Combining Percolator with X!Tandem for Accurate and Sensitive Peptide Identification

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.