title: PhosFox: a bioinformatics tool for peptide-level processing of LC-MS/MS-based phosphoproteomic data.
abstract: BACKGROUND
  It 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.
  
  
  RESULTS
  Toward 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.
  
  
  CONCLUSIONS
  PhosFox 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.
authors.affiliation: Institute of Biotechnology, University of Helsinki, P.O. Box 65 (Viikinkaari 1), FI-00014 Helsinki, Finland.
authors.forename: Sandra
authors.initials: S
authors.lastname: Söderholm
authors.affiliation: Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.
authors.forename: Petteri
authors.initials: P
authors.lastname: Hintsanen
authors.affiliation: Institute of Biotechnology, University of Helsinki, P.O. Box 65 (Viikinkaari 1), FI-00014 Helsinki, Finland.
authors.forename: Tiina
authors.initials: T
authors.lastname: Öhman
authors.affiliation: Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.
authors.forename: Tero
authors.initials: T
authors.lastname: Aittokallio
authors.affiliation: Institute of Biotechnology, University of Helsinki, P.O. Box 65 (Viikinkaari 1), FI-00014 Helsinki, Finland.
authors.forename: Tuula A
authors.initials: TA
authors.lastname: Nyman
keywords: Data processing and analysis; Database searching; LC-MS/MS; Phosphoproteomics