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

Soderholm S; Ohman T; Nyman TA; Aittokallio T; Hintsanen P

dc.contributor.authorSoderholm S
dc.contributor.authorOhman T
dc.contributor.authorNyman TA
dc.contributor.authorAittokallio T
dc.contributor.authorHintsanen P
dc.date.accessioned2022-10-28T14:31:18Z
dc.date.available2022-10-28T14:31:18Z
dc.identifier.urihttps://www.utupub.fi/handle/10024/171848
dc.description.abstractBackground: 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.
dc.publisherBIOMED CENTRAL LTD
dc.titlePhosFox: a bioinformatics tool for peptide-level processing of LC-MS/MS-based phosphoproteomic data
dc.identifier.urnURN:NBN:fi-fe2021042716063
dc.relation.volume12
dc.contributor.organizationfi=matematiikka|en=Mathematics|
dc.contributor.organization-code2606101
dc.converis.publication-id18053252
dc.converis.urlhttps://research.utu.fi/converis/portal/Publication/18053252
dc.identifier.jour-issn1477-5956
dc.okm.affiliatedauthorAittokallio, Tero
dc.okm.discipline111 Mathematicsen_GB
dc.okm.discipline111 Matematiikkafi_FI
dc.okm.discipline1182 Biokemia, solu- ja molekyylibiologiafi_FI
dc.okm.discipline1182 Biochemistry, cell and molecular biologyen_GB
dc.okm.internationalcopublicationnot an international co-publication
dc.okm.internationalityInternational publication
dc.okm.typeJournal article
dc.relation.articlenumberARTN 36
dc.relation.doi10.1186/1477-5956-12-36
dc.relation.ispartofjournalProteome Science
dc.year.issued2014


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