the manuscript stands. |
| Minor revision | The findings hold, and what remains is clarity, reporting detail or context that the authors can supply without further work at the bench or in the analysis. |
| Major revision | An analysis, a control or a validation the conclusions depend on is missing, and the work would stand if it were supplied. |
| Reject | The evidence does not support the claims, or the contribution falls outside the journal’s remit. |
Where the choice is genuinely finely balanced, saying so in the confidential comments, with the reason, helps the editor more than moving the recommendation a category.
Revisions
Coming back to a revised manuscript
A revised manuscript arrives with the authors’ response to the previous round. The task is narrower than the first review: whether each point raised has been answered, and whether the changes made have introduced anything new that needs attention.
Where the authors have answered a point with an argument rather than a change, the question is whether the argument holds. A reasoned disagreement, set out for the editor, is a complete answer to that round.
Points settled in the first round stay settled. Raising fresh requirements at a late round extends the process for the authors without improving the work, so a new point is worth making only where it bears on whether the conclusions stand.
Throughout
What holds from the moment you accept
- Confidentiality
- Submitted manuscripts are treated as confidential. Unpublished material stays within the assessment, and it is neither shared outside the review nor used in the reviewer’s own work.
- Manuscript files
- After submitting the review, reviewers should securely delete downloaded manuscript files and must not retain or use unpublished material.
- AI tools
- Reviewers must obtain journal permission before using AI to assist with a review. Any permitted use must be disclosed, and confidential manuscript content must not be uploaded where confidentiality cannot be assured. That requirement covers all unapproved externally hosted AI tools.
- Double-blind manuscripts
- For double-blind manuscripts, reviewers must not attempt to identify the authors.
- Review model
- Single-blind by default; double-blind review is available on request. Manuscripts that proceed to external peer review are normally evaluated by at least two independent subject-matter experts.
- Reviewer identity
- Reviewer identities are held in confidence under the single-blind model. A reviewer who wishes to be identified to the authors may ask the editor to sign the report on their behalf.
- Delegating a review
- Involving a colleague or a group member in a review is agreed with the editor beforehand, and everyone who contributed is named in the report.
The Editorial Policies give each of these in full, in the wording the journal publishes, and the For Editors page describes the same obligations from the editor’s side.
Concerns
When something in the manuscript looks wrong
A reviewer who suspects fabrication, falsification, plagiarism, image manipulation, undisclosed duplicate submission or an undeclared competing interest raises it with the editor rather than pursuing it with the authors. Concerns about a submitted or published manuscript are examined by the editorial office.
What helps is the specific observation and where it sits: the figure panel that repeats, the passage that matches an earlier paper, the dataset that appears elsewhere under different authorship. The editorial office takes the inquiry from there, and the identity of the person raising it is held in confidence.
Independence
What carries no weight in a review
An author’s payment status, membership, institution, funder, seniority, editorial board position or personal relationship to a reviewer carries no weight in the assessment of a manuscript, and confers no priority in review.
Reviewing for the journal likewise confers no advantage on a reviewer’s own submissions, which are handled exactly as any other manuscript is handled. The article processing charge of USD 2,100 is raised after a decision has been reached, by people other than the editors who reached it. Billing and fee-relief inquiries are handled by the editorial office and take no part in the editorial decision.
The governance safeguards behind that separation are described in the Editorial Policies.
Where to look
Taking a question further
The editorial office handles invitations, extensions, reassignment and any concern arising from a manuscript under review, and is the right first stop for a question this page leaves open.