The Manuscript Submission Process: Step-by-Step Guide for Authors

Submitting a manuscript to a scientific journal is not a single action — it is a structured sequence of decisions, preparations, and handoffs that can span weeks before a paper ever reaches a reviewer. The process varies by journal, discipline, and publication model, but the underlying architecture is largely consistent across the field. Getting it right the first time matters: desk rejection rates at high-profile journals routinely exceed 50%, meaning more than half of submitted papers never reach peer review at all.

Definition and scope

The manuscript submission process encompasses every step an author takes from selecting a target journal through the editorial system's acknowledgment of a complete, compliant submission. It is distinct from peer review — that begins only after a submission clears the editorial desk — and from the production process that follows acceptance. Think of submission as the intake phase: a structured handoff from author to journal, governed by each publisher's author guidelines and, increasingly, by automated compliance checks built into submission platforms like Editorial Manager, ScholarOne, and Open Journal Systems.

The scope of submission requirements has expanded considerably in the open science era. Journals affiliated with the federal open access mandate or with Plan S signatories often impose data availability statements, ORCID authentication, funding disclosure, and conflict-of-interest declarations as mandatory submission fields, not optional courtesy gestures.

How it works

A complete submission follows a defined sequence. Skipping or partially completing any step typically triggers an automatic hold or outright rejection before human eyes see the manuscript.

  1. Journal selection — Match the manuscript's scope, methodology, and audience to a specific journal's aims. The journal selection decision is the single highest-leverage choice in the process.
  2. Author guidelines review — Every journal publishes a detailed guide covering word limits, section structure, reference format, figure resolution (commonly 300 dpi minimum for print), and file type requirements.
  3. Manuscript preparation — Structure the paper per guidelines: typically Title, Abstract, Keywords, Introduction, Methods, Results, Discussion, Conclusion, Acknowledgments, References, and Supplementary Materials. See writing a scientific manuscript for structural standards.
  4. Cover letter drafting — A cover letter is not optional filler. Editors at journals like Nature and Science explicitly use it to assess scope fit and significance before reading the abstract.
  5. Co-author confirmation — All listed authors must meet the ICMJE (International Committee of Medical Journal Editors) authorship criteria: contribution to conception or execution, drafting or critical revision, final approval, and accountability for the work (ICMJE, 2023 Recommendations).
  6. Account creation and metadata entry — Most platforms require separate entry of title, abstract, keywords, author affiliations, and funding sources as structured fields — even if the same information appears in the manuscript file.
  7. File upload and format validation — Submission systems run automated checks on file format, embedded fonts, and figure resolution. A failed format check typically returns an error before any human review.
  8. Ethics and compliance declarations — IRB approval numbers, clinical trial registration identifiers (e.g., ClinicalTrials.gov IDs), and data availability statements are now mandatory fields at journals indexed in MEDLINE and most Web of Science Core Collection titles.
  9. Submission confirmation — A system-generated confirmation with a manuscript ID marks the official submission date, which matters for priority claims and DOI dating via persistent identifiers.

Common scenarios

Desk rejection is the fastest outcome — and not always a negative signal about quality. Editors reject out of scope or format non-compliant manuscripts within 3 to 10 business days at most major journals, sometimes within 24 hours. A desk rejection on scope grounds can and should be followed immediately by resubmission to a better-fit venue.

Revision requests before review — Some journals return manuscripts with requests to reformat citations, add missing declarations, or reduce word count before the paper enters the evaluation queue. This is distinct from a peer-review revision request and requires quick turnaround, typically within 5 business days.

Transfer offers — Several major publisher groups (Springer Nature, Elsevier, Wiley) offer formal manuscript transfer pipelines between journals within their portfolio. A rejection from Cell might come with an offer to transfer files directly to a specialty Cell Press title. The author retains control but must evaluate fit independently.

Preprint coexistence — Authors who deposited a preprint on bioRxiv, arXiv, or a similar server before formal submission should confirm the target journal's preprint policy. A majority of journals indexed in PubMed Central permit prior preprint posting, but specific embargo rules vary (bioRxiv policy database).

Decision boundaries

Two distinctions define where authors most often make costly errors.

Simultaneous versus sequential submission: Submitting the same manuscript to 2 or more journals at once — simultaneous submission — violates the ethical standards of effectively all indexed journals and overlaps with duplicate publication policy. Sequential submission (waiting for a decision before submitting elsewhere) is the required standard.

Complete versus provisional submission: Some platforms allow authors to save an incomplete submission and return to it. A saved draft is not a submitted manuscript and carries no submission date. Only a fully confirmed, system-acknowledged submission establishes the record. Authors navigating embargo windows or grant reporting deadlines should treat the confirmation email timestamp as the only document that matters.

The scientific journal publishing landscape is broad enough that no single journal's quirks represent universal norms. Practices that are mandatory at a high-impact medical journal — structured abstracts, CONSORT checklists, registered reports — may be absent or optional at a field-specific title in materials science or ecology. Reading the author guidelines for each target journal is not a courtesy — it is the minimum unit of submission preparation.

References

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