This script can be run after converting mzidentML results into the pepXML format with idconvert (Proteowizard) to append each spectrum result with the lines:
<analysis_result analysis="peptideprophet">
<peptideprophet_result probability="0" PEP="0">
</analysis_result>
Where the values for probability and PEP(e.g., "0") is replaced by the PSM confidence divided by 100. This makes the result file compatible with SpectraST.
Install tools:
# on archlinux
yaourt nodejs npm
# on ubuntu
sudo apt-get install nodejs npm
cd into directory with script
install node packages:
npm install jquery formattor [email protected]
edit proc.js with filenames
node proc.js