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QQsci-skill/references/submission-package-audit.md

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Submission Package Audit

Use this file when the user provides a full or partial submission package rather than only one manuscript file.

Typical files:

  • Manuscript.docx
  • Supplementary Information.docx
  • Highlights.docx
  • CoverLetter.docx
  • Figures.pptx
  • Supplementary Information.pptx
  • TOC.pptx

Core rule

Audit the files as one submission package. The main manuscript and main figures define the story; all other files must be consistent with them.

Do not check files independently if cross-file consistency matters.

Recommended order

  1. Manuscript.docx
  2. Figures.pptx
  3. Supplementary Information.docx
  4. Supplementary Information.pptx
  5. Highlights.docx
  6. CoverLetter.docx
  7. TOC.pptx

Rationale: the manuscript and main figures establish the scientific story, the SI documents support the claims, and the highlights, cover letter, and TOC must then align with that story.

File-specific checks

1. Manuscript.docx

Check:

  • central claim, novelty, target-journal fit, and story order
  • title, abstract, introduction gap, results logic, discussion boundary
  • claim-evidence alignment with figures and SI
  • DOI-only citation comment placement if requested
  • terminology, sample names, abbreviations, units, and spelling consistency
  • whether strong related papers expose missing evidence or weaker positioning

Default output:

  • annotated copy with Word native comments when editing is requested
  • Markdown reviewer report for global issues

2. Figures.pptx

Check:

  • main figure sequence matches manuscript Results order
  • each figure has one clear conclusion
  • panel labels, scale bars, axis labels, legends, units, and error bars
  • sample names and colors match manuscript and SI
  • resolution, font size, line width, contrast, cropping, and alignment risks
  • whether any panel lacks explanation in the text
  • whether any key claim in the text lacks a main or SI figure

3. Supplementary Information.docx

Check:

  • SI figure/table numbering and order
  • methods completeness and reproducibility
  • experimental details, controls, statistics, and raw/supporting data
  • cross-references from manuscript to SI
  • whether SI evidence actually supports main-text claims
  • consistency with Supplementary Information.pptx

4. Supplementary Information.pptx

Check:

  • SI figures match Supplementary Information.docx
  • figure numbering, captions, sample names, and units are consistent
  • control figures and supplementary mechanism evidence are present
  • image quality and visual style match main figures where appropriate

5. Highlights.docx

Check:

  • highlights reflect the manuscript's true novelty
  • claims are concrete and evidence-backed
  • no mismatch with abstract, cover letter, or target journal positioning
  • no empty phrases such as excellent performance without specifics
  • each highlight is short, distinct, and not redundant

6. CoverLetter.docx

Check:

  • target journal and article type are correct
  • novelty and significance match manuscript evidence
  • claims are not stronger than the data
  • relationship to strong related papers is clear without sounding defensive
  • required declarations are present if the journal requires them
  • tone is professional and concise

If target-journal rules may have changed, verify the current journal page before final submission advice.

7. TOC.pptx

Check:

  • graphical TOC communicates material design, mechanism, and application at a glance
  • it is consistent with manuscript title, abstract, and main figures
  • visual hierarchy is clear
  • text is minimal and readable
  • mechanism arrows, labels, material names, and device icons are accurate
  • it does not introduce claims absent from the manuscript

Cross-file consistency checks

Always check:

  • title consistency across manuscript, cover letter, TOC, and highlights
  • material names, sample labels, and abbreviations
  • figure numbering and panel references
  • SI numbering and manuscript callouts
  • performance values and units
  • target journal name and article type
  • novelty wording across abstract, highlights, cover letter, and TOC
  • terminology and spelling variants
  • whether DOI citation suggestions align with the claims being cited

Output package

Preferred outputs:

  • <manuscript-name>_comments.docx: Word native comments for sentence-level issues and DOI-only citation suggestions when requested
  • <manuscript-name>_reviewer_report.md: global review, comparative audit, figure/SI/package issues, and priority revision plan
  • optional <manuscript-name>_package_checklist.md: concise cross-file checklist

Never overwrite original files unless the user explicitly asks.

Report format

Use:

Package inventory
- Manuscript:
- Main figures:
- SI document:
- SI figures:
- Highlights:
- Cover letter:
- TOC:

Priority issues
| ID | Severity | File | Location | Problem | Fix | Cross-file impact |
|---|---|---|---|---|---|---|

Cross-file consistency
- ...

File-by-file findings
- Manuscript:
- Figures:
- SI document:
- SI figures:
- Highlights:
- Cover letter:
- TOC:

Next revision order
1. ...
2. ...
3. ...