Submit the technical note to the Journal of Proteome Research

[swaraj-neu]

Final formatting, author list, competing interests statement, data availability
statement, and submission.

Check the special issue requirements before submitting: open source licence, public
repository with documentation, install instructions, test data, and the full working tool
available to reviewers.

Hard deadline: November 2, 2026.

[swaraj-neu]

Pre-submission checklist: JPR technical note

Deadline: November 2, 2026. Journal of Proteome Research, Fifth Biennial Special
Issue on Software Tools and Resources.

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Template cleanup

• Strip the review annotation macros and every call to them: \todo{},
  \ov{}, \tw{}, \sp{}. Search the whole document, including the
  supplement.
• Restore the title page. The preamble currently discards the first page with
  \AtBeginDocument{\AtBeginShipoutNext{\AtBeginShipoutDiscard}}. Remove or
  comment that line.
• Add the graphical table of contents entry. JPR requires it. The block sits
  at the end of main.tex after the bibliography, currently commented out
  with a placeholder note.
• Convert Figure1.svg to PDF and switch \includesvg to
  \includegraphics. The svg package depends on Inkscape being available
  on the compile server, which is an avoidable dependency at submission.
• Prune unused packages from the preamble. Candidates: mhchem (chemical
  formulas), algorithm, algpseudocode, ulem (strikethrough),
  multirow. ACS asks that additional packages be loaded only when required.
• Reconsider fullpage. It overrides the ACS margins. Fine for drafting,
  worth removing so the layout matches what ACS expects.
• Check the bibliography filename case. main.tex calls
  \bibliography{Bibliography} while the file is bibliography.bib. It
  resolves in Overleaf but is fragile.
• Confirm supplement.tex compiles cleanly on its own. The main document
  pulls supplementary cross-references through xr and the .latexmkrc
  dependency, so if the supplement fails to build, references in the main
  text silently render wrong rather than erroring.

ACS LaTeX requirements

From the ACS submission guidance.

• All sections of the article in a single .tex file. Supporting information
  stays separate.
• References cited with \cite{} and a BibTeX database included in the
  archive.
• Captions written in the LaTeX document, not embedded in images.
• Minimal formatting. No layout-changing macros.
• Avoid extensive \newcommand and \def.
• U.S. Letter page size, not A4.

Submission artifacts

Two separate uploads.

• Manuscript file: a single .zip containing the main .tex, every
  referenced .tex, all .bib files, and all graphics. In Overleaf this is
  Menu, then Download, then Source.
• Manuscript PDF: your own generated PDF. In Overleaf, Download PDF.
• Verify the ZIP contains every referenced file. A missing graphic or .bib
  will stall the submission.

Special issue requirements

The call asks for these alongside the manuscript.

• Open source licence in the repository.
• Public GitHub repository with documentation and installation instructions.
• Test data included.
• The full working tool available free to reviewers.
• A stable citable release with a DOI, for example through Zenodo.
  Recommended rather than required.
• The architecture, algorithms, LLM approach, and validation described
  explicitly in the manuscript. The call names this directly, so the
  validation section carries real weight.

Manuscript metadata

• Author list and affiliations correct and in agreed order.
• Corresponding author and email set.
• Abstract written. Leave it until the paper is done.
• Keywords set.
• Competing interests statement.
• Data availability statement.
• Acknowledgements, including funding.