Hui Cui
Lanming Chen
Ying Yu
Michael O. Glocker
Lu Xie
aSchool of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
bShanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai 201203, China
cInstitute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
dCollege of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
eDepartment of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 30007, China
fProteome Center Rostock, University of Rostock, Rostock 18055, Germany
More InformationCorresponding author: E-mail address: yuying@tmu.edu.cn (Ying Yu);E-mail address: michael.glocker@med.uni-rostock.de (Michael O. Glocker);E-mail address: luxiex2017@outlook.com (Lu Xie)
Received Date: 2018-01-11
Accepted Date:2018-07-09
Rev Recd Date:2018-07-09
Available Online: 2018-07-19 Publish Date:2018-07-20
Abstract
Abstract
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 phosphopeptide, 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. PhoPepMass is available at https://www.scbit.org/phopepmass/index.html.Keywords: Phosphosite,
Phosphopeptide,
Phosphopeptide mass
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