Understanding the limit of open search in the identification of peptides with post-translational modifications -- A simulation-based study

Abstract

MotivationAnalyzing tandem mass spectrometry data to recognize peptides in a sample is the fundamental task in computational proteomics. Traditional peptide identification algorithms perform well when identifying unmodified peptides. However, when peptides have post-translational modifications (PTMs), these methods cannot provide satisfactory results. Recently, Chick et al., 2015 and Yu et al., 2016 proposed the spectrum-based and tag-based open search methods, respectively, to identify peptides with PTMs. While the performance of these two methods is promising, the identification results vary greatly with respect to the quality of tandem mass spectra and the number of PTMs in peptides. This motivates us to systematically study the relationship between the performance of open search methods and quality parameters of tandem mass spectrum data, as well as the number of PTMs in peptides.\n\nResultsThrough large-scale simulations, we obtain the performance trend when simulated tandem mass spectra are of different quality. We propose an analytical model to describe the relationship between the probability of obtaining correct identifications and the spectrum quality as well as the number of PTMs. Based on the analytical model, we can quantitatively describe the necessary condition to effectively apply open search methods.\n\nAvailabilitySource codes of the simulation are available at http://bioinformatics.ust.hk/PST.html.\n\nContactboningli@ust.hk or eeyu@ust.hk\n\nSupplementary informationSupplementary data are available at Bioinformatics online.