Scores tandem mass spectra against a peptide database, in which fragment ion probabilities, number of enzymatic termini of candidate peptides, matching quality and match pattern between experimental and theoretical spectrum were considered. PepSearch is a polypeptide identification software. Benchmarking the novel scorer on a large set of experimental mass spectrometry (MS)/MS spectra, it is doubted that this software run significantly better than the used software SEQUEST.
This work was supported by the grants from the National High Technology Research and Development Program of China (863 Program) (No. 2002AA234021), Knowledge Innovation Program of the Chinese Academy of Sciences (No. KJCX1-08), Shanghai Science and Technology Commission (No. 00JC14018), and the Major Program of the National Natural Science Foundation of China (No. 39990600-03).