PhoPepMass Edit

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Basic information
Short name PhoPepMass
Full name
Description A database and search tool assisting human phosphorylation peptide identification from mass spectrometry data.
URL https://www.scbit.org/phopepmass/index.html
Year founded
Last update & version
Availability Free to academic users only
Contact information
University/Institution hosted Shanghai Center for Bioinformation Technology
Address
City
Province/State
Country/Region China
Contact name Lu Xie
Contact email luxiex2017@outlook.com
Data information
Data object
  • Animal
Data type
  • Protein
Database category
  • Modification
Major organism
  • Homo sapiens
Keyword
  • phosphorylation
  • post-translational modifications
Publications
  • PhoPepMass: A database and search tool assisting human phosphorylation peptide identification from mass spectrometry data. [PMID: 30055873]
    Menghuan Zhang, Hui Cui, Lanming Chen, Ying Yu, Michael O Glocker, Lu Xie

    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.

    J Genet Genomics 2018:45(7)

    0 Citations (from Europe PMC, 2019-01-19)

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  • Created on: 2019-01-04
    • ***ina@***c.cn [2019-01-23]
    • ***d@***c.cn [2019-01-12]
    • ***d@***c.cn [2019-01-12]
    • ***d@***c.cn [2019-01-04]

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