This program reads the XML output of a Percolator analysis (Percolator run with the -X option), and filters the list of peptides by the user- supplied q-value and PSMs by the user-supplied q-value and generates a tab-delimited text file containing unmodified peptide sequences and associated spectral counts.
Ensure Java is installed on your system: https://java.com/en/download/
Download the .jar file from the latest release: https://github.com/metagomics/percolator-peptide-list-dumper/releases
Run with: java -jar peptideDumper.jar -p <peptide q-value cutoff> -s <psm q-value cutoff> -f <percolator output XML file>
For example: java -jar peptideDumper.jar -p 0.01 -s 0.01 -f percout.xml >peptide_psm_list.txt
To create a file called peptide_psm_list.txt containing the data.