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Process 'IonQuant' finished, exit code: 1 Process returned non-zero exit code, stopping

Status: Open.

#2832 In Nesvilab/FragPipe;

· hosizhao1999 opened on Jul 5, 2026

Large differences in protein identifications when using split database (msfragger.misc.slice-db) after "Not enough memory allocated to MSFragger"

Status: Open.

#2831 In Nesvilab/FragPipe;

· huhaining66 opened on Jul 4, 2026

Glycopeptide quantification using EThcD collision

Status: Open.

#2830 In Nesvilab/FragPipe;

· danyunghsu opened on Jul 4, 2026

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)

Status: Open.

#2814 In Nesvilab/FragPipe;

· jonghyeonseol opened on Jun 12, 2026

Extend TMT support for MBR

Status: Open.

#2773 In Nesvilab/FragPipe;

· seanh-funcphos opened on May 6, 2026

Peak boundaries in Skyline

Status: Open.

#2772 In Nesvilab/FragPipe;

· jd690764 opened on May 5, 2026

Add ProForma 2.1 Peptidoforms to FragPipe output

Status: Open.

#2733 In Nesvilab/FragPipe;

· mobiusklein opened on Apr 6, 2026

PTMprophet error

Status: Open.

#2717 In Nesvilab/FragPipe;

· jd690764 opened on Mar 27, 2026

PTM Assignment in Combined Peptide Results

Status: Open.

#2584 In Nesvilab/FragPipe;

· KZ-MS opened on Dec 8, 2025

Metadata-aware MBR

Status: Open.

#2564 In Nesvilab/FragPipe;

· leonardblaschek opened on Nov 25, 2025

example output data

Status: Open.

#2551 In Nesvilab/FragPipe;

· mffrank opened on Nov 20, 2025

Metaproteomics module test execution problem

Status: Open.

#2541 In Nesvilab/FragPipe;

· MiguelCos opened on Nov 13, 2025