A platform for high-throughput and ultrasensitive immunopeptidomics - Annotated MS2 spectra and FASTA databases

This repository contains annotated MS/MS spectra matched to immunopeptides in JY cells and U937 infection experiments. Per mass spectrometry run, a combined PDF shows all identifications by the four search engines using annotated spectra outputted by PDV (version 2.2.3). In addition, target and concatenated target-decoy FASTA databases used for the searches were included.