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TMT Integrator output files are only generating column headers with no data

Status: Open.

#2696 In Nesvilab/FragPipe;

· jessmajka opened on Mar 10, 2026

java.util.NoSuchElementException during Glycan Assignment in PTMShepherd (v23.0)

Status: Open.

#2695 In Nesvilab/FragPipe;

· cyH2001 opened on Mar 10, 2026

Phosphorylation site

Status: Open.

#2693 In Nesvilab/FragPipe;

· valersch13 opened on Mar 6, 2026

Timsdata unable to open files

Status: Open.

#2691 In Nesvilab/FragPipe;

· anfoss opened on Mar 5, 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

Summary report generation for DIA_Speclib_Quant workflow

Status: Open.

#2428 In Nesvilab/FragPipe;

· cutleraging opened on Sep 10, 2025