Proteomics pipeline, release p1.1
phalaena:pipeline:PA-PL-proteomics
Shotgun LC-MS/MS proteomics: spectral preprocessing, decoy-database search with Comet, an FDR filter step that does not filter (see FDR_FILTER), PSM export, plots, and a canonical summary.json. We read each mass-spectrum file (mzML, mzXML, or Thermo .raw), build a reversed-decoy concatenation of the user's FASTA, pick peaks, search target plus decoy with Comet, pass the hits to that filter step, export the PSMs as TSV, and emit summary/summary.json matching phalaena_backend/pipelines/SUMMARY_SCHEMA.md; the assistant reads this contract directly. Pipeline ID proteomics. Source: phalaena_backend/pipelines/3_proteomics/. API entry: phalaena_api/app/pipelines/proteomics.py.
- kind
- pipeline
- status
- draft
- github:phalaena-automata/monorepo/phalaena_backend/pipelines/3_proteomics
View Proteomics pipeline, release p1.1 on the Phalaena Wiki