Issues

• MSBooster 1.4.14 crashes with IllegalArgumentException: POSITIVE_INFINITY when saving the score histogram

  Nesvilab/FragPipe#2919 · Filter by author ZihengWu opened on Oct 29, 2026
  1

  

• Multi-CPU Windows machines won't use all cores

  Nesvilab/FragPipe#2915 · Filter by author danielgeiszler opened on Oct 26, 2026
  1

  

• Questions about Hyperscore calculation and peptide selection in MSFragger

  Nesvilab/FragPipe#2914 · Filter by author jingyiliu199703 opened on Oct 21, 2026
  6

  

• IonQuant TMT quant crash on timsTOF: Index -1 out of bounds

  Nesvilab/FragPipe#2905 · Filter by author eosullivan97 opened on Oct 8, 2026
  9

  

• Recurring non-zero exit code with FileNotFoundError

  Nesvilab/FragPipe#2891 · Filter by author KatjaBaerenfaller opened on Sep 21, 2026
  7

  

• Failed to initialize IonQuantAPI: null when GlycoShepherd 0.1.9 builds IonQuant indices (IonQuant 1.11.20, glyco-N-DIA / DIA-Umpire pseudo-MS2, FragPipe 24.1-build30)

  Nesvilab/FragPipe#2814 · Filter by author jonghyeonseol opened on Jun 12, 2026
  1

  

• Extend TMT support for MBR

  Nesvilab/FragPipe#2773 · Filter by author seanh-funcphos opened on May 6, 2026
  

• Peak boundaries in Skyline

  Nesvilab/FragPipe#2772 · Filter by author jd690764 opened on May 5, 2026
  

• Add ProForma 2.1 Peptidoforms to FragPipe output

  Nesvilab/FragPipe#2733 · Filter by author mobiusklein opened on Apr 6, 2026
  2

• PTMprophet error

  Nesvilab/FragPipe#2717 · Filter by author jd690764 opened on Mar 27, 2026
  

• PTM Assignment in Combined Peptide Results

  Nesvilab/FragPipe#2584 · Filter by author KZ-MS opened on Dec 8, 2025
  

• Metadata-aware MBR

  Nesvilab/FragPipe#2564 · Filter by author leonardblaschek opened on Nov 25, 2025

• example output data

  Nesvilab/FragPipe#2551 · Filter by author mffrank opened on Nov 20, 2025

• Metaproteomics module test execution problem

  Nesvilab/FragPipe#2541 · Filter by author MiguelCos opened on Nov 13, 2025
  

• O-Pair

  Nesvilab/FragPipe#2522 · Filter by author peteythecat1 opened on Oct 29, 2025
  15

  

• A Sectioning and Database Enrichment Approach using FragPipe

  Metaproteomics
  Nesvilab/FragPipe#2254 · Filter by author BPGA opened on Jun 6, 2025
  2

  

• Motif column - Phospho workflow

  IonQuant
  Nesvilab/FragPipe#2248 · Filter by author kaupuks opened on Jun 4, 2025
  

• FWHM in Summary report

  feature request
  Nesvilab/FragPipe#2165 · Filter by author pisistrato opened on May 5, 2025
  

• Unique Peptides only for Quant in FragPipe

  Nesvilab/FragPipe#2051 · Filter by author JohnSuberu opened on Feb 25, 2025
  3

  

• Protein coverage calculation

  Nesvilab/FragPipe#1810 · Filter by author apsteinberg opened on Oct 2, 2024
  5

  

• Combined unique peptides column is missing in combined_proteins.tsv

  Nesvilab/FragPipe#1808 · Filter by author SamueldelaCamaraFuentes opened on Oct 2, 2024
  

• How to set a modification not C-term?

  Nesvilab/FragPipe#1763 · Filter by author a995752924 opened on Aug 31, 2024
  3

  

• Can we get support for crosslinking MS?

  Nesvilab/FragPipe#1738 · Filter by author bluemooninvestor opened on Aug 20, 2024

• Questions about searching the Pierce iRT peptides.

  Nesvilab/FragPipe#1673 · Filter by author vindr20 opened on Jul 15, 2024
  18

  

• SaintExpress Analysis after GPF-DIA?

  feature requestFragPipe
  Nesvilab/FragPipe#1634 · Filter by author TTCooper-PhD opened on Jun 16, 2024
  2