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Combine open OpenDDA PRs and guide biologists from upload to analysis - #52

Merged

t0mdavid-m merged 28 commits into

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claude/project-thread-hepw99

Oct 30, 2026

Merged

Combine open OpenDDA PRs and guide biologists from upload to analysis#52
t0mdavid-m merged 28 commits into
mainfrom
claude/project-thread-hepw99

Commits on Oct 20, 2026
- Add an Identification QC page: score distribution, precursor error, PSMs per file
  claude
  committed
  1c21ffb
- Add a Proteins page: protein table with coverage, linked peptides and PSMs
  claude
  committed
  475436d
Commits on Oct 21, 2026
- Filtered PSMs: fragment mass error plot and b/y ion table for the selected PSM
  claude
  committed
  00fd972
Commits on Oct 23, 2026
- Add cRAP contaminants to the search database, flag and hide them in results
  claude
  committed
  24ba0fb
Commits on Oct 24, 2026
- Add a Run Overview page: key figures and a per-file summary
  claude
  committed
  9b7b41a
Commits on Oct 25, 2026
- Add a Samples page: PSMs, peptides and proteins per sample, by condition
  claude
  committed
  aed714c
Commits on Oct 26, 2026
- PSM tables: switch modifications between labels, ProForma and OpenMS; ProForma in exports
  claude
  committed
  a18ed80
Commits on Oct 28, 2026
- Add an Open Search preset and a Mass Shifts page with Unimod interpretation
  claude
  committed
  7e67b88
Commits on Oct 29, 2026
Commits on Oct 30, 2026
- Keep spike-in proteins out of the contaminants; annotated spectra on Identified proteins
  claude
  committed
  3c8d404