[A novel approach for peptide identification by tandem mass spectrometry].
High throughput scoring algorithms that are used to find the match of a tandem mass spectrum to a predicted mass spectrum of a peptide within a database have been applied in shotgun proteomics. However, these algorithms could produce a significant number of incorrect peptide identifications. Here a novel approach was developed to scoring 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. Benchmarking the novel scorer on a large set of experimental MS/MS spectra, it is demonstrated that PepSearch performs significantly better than the widely used software SEQUEST. The PepSearch software is available at http://compbio.sibsnet.org/projects/pepsearch.
Sheng
Quan-Hu
QH
Key Laboratory of Proteomics, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, the Chinese Academy of Sciences, Shanghai 200031, China.
Tang
Hai-Xu
HX
Xie
Tao
T
Wang
Lian-Shui
LS
Ding
Da-Fu
DF
D030562:Databases, Protein; D013058:Mass Spectrometry / Q000379:methods*; D015233:Models, Statistical; D010455:Peptides / Q000032:analysis*; D011338:Probability Theory; D040901:Proteomics
D010455:Peptides