title: Combining percolator with X!Tandem for accurate and sensitive peptide identification.
abstract: In this work, Percolator was successfully interfaced with X!Tandem using a PHP program to generate an improved search platform, X!Tandem Percolator. In order to achieve the best classification performance of peptide identifications in Percolator, a set of experimentally validated spectral identifications (34,993 MS/MS spectra) were used to guide the development of discriminatory features from X!Tandem search results. By comparing the features (e.g., Log(E) and mass error) of these experimentally validated peptide matches with those of false identifications, a comprehensive set of features can be chosen for Percolator in an objective and rational manner. The accuracy of X!Tandem Percolator was demonstrated by comparing the estimated q-value of the validated data set with the empirical q-value. By comparing the results from the X!Tandem Percolator and the original X!Tandem, superior sensitivity and specificity of the X!Tandem Percolator result was demonstrated on various shotgun proteomic data sets under different search conditions. In all of the cases studied in this work, X!Tandem Percolator could improve the number of peptide identifications at the same level of q-values.
authors.affiliation: Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada.
authors.forename: Mingguo
authors.initials: M
authors.lastname: Xu
authors.forename: Zhendong
authors.initials: Z
authors.lastname: Li
authors.forename: Liang
authors.initials: L
authors.lastname: Li
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D004926:Escherichia coli / Q000737:chemistry*; D029968:Escherichia coli Proteins / Q000302:isolation & purification*; D058977:Molecular Sequence Annotation; D010446:Peptide Fragments / Q000302:isolation & purification*; D040901:Proteomics; D012680:Sensitivity and Specificity; D012984:Software; D053719:Tandem Mass Spectrometry
chemical_list: D029968:Escherichia coli Proteins; D010446:Peptide Fragments