Pick most abundant bands

Description

This script determines the most abundant bands for every peptide or protein and rejects quantitation events that come from other bands (plus/minus a user-defined value). Protein information is exclusively taken from the quantitation events, from the PSM list files only peptide spectral counts are read, which can be promoted to protein spectral counts if there is a protein column in the quantitation events file.

Input files

• at least 1 quantitation events file (.csv)
• at least 1 PSM list file (.csv)

Output files

• Filtered results (most-abundant-bands.csv)

Context

Parameters

Scope

Specify whether the most abundant band should be picked on the peptide or protein level.

Choices: protein if available, else peptide (default), peptide, protein

Number of neighbor bands to include

Default: 1

Exclude bands

If certain band numbers should not be picked as the most abundant bands, specify the appropriate numbers here, separated by a comma.

Default: empty

Band ID

Default: empty

Source code

filter-qe-by-band.rb, filter-qe-by-band.yaml (GitHub)