Reproducible Proteomics Report

After biological interpretation has been summarized, the final step is to assemble a reproducible proteomics report.

This chapter converts the workflow outputs into a structured report that can be shared, reviewed, and regenerated.

The report brings together:

input files
filtering thresholds
differential abundance summary
ranked proteins
identifier cleaning summary
functional enrichment readiness
STRING network readiness
figures
biological interpretation
limitations
reproducibility notes

Starting Point

This chapter uses the biological interpretation summary created in Chapter 11:

results/biological-interpretation-summary.md

This file was generated by:

Rscript scripts/R/11-build-biological-interpretation-summary.R \
  results \
  results/biological-interpretation-summary.md

The report also uses the key workflow outputs created by earlier chapters.

Why a Reproducible Report Matters

A proteomics report should not be a manually assembled document with copied tables and screenshots.

A reproducible report should make it possible to answer:

What input files were used?
Which thresholds were applied?
Which proteins were significant?
Which figures were generated?
Which interpretation was written?
Can the report be regenerated later?

This is especially important for client reports, internal analyses, manuscripts, and future re-analysis.

Report Inputs

The report-building script expects these files when available:

results/differential-summary.tsv
results/ranked-significant-proteins.tsv
results/identifier-cleaning-summary.tsv
results/enrichment-input-summary.tsv
results/string-network-summary.tsv
results/visualization-summary.tsv
results/biological-interpretation-summary.md

It also checks for figures:

results/figures/volcano-plot.png
results/figures/top-significant-proteins.png
results/figures/regulation-summary.png

If a file is missing, the report records that it was not available instead of stopping.

Output Files

The report script creates a report source file and renders it to HTML.

reports/
├── proteomics-report.qmd
└── proteomics-report.html

The .qmd file is useful because it documents the report structure and can be edited or re-rendered.

The .html file is the shareable report output.

Report Script

The executable script is saved as:

scripts/R/12-build-reproducible-proteomics-report.R

The guide shows how to run the script. The full executable code is maintained in scripts/R/.

Running the Script

From the project root, run:

Rscript scripts/R/12-build-reproducible-proteomics-report.R \
  results \
  reports

The arguments are:

1st argument → results directory
2nd argument → report output directory

The script creates:

reports/proteomics-report.qmd
reports/proteomics-report.html

Report Sections

The generated report includes:

Executive summary
Input and output overview
Differential abundance summary
Ranked significant proteins
Identifier cleaning summary
Functional enrichment readiness
STRING network readiness
Figures
Biological interpretation
Limitations
Reproducibility notes

This makes the report both readable and auditable.

Biological Interpretation Section

The biological interpretation section is imported from:

results/biological-interpretation-summary.md

This means Chapter 11 acts as the interpretation-writing step, while Chapter 12 acts as the report-assembly step.

The relationship is:

biological-interpretation-summary.md
        ↓
proteomics-report.qmd
        ↓
proteomics-report.html

Figures in the Report

The report includes figures when they are available:

volcano-plot.png
top-significant-proteins.png
regulation-summary.png

If the figures are missing, the report still renders and notes that the figure files were not found.

Tables in the Report

The report includes small table previews for key outputs.

Large tables are not fully printed in the report. Instead, the report provides a preview and records the source file path.

This keeps the report readable while preserving access to the full result files.

Reproducibility Notes

The report includes a reproducibility section that records:

report generation date
results directory
report directory
source files used
R session information

This helps future users understand how the report was created.

Suggested Workflow

A complete reporting workflow is:

Rscript scripts/R/05-filter-differential-proteins.R \
  data/example/example-proteomics-results.csv \
  results \
  1 \
  0.05

Rscript scripts/R/06-rank-and-filter-dep.R \
  results/differential-proteins.tsv \
  results \
  10

Rscript scripts/R/07-clean-protein-identifiers.R \
  results/ranked-significant-proteins.tsv \
  results

Rscript scripts/R/08-prepare-functional-enrichment-inputs.R \
  results/cleaned-protein-identifiers.tsv \
  results

Rscript scripts/R/09-prepare-string-network-input.R \
  results/string-network-input.tsv \
  results

Rscript scripts/R/10-visualize-proteomics-results.R \
  results/differential-proteins.tsv \
  results \
  10

Rscript scripts/R/11-build-biological-interpretation-summary.R \
  results \
  results/biological-interpretation-summary.md

Rscript scripts/R/12-build-reproducible-proteomics-report.R \
  results \
  reports

Editing the Report

The generated report is a starting point.

For final delivery, review and refine:

biological interpretation
limitations
study-specific context
organism information
enrichment results
STRING network interpretation
final conclusion

The report should be reproducible, but biological interpretation should still be reviewed by a domain expert.

Looking Ahead

The next chapter provides a roadmap for expanding the system from results-first analysis to raw mass spectrometry data processing.

Processed result tables
        ↓
Reproducible report
        ↓
Future raw-data expansion