Issues

• Error in recursiveMassFilling.

  bug
  CompOmics/peptide-shaker#574 · Filter by author andmagdo opened on Jul 31, 2026
  2

  

• Required array length 2147483639 + 530 is too large

  enhancement
  CompOmics/peptide-shaker#572 · Filter by author max-l opened on Jul 3, 2026
  1

  

• How to specify the fasta path for ReportCli

  enhancement
  CompOmics/peptide-shaker#569 · Filter by author max-l opened on Jun 8, 2026
  1

  

• Trouble with passing results from searchgui to PeptideShaker

  help wanted
  CompOmics/peptide-shaker#563 · Filter by author justmpm opened on Feb 3, 2026
  8

  

• How to interpret Confidence scores? Especially when some datasets have the highest protein confidence at <100% (i.e. ~65% in one case)?

  CompOmics/peptide-shaker#558 · Filter by author PVlasov93 opened on Nov 11, 2025

• PRIDE reshake module access issues and future plans

  question
  CompOmics/peptide-shaker#557 · Filter by author Billsfriend opened on Oct 22, 2025
  1

  

• Precursor required to parse

  help wanted
  CompOmics/peptide-shaker#556 · Filter by author DiegoFGR15 opened on Sep 17, 2025
  2

  

• Cannot import/analyze data because "modificationScoring" is null, program stops at the peptide interference stage. Is there a way to fix this?

  help wanted
  CompOmics/peptide-shaker#555 · Filter by author PVlasov93 opened on Aug 24, 2025
  3

  

• Searches keep failing because "An error occurred: Two modifications found site 0 of peptide". Is there any way to fix this?

  help wanted
  CompOmics/peptide-shaker#554 · Filter by author PVlasov93 opened on Aug 24, 2025
  2

  

• FILTERING

  bug
  CompOmics/peptide-shaker#553 · Filter by author kazbek966 opened on Aug 22, 2025
  1

  

• 0% Validated Coverage and 0 Validated Peptides in PeptideShaker Reports 6 & 9

  help wanted
  CompOmics/peptide-shaker#552 · Filter by author umutcakir opened on Apr 3, 2025
  6

  

• Processing was cancelled

  help wanted
  CompOmics/peptide-shaker#547 · Filter by author Maiatallah opened on Jan 2, 2025
  3

  

• Error: No taxonomy found, Spectrum with title "___" not found

  help wanted
  CompOmics/peptide-shaker#545 · Filter by author jmattin2 opened on Nov 19, 2024
  1

  

• Question:

  help wanted
  CompOmics/peptide-shaker#543 · Filter by author JAEYOONSUNG opened on Nov 6, 2024
  1

  

• Spectrum not found when parsing sage results

  help wanted
  CompOmics/peptide-shaker#542 · Filter by author samgregoire opened on Oct 29, 2024
  3

  

• Peptideshaker found spectrum match null

  help wanted
  CompOmics/peptide-shaker#539 · Filter by author giovanni-cro opened on Sep 13, 2024
  2

  

• java.lang.StringIndexOutOfBoundsException

  bug
  CompOmics/peptide-shaker#537 · Filter by author jcanderan opened on Jul 17, 2024
  2

  

• MSFragger search result visualization

  help wanted
  CompOmics/peptide-shaker#535 · Filter by author Baopusr opened on Mar 9, 2024
  6

  

• Error in PTM mapping

  bug
  CompOmics/peptide-shaker#526 · Filter by author elrubio opened on Sep 30, 2023
  1

  

• PeptideShaker importing error from SearchGUI output

  bug
  CompOmics/peptide-shaker#512 · Filter by author fengx90 opened on Apr 20, 2023
  3

  

• "spectrumMatch" is null error when trying to view identifications from searchGUI files

  help wanted
  CompOmics/peptide-shaker#509 · Filter by author mlmarshall opened on Apr 5, 2023
  1

  

• Peptide-shaker doesn't progress from "Importing PSMs from mgf.comet.pep.xml.gz"

  help wanted
  CompOmics/peptide-shaker#496 · Filter by author MigRibe opened on Nov 15, 2022
  27

  

• Peptideshaker run issues

  bug
  CompOmics/peptide-shaker#495 · Filter by author carolinelennartsson opened on Nov 2, 2022
  3

  

• Parsing mzIdentML is whitespace sensitive

  enhancement
  CompOmics/peptide-shaker#493 · Filter by author lazear opened on Oct 30, 2022
  3

  

• Export MGF with annotated fragment ions?

  enhancement
  CompOmics/peptide-shaker#482 · Filter by author denisbeslic opened on Apr 4, 2022
  1