After a desk rejection: revise, transfer or appeal?

Read the decision letter before changing the manuscript. Not every message that stops a submission is a rejection, and not every rejection identifies a flaw in the underlying study. The next step depends on what the editor actually decided and why.

Set aside the temptation to send the paper immediately to the next title on a list. First classify the decision, identify which concerns travel with the manuscript and decide whether a revision, transfer or appeal addresses them. This guide offers a decision procedure, not a prediction of acceptance at another journal.

Identify which decision you received

A technical return requests information or changes needed to process the submission. An editorial rejection before external review ends consideration at that stage. A rejection following review may include external assessments as well as the editor’s judgement. A revision invitation keeps open a route for reconsideration under stated conditions.

Read the actual instructions and system status together. If they conflict, ask the journal office to clarify whether the manuscript remains under consideration. Do not infer a universal meaning from a familiar status label across different submission systems.

PLOS One’s published process distinguishes initial checks, which can result in a return for clarification, from editorial assessment and later decisions. It is a useful example of why “returned” and “rejected” should not be treated as synonyms. 1

Save the decision letter, submitted files and any reviews together. Mark which version received the decision. If a collaborator opens an older draft while interpreting the feedback, the team can waste time answering concerns about text that was never submitted or has already changed.

Translate the reason into a manuscript question

Write the editor’s stated reason in one column and the question it raises for the team in another. Keep quotations from the private decision letter within the team rather than circulating them publicly.

A scope rejection asks whether the paper addresses the journal’s readership or remit. An article-type rejection asks whether the format is eligible. A concern about evidential support asks whether the manuscript’s conclusions are justified. A missing reporting item asks whether the reader has enough information to evaluate the work. These questions lead to different actions.

Do not automatically treat every rejection as a request for more experiments. Nor should you assume that a different journal will overlook a material problem. Separate venue-specific expectations from issues that would matter wherever the work is published.

If the letter is brief, use the journal’s published criteria to interpret it cautiously. Do not invent a hidden reason such as reviewer hostility or institutional bias without evidence. A short letter may leave uncertainty; that is a reason to review the submission and fit, not to fill the gap with a confident story.

Scope and article type: when a new destination makes sense

Re-read the journal’s current aims and accepted article types. Compare them with the actual submission, not the paper you hoped the editor would see. Was the research question clear in the title and abstract? Did the cover letter explain a contribution relevant to the journal’s readers?

PLOS One’s criteria, for example, distinguish types such as systematic reviews and certain protocols from formats it does not ordinarily consider. That is a specific editorial policy, not a general rule about whether those other formats are valuable scholarship. 2

If the mismatch is real, choose a journal that considers the paper’s actual form. Do not relabel a narrative discussion as a systematic review or omit necessary limitations to make the work appear broader. A new destination may require different framing, but it should not require misdescribing the study.

Use the shortlist procedure to revisit audience and methods. Look at recent comparable articles and written criteria. Record why the next journal is a better fit so that the team is making a new decision rather than repeating the old one with a different name.

Reporting problems: repair the paper before moving it

An editor may be unable to assess a study because essential information is missing. Identify whether the missing information exists in the study records and can be reported accurately. Adding an explanation is different from discovering that a necessary procedure was never performed.

EQUATOR distinguishes reporting guidelines from study-design standards and quality-appraisal tools. In health research, an appropriate guideline can help identify what the manuscript needs to describe, but a completed checklist cannot repair a design flaw or certify the findings. 3

Check the current guideline and any relevant extension for the study type. Link each item to a section, table or supplementary file. If an item does not apply, explain why. If it was not done, report that honestly rather than writing a retrospective description that implies it was planned or completed.

Read the abstract and discussion again after correcting the methods. Sometimes the necessary revision is a narrower claim rather than a longer description. Ask a co-author with relevant methodological expertise to confirm that the revised interpretation matches the evidence.

Data and ethics concerns need their own review

Do not treat concerns about approvals, consent, registration or access to underlying data as cosmetic submission problems. Identify the factual record and consult the relevant institutional support before deciding how to respond.

PLOS’s data policy illustrates the distinction between a general wish to share and a specific required statement about access, including circumstances involving legal or ethical restrictions. A manuscript should not promise unrestricted access to data that cannot responsibly be released. 4

Gather the applicable approvals, protocols, permissions and data-access arrangements. Determine which statements need correction and whether the issue affects the study’s interpretation or suitability for publication. Where the answer is uncertain, seek appropriate institutional advice rather than submitting elsewhere with the same unresolved assertion.

Keep the editor informed if a requested clarification is taking time and the manuscript remains active. If the decision is final, resolve the underlying issue before making new declarations at another journal. A change of venue does not remove the author’s responsibility for the submission’s accuracy.

A decision guide after the first reading

Use this sequence with the decision letter in front of you. It is a planning tool, not a journal policy.

