Issues

• MaxQuant 2.8.1.0 on Linux: freshly generated Thermo RAW .index is ~1 KB and contains no scan table

  MaxQuant
  cox-labs/CoxLab_Bug_Reporting#232 · Filter by author s268490t-cpu opened on Sep 21, 2026
  3

  

• proteinGroups.txt and other files were empty when using Maxquant running 84 samples on linux

  MaxQuant
  cox-labs/CoxLab_Bug_Reporting#230 · Filter by author lishr0007-spec opened on Sep 4, 2026
  7

  

• Prepare protein assembly error Maxquant

  MaxQuant
  cox-labs/CoxLab_Bug_Reporting#229 · Filter by author doanthaodinh opened on Sep 1, 2026
  3

  

• Perseus 2.1.4.0 and 2.1.5.0 exception 0xc0000409 in ucrtbase.dll, version: 10.0.17763.9020

  Perseus
  cox-labs/CoxLab_Bug_Reporting#228 · Filter by author magnush0lm opened on Aug 31, 2026
  5

  

• what is calculated by post hoc tukey test in Perseus

  Perseus
  cox-labs/CoxLab_Bug_Reporting#227 · Filter by author hrezvani2112 opened on Aug 28, 2026

• Feature Request: Combine columns values

  Perseus Feature Request
  cox-labs/CoxLab_Bug_Reporting#221 · Filter by author dudumello opened on Jul 17, 2026
  5

• MaxQuant 2.6.7.0 and 2.7.5.0 are completely unusable for TMT data aquired on an Astral

  MaxQuant
  cox-labs/CoxLab_Bug_Reporting#214 · Filter by author seanh-funcphos opened on May 5, 2026

• Mitochondrial Complex II Ontology is Outdated

  Perseus
  cox-labs/CoxLab_Bug_Reporting#211 · Filter by author DarioS opened on Apr 17, 2026

• Single Sample Pathway Analysis

  Perseus Feature Request
  cox-labs/CoxLab_Bug_Reporting#210 · Filter by author DarioS opened on Apr 2, 2026

• MaxQuant_2.7.5.0 could not find file "…/andromeda/aplfiles” during MSMS_first_search

  MaxQuant
  cox-labs/CoxLab_Bug_Reporting#209 · Filter by author sknodel779 opened on Apr 1, 2026
  1

  

• Two-sample Tests Documentation is Vague

  Perseus
  cox-labs/CoxLab_Bug_Reporting#207 · Filter by author DarioS opened on Mar 22, 2026
  1

• Generic Matrix export decimal separator bug

  Perseus
  cox-labs/CoxLab_Bug_Reporting#206 · Filter by author Ferienkrebs opened on Mar 18, 2026

• Load local modifications from custom dir

  MQ Feature Request
  cox-labs/CoxLab_Bug_Reporting#205 · Filter by author bernt-matthias opened on Mar 18, 2026
  2

  

• ProForma 2 support in MaxQuant output

  MQ Feature Request
  cox-labs/CoxLab_Bug_Reporting#204 · Filter by author mobiusklein opened on Mar 11, 2026

• MaxQuant 2.7.5.0 crashing on Start

  MaxQuant
  cox-labs/CoxLab_Bug_Reporting#202 · Filter by author medcbau opened on Mar 7, 2026
  1

  

• MaxDIA library prediction error for SCIEX wiff files

  MaxQuant
  cox-labs/CoxLab_Bug_Reporting#201 · Filter by author Katherinebtan opened on Mar 4, 2026

• Tims-MaxDIA runtime extremely long; advice on bottlenecks / hardware upgrades

  MaxQuant
  cox-labs/CoxLab_Bug_Reporting#200 · Filter by author k-Vartika opened on Feb 23, 2026
  1

• MaxDIA Library Prediction Error

  MaxQuant
  cox-labs/CoxLab_Bug_Reporting#198 · Filter by author euniceseo opened on Feb 3, 2026

• MaxQuant 2.7.x on Linux: MSMS first search crashes with “Could not find file '/…/andromeda/aplfiles'” – appears to be raw‑file‑specific

  MaxQuant
  cox-labs/CoxLab_Bug_Reporting#196 · Filter by author aretaon opened on Jan 14, 2026
  2

  

• stay at "creating peptide list"&"Preparing searches" step without bug reported. same like same #117

  MQ Feature Request
  cox-labs/CoxLab_Bug_Reporting#195 · Filter by author sunlu131 opened on Dec 24, 2025
  2

• Error while saving PDF or SVG for MS/MS spectra

  MaxQuant
  cox-labs/CoxLab_Bug_Reporting#194 · Filter by author Kritika-Ch opened on Dec 18, 2025

• Correcting errors for DDA FAIMS data

  MaxQuant
  cox-labs/CoxLab_Bug_Reporting#192 · Filter by author YiChan-ovo opened on Dec 12, 2025

• MaxLynx crashes for DHSO and BMSO

  MaxQuant
  cox-labs/CoxLab_Bug_Reporting#191 · Filter by author pisistrato opened on Dec 7, 2025
  2

  

• MaxDIA fails with "could not find file ...\combined\pd_0" error

  MaxQuant
  cox-labs/CoxLab_Bug_Reporting#190 · Filter by author LisJakobsen opened on Nov 17, 2025

• Ratio calculation in PTM analysis

  MaxQuant
  cox-labs/CoxLab_Bug_Reporting#186 · Filter by author goma2541 opened on Oct 28, 2025