Monitoring Functional Post-Translational Modifications Using a Data-Driven Proteome Informatic Pipeline Based on PEIMAN2

Abstract

Post-translational modifications (PTMs) are under significant focus in molecular biomedicine due to their importance in signal transduction in most cellular and organismal processes. Characterization of PTMs, discrimination between functional and inert PTMs, quantification of their occupancies and PTM crosstalk are demanding tasks in each biosystem. On top of that, the study of each PTM often necessitates a particular laborious experimental design. Here, we present a PTM-centric proteome informatic pipeline for prediction of most probable and relevant PTMs in mass spectrometry-based proteomics data. Upon prediction, such PTMs can be incorporated in a refined database search. To demonstrate the applicability of our approach, using expression profiling, we identified cellular proteins that are differentially regulated in response to multikinase inhibitors dasatinib and staurosporine. Computational enrichment analysis was employed to determine the potential PTMs of protein targets for both drugs. Finally, we conducted an additional round of database search with the predicted probable PTMs. Our pipeline helped analyze the enriched PTMs and even detected proteins that were not picked up in the initial search. Our findings support the idea of PTM-centric searching of MS data in proteomics based on computational enrichment analysis and we believe this strategy should be incorporated in futuristic proteomics search engines.