bsphinney

Run an end-to-end proteomics search + differential expression analysis from raw mass-spec data. Use this whenever the user wants to "analyze my proteomics data", "search these raw files", "run my DIA/DDA data", "find differentially expressed proteins", "process this timsTOF/Astral/Orbitrap run", or points at a folder of .raw / .d / .mzML files and asks what's in it. Detects acquisition + instrument, fetches a Brett-validated workflow from the DE-LIMP repo, downloads the pinned search engine, runs DIA-NN (DIA) or Sage (DDA), then limpa/limma DE — with full provenance back to the validated workflow. Also use it to "write the LC-MS methods section" / "generate a publication-ready methods section with the instrument grant acknowledgment" from facility raw data (UC Davis Proteomics Core).