Candidate Peptides Discriminability-based Protein Identificationalgorithm For Tandem Mass Spectrometry

Since the soft ionization techniques has come true, biological mass spectrometryhas decreased the impurity and maintained integrity of the peptides molecules, thesechanges make biological mass spectrometry has become one of the most importanttechnologies in proteomic analysis. Tandem mass spectrometry (LC-MS/MS), whichis one of technologies of biological mass spectrometry, is a major tool for the analysisof peptide mixtures from protein samples. Mass spectrometry data processing is toinfer the protein composition of the sample from the data with the complex noise orwith some information missing, and one of most fundamental steps is identifiedpeptides from the fragmentation spectra. Database search is the main method of massspectrometry data processing, and the basic process is to map score the experimentalspectrum with the theoretical fragment spectrum and score, then choose the matchingwith the highest score as candidate peptides of the searching results. Now there arelots of algorithms identifying peptides from mass spectrum, e.g. Sequest, OMSSA,X!Tandem, Mascot, MassWiz, etc. Although there are many methods to qualitycontrol overall, the method of identification results is mainly used random databasemethod to calculate False Positive Rate(FPR). However, these algorithms are mainlyconsidered the peak-matches or not of experimental mass spectrometry, littleconsidered the consecutive matches or the consideration is not comprehensive enoughentirety.In this paper, we presented a novel concept model and a new proteinidentification algorithm Dispec based on DiLS-Discriminating Labeled Spectra, inwhich the labeling information of every peak reflects the discriminability of candidatepeptides. This algorithm takes three aspects of discriminability into consideration: ionmatches discriminability, intensity discriminability of different intervals and thetheoretical fragment ions and the experimental spectrum m/z error discriminability.Compared with two widely used algorithms-Mascot algorithm and Sequest algorithm,we validated the accuracy, robustness and compatibility of Dispec algorithm, theidentified results-including the number of spectrum, the reliability of peptides and thenumber of peptides, are higher than other identification algorithms of protein tandemmass spectrometry.