SimPhospho: a software tool enabling confident phosphosite assignment

Journal article


Suni, Veronika, Suomi, Tomi, Tsubosaka, Tomoya, Imanishi, Susumu Y., Elo, Laura L. and Corthals, Garry L. 2018. SimPhospho: a software tool enabling confident phosphosite assignment. Bioinformatics. 34 (15), pp. 2690 - 2692. https://doi.org/10.1093/bioinformatics/bty151
AuthorsSuni, Veronika, Suomi, Tomi, Tsubosaka, Tomoya, Imanishi, Susumu Y., Elo, Laura L. and Corthals, Garry L.
Abstract

Motivation: Mass spectrometry combined with enrichment strategies for phosphorylated peptides has been successfully employed for two decades to identify sites of phosphorylation. However, unambiguous phosphosite assignment is considered challenging. Given that site-specific phosphorylation events function as different molecular switches, validation of phosphorylation sites is of utmost importance. In our earlier study we developed a method based on simulated phosphopeptide spectral libraries, which enables highly sensitive and accurate phosphosite assignments. To promote more widespread use of this method, we here introduce a software implementation with improved usability and performance. Results: We present SimPhospho, a fast and user-friendly tool for accurate simulation of phosphopeptide tandem mass spectra. Simulated phosphopeptide spectral libraries are used to validate and supplement database search results, with a goal to improve reliable phosphoproteome identification and reporting. The presented program can be easily used together with the Trans-Proteomic Pipeline and integrated in a phosphoproteomics data analysis workflow. Availability and implementation: SimPhospho is open source and it is available for Windows, Linux and Mac operating systems. The software and its user’s manual with detailed description of data analysis as well as test data can be found at https://sourceforge.net/projects/simphospho/. Supplementary information: Supplementary data are available at Bioinformatics online.

Year2018
JournalBioinformatics
Journal citation34 (15), pp. 2690 - 2692
PublisherOxford University Press
ISSN1367-4803
Digital Object Identifier (DOI)https://doi.org/10.1093/bioinformatics/bty151
Scopus EID2-s2.0-85055121040
Open accessOpen access
Page range2690 - 2692
Research GroupMary MacKillop Institute for Health Research
Publisher's version
License
Place of publicationUnited Kingdom
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https://acuresearchbank.acu.edu.au/item/8v60q/simphospho-a-software-tool-enabling-confident-phosphosite-assignment

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