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MSFragger crashing exit code 1

Status: Open.

#2705 In Nesvilab/FragPipe;

· slug-lover opened on Mar 21, 2026

Basic-Search

Status: Open.

#2703 In Nesvilab/FragPipe;

· Ingeborg3 opened on Mar 19, 2026

OutOfMemoryError: Java heap space

Status: Open.

#2701 In Nesvilab/FragPipe;

· gukongxin opened on Mar 18, 2026

FragPipe v24.0 DIA run fails: missing .psmpkl file

Status: Open.

#2699 In Nesvilab/FragPipe;

· jingyiliu199703 opened on Mar 16, 2026

skyline document not generated in FragPipe 23.1, with Skyline 25.1.0.237

Status: Open.

#2698 In Nesvilab/FragPipe;

· jxu-11 opened on Mar 16, 2026

SILAC-TMT hyperplex

Status: Open.

#2625 In Nesvilab/FragPipe;

· JohnSuberu opened on Jan 16, 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

O-Pair

Status: Open.

#2522 In Nesvilab/FragPipe;

· peteythecat1 opened on Oct 29, 2025

Fragpipe V23.1 crashes with DDA+ in hybrid DIA

Status: Open.

#2520 In Nesvilab/FragPipe;

· NikolaMonteverde opened on Oct 29, 2025