PhoPepMass： A database and search tool assisting human phosphorylation peptide identification from mass spectrometry data  

作　　者：Menghuan Zhang Hui Cui Lanming Chen Ying Yu Michael O. Glocker Lu Xie 

机构地区：[1]School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China [2]Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai 201203, China [3]Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China [4]College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China [5]Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 30007, China [6]Proteome Center Rostock, University of Rostock, Rostoek 18055, Germany

出　　处：《Journal of Genetics and Genomics》2018年第7期381-388,共8页遗传学报（英文版）

基　　金：supported by National Key Research and Development Program of China (2016YFC0904101);Chinese Human Proteome Projects (CNHPP: 2014DFB30020, 2014DFB30030);Shanghai Municipal Science and Technology Commission of China (No. 17ZR1420300);National Hi-Tech Program (2015AA020101)

摘　　要：Protein phosphorylation, one of the most important protein post-translational modifications, is involved in various biological processes, and the identification of phosphorylation peptides （phosphopeptides） and their corresponding phosphorylation sites （phosphosites） will facilitate the understanding of the molecular mechanism and function of phosphorylation. Mass spectrometry （MS） provides a high- throughput technology that enables the identification of large numbers of phosphosites. PhoPepMass is designed to assist human phosphopeptide identification from MS data based on a specific database of phophopeptide masses and a multivariate hypergeometric matching algorithm. It contains 244,915 phosphosites from several public sources. Moreover, the accurate masses of peptides and fragments with phosphosites were calculated. It is the first database that provides a systematic resource for the query of phosphosites on peptides and their corresponding masses. This allows researchers to search certain proteins of which phosphosites have been reported, to browse detailed phosphopeptide and fragment information, to match masses from MS analyses with defined threshold to the corresponding phos- phopeptide, and to compare proprietary phosphopeptide discovery results with results from previous studies. Additionally, a database search software is created and a ＂two-stage search strategy＂ is suggested to identify phosphopeptides from tandem mass spectra of proteomics data. We expect PhoPepMass to be a useful tool and a source of reference for proteomics researchers.Protein phosphorylation, one of the most important protein post-translational modifications, is involved in various biological processes, and the identification of phosphorylation peptides （phosphopeptides） and their corresponding phosphorylation sites （phosphosites） will facilitate the understanding of the molecular mechanism and function of phosphorylation. Mass spectrometry （MS） provides a high- throughput technology that enables the identification of large numbers of phosphosites. PhoPepMass is designed to assist human phosphopeptide identification from MS data based on a specific database of phophopeptide masses and a multivariate hypergeometric matching algorithm. It contains 244,915 phosphosites from several public sources. Moreover, the accurate masses of peptides and fragments with phosphosites were calculated. It is the first database that provides a systematic resource for the query of phosphosites on peptides and their corresponding masses. This allows researchers to search certain proteins of which phosphosites have been reported, to browse detailed phosphopeptide and fragment information, to match masses from MS analyses with defined threshold to the corresponding phos- phopeptide, and to compare proprietary phosphopeptide discovery results with results from previous studies. Additionally, a database search software is created and a ＂two-stage search strategy＂ is suggested to identify phosphopeptides from tandem mass spectra of proteomics data. We expect PhoPepMass to be a useful tool and a source of reference for proteomics researchers.

关 键 词：Phosphosite PHOSPHOPEPTIDE Phosphopeptide mass 

分 类 号：Q1[生物学—普通生物学]