What Is a Preflight Check, and Why It Could Save Your Paper From Desk Rejection

"Preflight" is borrowed from aviation on purpose — it's the checklist you run before takeoff, not after something's already gone wrong. In document conversion, a preflight check means validating your manuscript's structure, citations, figures, and images before you generate the final file, so problems surface as an editable warning instead of a rejected submission.

What actually gets checked

Stemdoc's preflight runs six categories of checks:

• Structure (STR) — flags missing sections your document type typically requires, like an Abstract or a References section.
• Citations (CIT) — catches citation keys with no matching bibliography entry, bibliography entries that are never cited, and ordering issues for citation styles that require it.
• Bibliography quality (REF) — checks cross-reference labels resolve correctly, flags a self-citation rate above 30%, missing DOIs, and a reference list where more than 40% of sources are over 15 years old.
• Figures (FIG) — figures referenced in text but never uploaded, uploaded images never referenced, filename case mismatches, and missing captions.
• Images (IMG) — unsupported file formats, low-DPI images that won't print cleanly, and files that can't be read at all.
• Security (SEC) — blocks PDF images carrying embedded JavaScript, a real (if rare) attack vector in academic submission pipelines.

Errors vs. warnings

Not every flag blocks you. Errors stop conversion because they'd produce a broken document — an unresolved citation, a figure reference with nothing to point to. Warnings are informational: they won't stop your conversion, but they're exactly the kind of thing a journal's editorial office would flag back to you, so it's worth reading them before you submit rather than after.

Where LMS-specific rules come in

Beyond the general checks, Stemdoc layers on publisher-specific rules when you select a submission target — arXiv, MDPI, PLOS, Frontiers, Elsevier, IEEE, Springer Nature, Wiley, Taylor & Francis, ACM, NeurIPS, ICML, APS, Nature Portfolio, and more, including generic Thesis/Dissertation formatting. Each has its own quirks; arXiv, for instance, needs a compiled .bbl file rather than a raw .bib — more on that here.

Preflight is available in Advanced mode, alongside the Text, Images, and Citations tabs — run it before you convert, not after you've already downloaded a file with a broken reference list.