Issues

• Parallelize per-file feature detection in ProteomicsLFQ

  enhancement
  bigbio/quantms#739 · Filter by author chunxubioinfor opened on Oct 7, 2026
  3

• Keep decoy protein hits (with q/PEP) in protein-level output for atlas protein FDR

  bigbio/quantms#737 · Filter by author ypriverol opened on Oct 7, 2026
  1

• Segfault in QTClusterFinder/FeatureGroupingAlgorithmQT during ProteomicsLFQ cross-run alignment with Sage identifications

  bug
  bigbio/quantms#735 · Filter by author chunxubioinfor opened on Sep 28, 2026
  4

  

• Update figure to remove MSstats and DIANN from the workflow

  bigbio/quantms#703 · Filter by author ypriverol opened on Apr 15, 2026

• quantms comet version is null in pmultiqc

  Bug fixhigh-priority
  bigbio/quantms#698 · Filter by author ypriverol opened on Apr 13, 2026
  

• CI failure: OpenMS container cannot create config directory

  bigbio/quantms#691 · Filter by author ypriverol opened on Apr 3, 2026

• Package pkg_resources not found when running quantmsutilsc

  bug
  bigbio/quantms#685 · Filter by author apalleja opened on Mar 12, 2026
  5

• in the main figures we should add pmultiqc as last step

  enhancement
  bigbio/quantms#658 · Filter by author ypriverol opened on Feb 13, 2026
  1

• Update parameters that are going to pmultiqc

  bigbio/quantms#654 · Filter by author ypriverol opened on Jan 21, 2026 · Release 1.8.0

• Discuss: Targeted proteomics support in quantms ecosystem.

  enhancement
  bigbio/quantms#648 · Filter by author thanadol-git opened on Jan 16, 2026
  77

  

• Put SDRF creation skill on Claude marketplace

  bigbio/quantms#647 · Filter by author jpfeuffer opened on Jan 14, 2026
  1

• Discuss SDRF validation scope

  bigbio/quantms#646 · Filter by author jpfeuffer opened on Jan 14, 2026
  1

• Add extensive documentation on how to structure biological and technical replicates for MSstats or general diff. expr. usage

  bigbio/quantms#645 · Filter by author jpfeuffer opened on Jan 14, 2026

• Deprecate openms tsv as an option for SDRF input and allow csv AND tsv

  bigbio/quantms#638 · Filter by author jpfeuffer opened on Jan 13, 2026
  7

  

• Conform with upcoming big nf-core requirements

  enhancementlow-priority
  bigbio/quantms#607 · Filter by author jpfeuffer opened on Nov 3, 2025

• Add protein quantification

  enhancement
  bigbio/quantms#592 · Filter by author enryH opened on Oct 21, 2025
  6

  

• Layout how parameters are combined

  enhancement
  bigbio/quantms#591 · Filter by author enryH opened on Oct 21, 2025
  10

  

• [FEATURE] Better error message when running quantms with no input

  enhancement
  bigbio/quantms#584 · Filter by author fabianegli opened on Sep 25, 2025
  

• quantms.io protein groups representation.

  enhancementhigh-priority
  Feature

  bigbio/quantms#559 · Filter by author ypriverol opened on Jun 4, 2025
  4

  

• Discussion about ConsesusID vs UniScore

  enhancementlow-priorityresearch-projects
  bigbio/quantms#558 · Filter by author ypriverol opened on Jun 3, 2025

• msgf+ needs the disassociation method/fragmentation methods

  enhancementlow-priority
  Feature

  bigbio/quantms#532 · Filter by author ypriverol opened on May 9, 2025
  1

• Does not add second enzyme to Comet search

  bughigh-priority
  bigbio/quantms#529 · Filter by author MetteBoge opened on May 8, 2025
  7

  

• Phospho decoy algorithm based on Ascore in OpenMS

  enhancement
  bigbio/quantms#497 · Filter by author ypriverol opened on Mar 21, 2025
  

• MSstats issues and refactoring

  documentationenhancementhigh-priorityquestion
  Task

  bigbio/quantms#493 · Filter by author ypriverol opened on Mar 10, 2025
  

• Support for different parameters (I.e. different PTMs and Enzymes)

  enhancement
  bigbio/quantms#478 · Filter by author kai-lawsonmcdowall opened on Feb 5, 2025