Deephos: predicted spectral database search for TMT-labeled phosphopeptides and its false discovery rate estimation

Abstract

Abstract Motivation Tandem mass tag (TMT)-based tandem mass spectrometry (MS/MS) has become the method of choice for the quantification of post-translational modifications in complex mixtures. Many cancer proteogenomic studies have highlighted the importance of large-scale phosphopeptide quantification coupled with TMT labeling. Herein, we propose a predicted Spectral DataBase (pSDB) search strategy called Deephos that can improve both sensitivity and specificity in identifying MS/MS spectra of TMT-labeled phosphopeptides. Results With deep learning-based fragment ion prediction, we compiled a pSDB of TMT-labeled phosphopeptides generated from ∼8000 human phosphoproteins annotated in UniProt. Deep learning could successfully recognize the fragmentation patterns altered by both TMT labeling and phosphorylation. In addition, we discuss the decoy spectra for false discovery rate (FDR) estimation in the pSDB search. We show that FDR could be inaccurately estimated by the existing decoy spectra generation methods and propose an innovative method to generate decoy spectra for more accurate FDR estimation. The utilities of Deephos were demonstrated in multi-stage analyses (coupled with database searches) of glioblastoma, acute myeloid leukemia and breast cancer phosphoproteomes. Availability and implementation Deephos pSDB and the search software are available at https://github.com/seungjinna/deephos.