Unrestricted identification of post-translational modifications with listing and coupling of mass shift using tandem MS

Abstract

Post-Translational Modification (PTM) identification remains a complex process in proteome analysis. Restrictive search algorithms that consider only a small number of PTMs are widely used though they cannot identify unexpected PTMs. To cover unexpected modifications, unrestrictive search algorithms have been introduced, but they are limited in terms of the shift mass range or when using prior information such as the precursor mass or the PTM frequency matrix. An improved unrestrictive PTM search algorithm that enables the identification and sequence mapping of PTMs of candidate proteins or peptides found by protein identification algorithms is developed in this study. The proposed algorithm calculates all possible mass shifts and generates mass shift lists. The scores of the mass shift lists are calculated and PTMs are identified with their sequence location. With this algorithm, it is possible to consider all possible mass shifts without restriction and detect previously unidentified PTMs in the mass spectra.