What the letter establishes	First action	Possible next route
Files or information are missing; submission remains active	Complete the specific request	Return through the existing submission
Clear mismatch with scope or article type	Reassess journal fit	Revise framing and submit to a suitable venue
Reporting gaps obscure an otherwise assessable study	Audit records and reporting	Revise before any resubmission
A material methodological or integrity issue is raised	Evaluate the issue with the right expertise	Further work, narrower claims or pause
A consequential factual misunderstanding appears in the decision	Check the submitted version and appeal policy	Focused clarification or formal appeal
A transfer is offered	Check the receiving journal independently	Accept or decline the transfer offer

If several rows apply, address the issue with the greatest consequence first. An appealing transfer offer should not distract from an unresolved problem with the data. A scope mismatch should not trigger an elaborate appeal if the journal’s written remit plainly excludes the article.

Agree on one route with the co-authors and record who will carry it out. Parallel, uncoordinated messages to different editors can create confusion about what the authors are requesting.

Evaluate a transfer as a new journal choice

A transfer may reduce administrative work by moving files or review material, but it is not the same as acceptance. Read what the offer says will move, what consent is needed and what the receiving journal will assess independently.

Check the receiving journal’s scope, article types, charges, licences, indexing and data requirements. Reconfirm institutional funding if the title or publishing route changes. Do not assume an agreement covering the first journal also covers the second.

Inspect the transferred files before finalising the submission. Remove obsolete cover-letter references and update journal-specific statements. Ensure the manuscript still reflects the co-authors’ agreed revisions and that the author list, affiliations and disclosures are correct.

If reviews transfer, decide how the new submission should address them under the receiving journal’s instructions. Do not conceal a substantive issue simply because a different editor will handle the paper. Conversely, do not claim that transferred reviews oblige the new journal to reach a particular decision.

Declining a transfer can be reasonable when another journal fits better. Make that choice on evidence about the destination rather than on the convenience or prestige of the original publisher’s invitation.

Appeal only when the policy and evidence support it

An appeal should identify something that could change the decision: a consequential factual error, a demonstrable misunderstanding of the submitted work or another ground recognised by the journal’s policy. Disappointment, urgency and the amount of effort invested in the study do not by themselves answer the editor’s reasoning.

PLOS One requires a formal written appeal through its stated process and treats the manuscript as still under consideration during the appeal. Its appeal decision is final. Other journals may use different grounds, forms and timelines, so read the target policy before writing. 1

Check the submitted version carefully. Was the information really present and easy to find, or only clear in your internal understanding of the project? If the paper did not explain a crucial point, acknowledge that and describe the correction rather than insisting the editor should have inferred it.

Do not submit the paper elsewhere while an appeal leaves it under active consideration. Establish its status first. If you decide to stop the appeal and move on, follow the journal’s process and retain written confirmation where appropriate.

A focused appeal outline

This is a blank structure to adapt only where the journal permits an appeal:

We request reconsideration of decision [identifier and date] on the following ground permitted by your policy: [ground].

The decision states [specific point]. In the submitted version, [section or evidence] addresses this point by [brief explanation]. We believe the distinction matters because [effect on the decision].

We propose [specific clarification or correction]. The remaining concerns are [acknowledged issues and response]. We understand that reconsideration does not guarantee external review or acceptance.

Keep the request bounded. A concise account of one material issue is easier to assess than a document arguing against every unfavourable phrase. Have a co-author check tone and accuracy before sending it.

Record what you decided not to change

Keep a brief internal note of concerns the team considered but did not act on, with the reason. This can distinguish a deliberate scientific judgement from an overlooked comment when another journal later raises a similar issue.

The note should not become a defensive dossier against the editor. State the question, relevant evidence and the team’s conclusion. Revisit that conclusion if the manuscript or evidence changes. If the same concern appears repeatedly, examine whether the explanation is reaching readers clearly enough, even if the team still considers its scientific position sound.

Audit the package before the next submission

Whether you revise for the same journal or choose another, inspect the whole package. A corrected manuscript can be undermined by an outdated abstract, supplement or form entry.

Package element	Question for the team
Title and abstract	Do they state the actual design and supported contribution?
Methods and reporting checklist	Can each necessary detail be located?
Results, tables and figures	Do labels, denominators and descriptions agree?
Discussion	Are claims proportionate and limitations explicit?
Data and code statements	Do links and access conditions match reality?
Author information	Has everyone approved the current version and declarations?
Cover letter	Does it address this journal without overstating novelty?
Supplementary files	Are they current, named clearly and cited correctly?
Prior submission status	Is the earlier consideration closed or otherwise resolved?

For a revision at PLOS One, the specific instructions require a response and both marked and clean manuscript copies; existing supporting files can carry forward unless replaced. That is a reminder to inspect inherited files rather than assuming the system has selected the right versions. 5

End the audit by opening the generated submission PDF or equivalent preview. Read it as the editor will see it. Confirm that the files, order and references are intact before completing the submission. The useful outcome of a rejection review is a better-supported next decision and a coherent manuscript package, not simply another submission date.