ANSVMSCORERFORMORESENSITIVEANDRELIABLEPEPTIDEIDENTIFICATIONVIATANDEMMASSSPECTR.pdfVIP

AN SVM SCORER FOR MORE SENSITIVE AND RELIABLE PEPTIDE IDENTIFICATION VIA TANDEM MASS * SPECTROMETRY 1, 2 † 1, 2 1 1 3 HAIPENG WANG , YAN FU , RUIXIANG SUN , SIMIN HE , RONG ZENG , 1, 2 and WEN GAO 1Digital Technology Lab, Institute of Comp uting Technology, Chinese Academy of Sciences, Beijing 100080, China 2 Graduate University of Chinese Academy of Sciences, Beij ing 100039, China 3Research Center f or Proteome Analysis, Key Lab of Proteomics, Institute of Biochemistry and Cell Biology, Shanghai Institutes fo r Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China Tandem mass spectrometry (MS/MS) has become increasingly important and indispensable in high-throughput proteomics for identifying complex protein mixtures. Database searching is the standard method to accomplish this purpose. A key sub-routine, peptide identification, is used to generate a list of candidate peptides from a protein database according to an experimental MS/MS spectrum, and then validate these candidate peptides for protein identification. Although currently there are many algorithms for peptide identification, most of them either lack an effective validation module or only validate the first-ranked peptide, thus leading to a low identification reliability or sensitivity. This paper