When answering peer review questions, reply point-by-point with gratitude, evidence, and clear changes that map to each comment.
Peer review can feel daunting on the first read. Questions keep coming, some simple, some thorny. A solid plan makes the heavy lift lighter. This guide turns feedback into a clean, persuasive reply set that moves your paper forward.
Editors and reviewers want clarity, traceability, and a professional tone. Many journals ask for a point-by-point response that quotes each comment and shows the exact change. You can see this approach in Springer Nature’s revising and responding guide and in Elsevier Researcher Academy advice.
Answering Peer Review Questions Step-By-Step
Skim, Sort, And Cool Off
Read the decision letter and all reports from start to finish without writing a word. Step away for a few hours. When you return, tag each point as major, moderate, or minor. Group similar items across reviewers. That bird’s-eye view keeps you from fixing the same issue three times.
Map Every Comment To An Action
Create a working table that pairs each reviewer question with your planned action. This becomes your to-do list and later the spine of your response letter.
| Comment Type | What It Signals | First Move |
|---|---|---|
| Missing citation | Evidence gap | Add a current source or justify choice with context. |
| Unclear method | Reproducibility risk | Expand steps, parameters, and software versions. |
| Stats concern | Validity question | Re-run checks, report exact tests and effect sizes. |
| Scope creep | Beyond study aim | Explain boundaries and refine the claim. |
| Contradictory result | Interpretation issue | Compare with prior work and narrow the wording. |
| Sample size | Power question | Report calculations; add data if available. |
| Writing clarity | Readability issue | Rewrite the passage; fix grammar and flow. |
| Figure quality | Legibility problem | Increase resolution; simplify labels. |
| Ethics/consent | Compliance check | Add approvals, registry IDs, and consent text. |
| Novelty claim | Overstatement risk | Tone down claims; show precise contribution. |
Draft A Point-By-Point Response
Most journals want a response letter that mirrors each comment and your reply. Use clear labels, quote the reviewer verbatim (short quotes), and reference page and line numbers for every change. Keep the voice calm and direct.
Use Clear Labels And Line Numbers
Number the comments: R1-C1, R1-C2, R2-C1, and so on. When you cite a change, point to the exact page and line range in the revised manuscript. That single habit saves editors time and shows control of the revision.
Quote, Reply, Then Show The Change
Structure each item as three blocks: the quoted comment, your reply, and a short “Change made” note. This format is easy to scan and reduces back-and-forth.
Tone, Evidence, And Boundaries
Stay Polite, Even When You Disagree
Thank the reviewer before you answer. If a point rests on a misunderstanding, take the blame for not being clear and improve the wording in the paper. Keep any disagreement factual and measured. Respect wins trust.
Show Proof Fast
Back claims with data, citations, or short calculations. Where a request needs new analyses, add them and report the outcome. If you can’t include raw data due to policy, say so and offer a path to access if the journal allows.
When A Request Isn’t Feasible
Some asks don’t fit the study aim, budget, or timeline. Explain the constraint in plain terms, give any supporting reference, and show what you did instead. Propose a line that acknowledges limits in the Discussion.
Structure Of A Response Letter That Works
Cover Letter To The Editor
Open with sincere thanks. Give a short, crisp overview of major changes: new analyses, added datasets, trimmed claims, and major rewrites. State that a detailed point-by-point file follows.
The Point-By-Point File
Present each reviewer in turn. Keep your replies concise and complete. Bold your responses or use a tint box so they don’t blend with the quotes.
Marked And Clean Manuscripts
Upload a marked version with tracked changes or highlights plus a clean version. That pair lets editors verify edits quickly.
Workflow Timeline And File Naming
Set a simple schedule. Day 1–2: read, cool off, and sort. Day 3–5: run analyses and draft replies to major points. Day 6–7: finish minor fixes and polish. Add a buffer for co-author input and sign-off.
Name files so the editor never guesses. Use a pattern like Manuscript_TrackChanges_DATE, CleanManuscript_DATE, ResponseToReviewers_DATE, and Supp_Figures_DATE. Inside the response file, add a short contents list that maps sections and reviewer labels.
Common Reviewer Questions And Ready Moves
Most threads fall into a few buckets. If a reviewer asks for stronger positioning, add a short paragraph in the Introduction that frames the gap and cites recent work. If the question is about claims, narrow verbs and hedge where the data warrant caution. When a figure confuses readers, reduce panels, boost font size, and move detail to the supplement.
