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How to specify the fasta path for ReportCli

enhancement

Status: Open.

#569 In CompOmics/peptide-shaker;

· max-l opened on Jun 8, 2026

Trouble with passing results from searchgui to PeptideShaker

help wanted

Status: Open.

#563 In CompOmics/peptide-shaker;

· justmpm opened on Feb 3, 2026

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

Status: Open.

#558 In CompOmics/peptide-shaker;

· PVlasov93 opened on Nov 11, 2025

PRIDE reshake module access issues and future plans

question

Status: Open.

#557 In CompOmics/peptide-shaker;

· Billsfriend opened on Oct 22, 2025

Precursor required to parse

help wanted

Status: Open.

#556 In CompOmics/peptide-shaker;

· DiegoFGR15 opened on Sep 17, 2025

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

help wanted

Status: Open.

#555 In CompOmics/peptide-shaker;

· PVlasov93 opened on Aug 24, 2025

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

help wanted

Status: Open.

#554 In CompOmics/peptide-shaker;

· PVlasov93 opened on Aug 24, 2025

FILTERING

bug

Status: Open.

#553 In CompOmics/peptide-shaker;

· kazbek966 opened on Aug 22, 2025

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

help wanted

Status: Open.

#552 In CompOmics/peptide-shaker;

· umutcakir opened on Apr 3, 2025

Processing was cancelled

help wanted

Status: Open.

#547 In CompOmics/peptide-shaker;

· Maiatallah opened on Jan 2, 2025

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

help wanted

Status: Open.

#545 In CompOmics/peptide-shaker;

· jmattin2 opened on Nov 19, 2024

Question:

help wanted

Status: Open.

#543 In CompOmics/peptide-shaker;

· JAEYOONSUNG opened on Nov 6, 2024