All pull requests

Pull requests

• Read TMT reporter ions one scan at a time, and stop a search keeping each searched file's data until it ends

  ready for reviewready-for-agent
  #2924·trishorts opened Oct 26, 2026Contributor·

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• Write a rescued protein group once, not once for each accession it lost

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  #2923·trishorts opened Oct 26, 2026Contributor·

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• Test that a LowCID TMT search reads reporter ions from the stored scans, not the binned ones

  ready for reviewready-for-agent
  #2922·trishorts opened Oct 26, 2026Contributor·

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• List unique and shared peptides in the glyco protein tables, and test per-file peptide lists on two different files

  ready for reviewready-for-agent
  #2920·trishorts opened Oct 25, 2026Contributor·

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• When PEP filtering cannot be done, say what was done instead, and stop dropping every match

  ready for reviewready-for-agent
  #2919·trishorts opened Oct 25, 2026Contributor·

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• Quantify a PSM ambiguous only in where its modifications sit, for its one protein group

  ready for reviewready-for-agent
  #2917·trishorts opened Oct 20, 2026Contributor·

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• Call a peptide unique when no other protein group contains it

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  #2916·trishorts opened Oct 20, 2026Contributor·

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• GPTMD: try each database modification at the peptide's other residues, and add the sites that tie or beat it

  ready for reviewready-for-agent
  #2913·trishorts opened Oct 18, 2026Contributor·

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• When PEP filtering is requested, one filter (PEP q-value, else q-value notch, else q-value; strict <) decides identification everywhere

  ready for reviewready-for-agent
  #2909·trishorts opened Oct 16, 2026Contributor·

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• Re-write TmtDesign.txt for the calibrated files, so a TMT search after calibration quantifies its channels

  ready for reviewready-for-agent
  #2904·trishorts opened Oct 10, 2026Contributor·

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• Metadraw Occupancy

  ready-for-humanVisualizationWIP
  #2900·nbollis opened Oct 10, 2026Member·

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• Add a library-based DIA search engine: the walking skeleton

  #2863·trishorts opened Sep 30, 2026Contributor·

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• Write entrapment in the Decoy/Contaminant/Target columns, and keep MetaDraw showing it

  ready for reviewready-for-agent
  #2854·trishorts opened Sep 25, 2026Contributor·

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• Run the non-specific search over nucleic acids (singleN / singleC)

  #2830·trishorts opened Sep 17, 2026Contributor·

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• Refuse RNA seed digestion outside the non-specific search

  ready for reviewready-for-agent
  #2829·trishorts opened Sep 17, 2026Contributor·

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• Add a GPTMD filter that rejects substitutions which move a cleavage site

  #2828·acesnik opened Sep 17, 2026Contributor·

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• Don't annotate an MS3 child scan against a peptide it isn't evidence for

  #2827·acesnik opened Sep 17, 2026Contributor·

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• Name the spectra file in calibration warnings

  #2825·acesnik opened Sep 17, 2026Contributor·

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• Let the search task window set match-between-runs and normalization for SILAC

  #2824·acesnik opened Sep 17, 2026Contributor·

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• Move Max Threads out of Fragment Ion Search Parameters in the calibrate, XL and glyco task windows

  #2822·acesnik opened Sep 17, 2026Contributor·

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• Write one SDRF row per sample per channel for a TMT search

  ready for reviewready-for-agent
  #2817·trishorts opened Sep 15, 2026Contributor·

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• Key the index cache on database content, and stop abandoning the lookup early

  ready for reviewready-for-agent
  #2808·trishorts opened Sep 10, 2026Contributor·

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• Detach CMD's handlers from the static engine and task events

  #2799·acesnik opened Sep 5, 2026Contributor·

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• Make the rewritten experimental design name the files that were written

  #2784·acesnik opened Aug 31, 2026Contributor·

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• Let the user choose or supply the FASTA header regexes

  #2782·acesnik opened Aug 30, 2026Contributor·

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