Compare PSM and modifications
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)