PSM Validation Tool

The PSM validation tool verifies PSM scans against the ion fragmentation of the associated peptide squence.

Inputs

• MZSQLite database generated in a Galaxy workflow
• Tabular file of peptide sequences

By default the tool will fragment peptde into

• b and y ions
• b-H2O, b-NH3, y-H2O, y-NH3
• Internals

You can disable internals and neutral loss ions.

Output

A self-contained HTML report that includes:

• All PSMs for peptides of interest with PSM identifiers
• PSM PeptideShaker scores are presented
• MSMS interactive graphs with
  • PSM scan mz and intensities
  • All matching ion fragments
• Ion fragment table
  • Color coded for matching fragments
  • Internal values and color coded for internal matches