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Does --group apply only PSM-level FDR filtering, not peptide-level FDR?

Status: Open.

#2610 In Nesvilab/FragPipe;

· JWJW1 opened on Jan 8, 2026

error on 'DIA-quant propagate information'

Status: Open.

#2609 In Nesvilab/FragPipe;

· brasman1984 opened on Jan 8, 2026

Philosopher filter crashes (slice bounds out of range [-6:]) with custom FASTA generated from J2-seq, despite valid FASTA formats

Status: Open.

#2608 In Nesvilab/FragPipe;

· Siyang-nju opened on Jan 8, 2026

FileNotFoundError: [WinError 206] The filename or extension is too long

Status: Open.

#2602 In Nesvilab/FragPipe;

· dtabang opened on Dec 23, 2025

Wrong quantification for extreme ratio in SILAC H/L mixtures

Status: Open.

#2593 In Nesvilab/FragPipe;

· pisistrato opened on Dec 12, 2025

write sub-mzml files for timstof data

Status: Open.

#2592 In Nesvilab/FragPipe;

· jd690764 opened on Dec 12, 2025

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

Split database causes inconsistent mapped proteins for some peptides

Status: Open.

#2524 In Nesvilab/FragPipe;

· NikolaMonteverde opened on Oct 31, 2025

O-Pair

Status: Open.

#2522 In Nesvilab/FragPipe;

· peteythecat1 opened on Oct 29, 2025