10 Issues closed by 4 people

• DIA_SpecLib_Quant_diaPASEF java error

  #2380 closed Aug 19, 2025

• Java related issues using Fragpipe v23

  #2374 closed Aug 19, 2025

• MaxLFQ without prefractionation

  #2379 closed Aug 19, 2025

• DDA/DIA Hybrid analysis file handling

  #2377 closed Aug 16, 2025

• ERROR - MSFragger path or version does not exist.

  #2375 closed Aug 16, 2025

• peptide N terminal PTM site localization

  #2367 closed Aug 16, 2025

• Location of Temp Folder duing WorkspaceCleanInit

  #2366 closed Aug 16, 2025

• Combining separate TMT-plex MSFragger searches for global FDR and quantification?

  #2365 closed Aug 14, 2025

• MSBooster crashes with UniSpec models for MS2 on timsTOF Pro2

  #2360 closed Aug 14, 2025

• MSBooster Issue > Koina server may be running slow - Remote host terminated the handshake

  #2371 closed Aug 14, 2025

7 Issues opened by 7 people

• libgomp.so.1: No such file or directory

  #2382 opened Aug 20, 2025

• diaPASEF/quantification mapping issue

  #2381 opened Aug 19, 2025

• Validating WGS/RNA-Seq Derived Neoantigen Sequences

  #2378 opened Aug 16, 2025

• DIA_SpecLib_Quant_diaPASEF producing PeptideProphet error when Percolator is enabled

  #2376 opened Aug 14, 2025

• TMTIntegrator failed

  #2373 opened Aug 14, 2025

• Fragpipe rejects Fasta file

  #2372 opened Aug 14, 2025

• interact.pep.xml outputs already FDR-filtered? And different contents of .tsv and .pepXML MSFragger outputs

  #2370 opened Aug 13, 2025

4 Unresolved conversations

Sometimes conversations happen on old items that aren’t yet closed. Here is a list of all the Issues and Pull Requests with unresolved conversations.

• issues with tmt and faims search

  #2369 commented on Aug 14, 2025 • 0 new comments

• Headless FragPipe run under Apptainer fails DIANN version validation & Spectral Library Generation

  #2364 commented on Aug 14, 2025 • 0 new comments

• SaintExpress Analysis after GPF-DIA?

  #1634 commented on Aug 19, 2025 • 0 new comments

• MSBooster failing for model 'AlphaPept_ms2_generic'

  #2312 commented on Aug 19, 2025 • 0 new comments