When comments ask for context, add a short related-work bridge at the end of the Results to connect your findings to the field. If a term caused confusion, add a one-line definition on first use and keep it steady across the paper. When an edit touches many places, track a compact list of pages and lines so you can reference them in one go.
Make Your Manuscript Changes Obvious
Use tracked changes or highlights in the marked file. In figures, annotate new panels with simple labels such as “Added per R2-C4.” In tables, add footnotes to mark updated numbers. Small cues help editors confirm edits within minutes.
When a change spans sections, add a one-line note in the response file that lists all affected pages. That way the editor doesn’t hunt through the PDF to piece it together.
Data, Code, And Materials
Many journals ask for open data or at least a path for access. If you can share, link a repository and include a README that matches variable names to the paper. If policies limit sharing, say so in plain terms and provide a minimal de-identified set or full code so others can rerun your analyses.
Keep versions tight. Freeze the code used for new runs and tag a release. Note package versions in the Methods. Small details prevent confusion in later rounds.
Editor Signals That Speed Decisions
Editors value replies that are easy to verify. Clear labels, exact page and line pointers, and a short overview of major changes reduce friction. A respectful tone across the file matters as well; many guides, including those from leading publishers, stress this point, and steady review timing.
Answering Peer Review Questions With Clarity
Use short starters to handle common lines of questioning and keep a calm tone. These lines save time and keep replies tidy.
Tricky Cases And Smart Moves
Conflicting Reviews
State the conflict in one line. Choose a path, explain the trade-off, and adjust the text so the reader sees the logic. Invite the editor to guide you if needed.
Requests Beyond The Study Scope
Show that you understand the value of the idea, then place it in a short “Next steps” note or a limit paragraph. Keep your main claim tight and document the reason for not running the extra work now.
New Experiments And Added Analyses
When you add work, keep records. Name files clearly, note seeds and versions, and update figure captions. If results shift the story, adjust the Abstract and Conclusions.
Language, Style, And Formatting
If reviewers flag grammar, run a full edit. Fix tense, voice, and structure. Shorten long sentences. Replace jargon where plain words will do. Good prose eases later rounds.
Final Checks Before Re-Submission
Before you hit send, run a fast audit:
- Every reviewer point has a matching reply and a change in the manuscript or a clear rationale.
- Page and line numbers point to each change.
- New figures and tables meet journal specs and file limits.
- Data, code, and materials are linked or archived as the journal requests.
- The cover letter lists major changes in plain language.
Take one more break. Read your response file fresh, out loud if you can. Tighten any long lines.
| Situation | Useful Openers | Pitfall To Avoid |
|---|---|---|
| Conflicting advice | “We thank both reviewers. The requests differ on X; we followed Y and explain below.” | Picking a side without rationale. |
| Request beyond scope | “We agree this path is interesting. Our study targets Z; we now state this boundary on p. X.” | Dismissing the idea outright. |
| Method clarity | “We expanded the protocol with step-by-step settings and software versions (p. X).” | Vague promises to clarify. |
| Stats choice | “We re-ran the analysis with the suggested test; results match and are now reported on p. X.” | Defending a test with no data. |
| New experiment | “Resources limit new wet-lab work. We added a power check and a sensitivity run to answer the concern.” | Blaming reviewers or budget. |
| Language edits | “We edited the full text for grammar and flow; main lines rewritten on pp. X–Y.” | Claiming edits with no pointers. |
| Citation gap | “We added recent work that covers this angle and cite it in the Introduction and Discussion.” | Padding with unrelated sources. |
| Data access | “Data share is limited by policy; a de-identified set and code are now in the repository.” | Ignoring journal data rules. |
Short Response Letter Sample
R1-C3: “The method section is thin; main parameters are missing.”
Response: Thank you for pointing this out. We expanded the protocol with exact settings, seed values, and software versions. Change made: Methods, p. 5, lines 112–148.
R2-C2: “The claim of novelty is too strong.”
Response: You’re right that our phrasing overstated the advance. We now present the contribution as incremental and cite recent related work. Change made: Introduction, p. 2, lines 36–49; Discussion, p. 14, lines 320–334.