PhosFox: a bioinformatics tool for peptide-level processing of LC-MS/MS-based phosphoproteomic data

Proteome Science

Methodology

Petteri Hintsanen¹  Tero Aittokallio¹  Sandra Söderholm²  Tiina Öhman²  Tuula A Nyman² 

[1] Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland;Institute of Biotechnology, University of Helsinki, P.O. Box 65, (Viikinkaari 1), FI-00014, Helsinki, Finland;

关键词: Database searching;    Phosphoproteomics;    LC-MS/MS;    Data processing and analysis;   

DOI  :  10.1186/1477-5956-12-36

 received in 2014-03-26, accepted in 2014-06-19,  发布年份 2014

来源: Springer

【 摘 要 】

BackgroundIt is possible to identify thousands of phosphopeptides and –proteins in a single experiment with mass spectrometry-based phosphoproteomics. However, a current bottleneck is the downstream data analysis which is often laborious and requires a number of manual steps.ResultsToward automating the analysis steps, we have developed and implemented a software, PhosFox, which enables peptide-level processing of phosphoproteomic data generated by multiple protein identification search algorithms, including Mascot, Sequest, and Paragon, as well as cross-comparison of their identification results. The software supports both qualitative and quantitative phosphoproteomics studies, as well as multiple between-group comparisons. Importantly, PhosFox detects uniquely phosphorylated peptides and proteins in one sample compared to another. It also distinguishes differences in phosphorylation sites between phosphorylated proteins in different samples. Using two case study examples, a qualitative phosphoproteome dataset from human keratinocytes and a quantitative phosphoproteome dataset from rat kidney inner medulla, we demonstrate here how PhosFox facilitates an efficient and in-depth phosphoproteome data analysis. PhosFox was implemented in the Perl programming language and it can be run on most common operating systems. Due to its flexible interface and open source distribution, the users can easily incorporate the program into their MS data analysis workflows and extend the program with new features. PhosFox source code, implementation and user instructions are freely available from https://bitbucket.org/phintsan/phosfox.ConclusionsPhosFox facilitates efficient and more in-depth comparisons between phosphoproteins in case–control settings. The open source implementation is easily extendable to accommodate additional features for widespread application use cases.

【 授权许可】

Unknown   
© Söderholm et al.; licensee BioMed Central Ltd. 2014. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.