Digging deeper into the immunopeptidome with TripleToolWF

While the field of immunopeptidomics has matured substantially over the last years, high input amounts of cellular or tissue material are still required to obtain a somewhat complete profile of the immunopepti-dome. Here we present a simple platform termed TripleToolWF (derived from Triple Tool workflow) to increase the number of identified and quantified immunopeptides combining the outputs of three search engines such as PEAKS Online 12, Sequest HT with INFERYS rescoring and MSFragger. For assessing the false discovery rate (FDR) an entrapment approach is used. The platform improved peptide identifica-tions by 6-14% and peptide quantitations by 11-25% compared to the best individual search