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Proteomics. 2015 Mar;15(5-6):950-63. doi: 10.1002/pmic.201400372. Epub 2015 Feb 17.

Computational phosphoproteomics: from identification to localization.

Author information

1
Faculty of Life Sciences, University of Manchester, Manchester, UK.

Abstract

Analysis of the phosphoproteome by MS has become a key technology for the characterization of dynamic regulatory processes in the cell, since kinase and phosphatase action underlie many major biological functions. However, the addition of a phosphate group to a suitable side chain often confounds informatic analysis by generating product ion spectra that are more difficult to interpret (and consequently identify) relative to unmodified peptides. Collectively, these challenges have motivated bioinformaticians to create novel software tools and pipelines to assist in the identification of phosphopeptides in proteomic mixtures, and help pinpoint or "localize" the most likely site of modification in cases where there is ambiguity. Here we review the challenges to be met and the informatics solutions available to address them for phosphoproteomic analysis, as well as highlighting the difficulties associated with using them and the implications for data standards.

KEYWORDS:

Bioinformatics; Data processing and analysis; Phosphoproteomics; Technology

PMID:
25475148
PMCID:
PMC4384807
DOI:
10.1002/pmic.201400372
[Indexed for MEDLINE]
Free PMC Article

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