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dc.contributor.authorPrieto Agujeta, Gorka ORCID
dc.contributor.authorAloria Escolastico, Kerman
dc.contributor.authorOsinalde Moraleja, Nerea ORCID
dc.contributor.authorFullaondo Elordui-Zapaterieche, Asier ORCID
dc.contributor.authorArizmendi Bastarrika, Jesús María ORCID
dc.contributor.authorMatthiesen, Rune
dc.date.accessioned2013-05-14T18:24:27Z
dc.date.available2013-05-14T18:24:27Z
dc.date.issued2012-11-05
dc.identifier.citationBMC Bioinformatics 13(288) : (2012)es
dc.identifier.issn1471-2105
dc.identifier.urihttp://hdl.handle.net/10810/10070
dc.description.abstractBackground Protein inference from peptide identifications in shotgun proteomics must deal with ambiguities that arise due to the presence of peptides shared between different proteins, which is common in higher eukaryotes. Recently data independent acquisition (DIA) approaches have emerged as an alternative to the traditional data dependent acquisition (DDA) in shotgun proteomics experiments. MSE is the term used to name one of the DIA approaches used in QTOF instruments. MSE data require specialized software to process acquired spectra and to perform peptide and protein identifications. However the software available at the moment does not group the identified proteins in a transparent way by taking into account peptide evidence categories. Furthermore the inspection, comparison and report of the obtained results require tedious manual intervention. Here we report a software tool to address these limitations for MSE data. Results In this paper we present PAnalyzer, a software tool focused on the protein inference process of shotgun proteomics. Our approach considers all the identified proteins and groups them when necessary indicating their confidence using different evidence categories. PAnalyzer can read protein identification files in the XML output format of the ProteinLynx Global Server (PLGS) software provided by Waters Corporation for their MSE data, and also in the mzIdentML format recently standardized by HUPO-PSI. Multiple files can also be read simultaneously and are considered as technical replicates. Results are saved to CSV, HTML and mzIdentML (in the case of a single mzIdentML input file) files. An MSE analysis of a real sample is presented to compare the results of PAnalyzer and ProteinLynx Global Server. Conclusions We present a software tool to deal with the ambiguities that arise in the protein inference process. Key contributions are support for MSE data analysis by ProteinLynx Global Server and technical replicates integration. PAnalyzer is an easy to use multiplatform and free software tool.es
dc.description.sponsorshipProteomics Core Facility-SGIKER is member of ProteoRed-ISCIII and is supported by UPV/EHU, MCINN, GV/EJ, ERDF and ESF. JMA is supported by the Department of Industry of the Basque Government (ETORTEK grant IE09-256).RM is supported by Fundação para a Ciência e a Tecnologia (FCT) Ciência 2007 and by European Social Fund. IPATIMUP is an Associate Laboratory of the Portuguese Ministry of Science, Technology and Higher Education and is partially supported by FCT. RM is further supported by FCT grants (PTDC/QUI-BIQ/099457/2008 and PTDC/EIA-EIA/099458/2008).es
dc.language.isoenges
dc.publisherBioMed Centrales
dc.rightsinfo:eu-repo/semantics/openAccesses
dc.titlePAnalyzer: A software tool for protein inference in shotgun proteomicses
dc.typeinfo:eu-repo/semantics/articlees
dc.rights.holder© 2012 Prieto et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.es
dc.relation.publisherversionhttp://www.biomedcentral.com/1471-2105/13/288es
dc.identifier.doi10.1186/1471-2105-13-288
dc.departamentoesBioquímica y biología moleculares_ES
dc.departamentoesIngeniería de comunicacioneses_ES
dc.departamentoesGenética, antropología física y fisiología animales_ES
dc.departamentoeuBiokimika eta biologia molekularraes_ES
dc.departamentoeuKomunikazioen ingeniaritzaes_ES
dc.departamentoeuGenetika,antropologia fisikoa eta animalien fisiologiaes_ES
dc.subject.categoriaBIOCHEMISTRY AND MOLECULAR BIOLOGY
dc.subject.categoriaMOLECULAR BIOLOGY
dc.subject.categoriaCOMPUTER SCIENCE APPLICATIONS


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