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Error with DIA data analysis

Status: Open.

#2657 In Nesvilab/FragPipe;

· Jamiearmzy opened on Feb 5, 2026

Why Is MSFragger Called Instead of MSFragger-DIA When Running DIA_SpecLib_Quant via FragPipe CLI?

Status: Open.

#2656 In Nesvilab/FragPipe;

· jingyiliu199703 opened on Feb 5, 2026

Charged cysteine monolinks in spectral library generation

Status: Open.

#2655 In Nesvilab/FragPipe;

· chloe-pepper opened on Feb 4, 2026

Glycolibrary reuse

Status: Open.

#2654 In Nesvilab/FragPipe;

· ecamafeita opened on Feb 3, 2026

OSError: [Errno 22]

Status: Open.

#2653 In Nesvilab/FragPipe;

· mmcilvin opened on Feb 2, 2026

Missing Ion Mobility and CV values from library in hybridDIA v23.1

Status: Open.

#2652 In Nesvilab/FragPipe;

· NikolaMonteverde opened on Feb 2, 2026

Protein identification discrepancy

Status: Open.

#2650 In Nesvilab/FragPipe;

· SamueldelaCamaraFuentes opened on Jan 28, 2026

SpecLib Problem w/ FP24

Status: Open.

#2649 In Nesvilab/FragPipe;

· jjGG opened on Jan 27, 2026

Export matched fragments (and batch spectra export) not reporting c- and z-ions

Status: Open.

#2647 In Nesvilab/FragPipe;

· iahendriks opened on Jan 26, 2026

SILAC-TMT hyperplex

Status: Open.

#2625 In Nesvilab/FragPipe;

· JohnSuberu opened on Jan 16, 2026

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