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Patch capped MS1 from the Thermo RAW; IonQuant-like precursor MS1 estimator - #21
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…uant-like precursor MS1 estimator spectrum_cache.patch_ms1 / patch-ms1 replaces each MS1 scan's peaks with the full centroid list from the RAW (thermo_raw: RawFileReader under Mono, DLLs found not shipped, reference/exception peaks included as msconvert's vendor peak picking writes them). It refuses anything but a most-intense cap: same scans and RTs, cached peaks are RAW peaks, re-capping reproduces the cache bit for bit, MS2 digest unchanged. mz_mode=calibrated handles MSFragger *_calibrated.mzML caches with the scan's own calibration curve. open_spectra(ms1_cap=N) serves the capped view; ms1_cap_status / warn_if_ms1_capped report the state. ms1quant ports NGlycoMM's IonQuant-mimicking extractor (top-3 isotope-cluster scans, nearest peak per isotope), parameters from fragpipe.workflow, with an apex_floor_ratio / cap_censored flag on capped MS1. Verified: on 12 OGlyco runs every cached MS1 peak is a RAW peak at 0 ppm, each capped scan is the RAW's top 1,000, re-capped view == mzML on ~3,800 sampled scans, MS2 byte-identical; the port equals NGlycoMM's extractor on 9,215/9,215 precursors; 272 offline tests pass. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Adds spectrum_cache.patch_ms1 (with thermo_raw), the ms1_cap re-capped view, ms1_cap_status, and ms1quant. Verified on 12 OGlyco runs and NGlycoMM; see the commit message.
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