Compare PSM and modifications

Description

This script compares peptide-spectral matches (PSM) from OMSSA and SEQUEST on both protein and peptide levels and also shows details about modifications.
Note: SEQUEST results must be in CSV format, which can be obtained by manually exporting SEQUEST results from a SRF file.

Input files

• optional: OMSSA results files (.csv)
• optional: SEQUEST results files (.csv)

Output files

• HTML report (compare-psm-mod-report.html)
• Peptide level CSV report (peptide-level-comparison.csv)
• Protein level CSV report (protein-level-comparison.csv)

Context

Parameters

SEQUEST format

Choices: SRF exported (default), TPP

Substitute long names with numbers

Default: false

Strip proteins at first whitespace

SEQUEST seems to print the protein ID up to the first whitespace instead of the complete protein name. Activate this flag to make OMSSA protein IDs compatible to SEQUEST.

Default: true

Source code

compare-psm-mod.rb, compare-psm-mod.yaml (GitHub)