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

Menghuan Zhang; Hui Cui; Lanming Chen; Ying Yu; Michael O. Glocker; Lu Xie

doi:10.1016/j.jgg.2018.07.005

Volume 45 Issue 7

Jul. 2018

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

doi: 10.1016/j.jgg.2018.07.005

Menghuan Zhang^{a, b, #},
Hui Cui^{a, b, c, #},
Lanming Chen^d,
Ying Yu^e,
Michael O. Glocker^f,
Lu Xie^b

a
School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
b
Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai 201203, China
c
Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
d
College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
e
Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 30007, China
f
Proteome Center Rostock, University of Rostock, Rostock 18055, Germany

More Information

Corresponding 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.
- Phosphosite,
- Phosphopeptide,
- Phosphopeptide mass

These authors contributed equally to this work.

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References(27)

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