title: ProCon - PROteomics CONversion tool.
abstract: With the growing amount of experimental data produced in proteomics experiments and the requirements/recommendations of journals in the proteomics field to publicly make available data described in papers, a need for long-term storage of proteomics data in public repositories arises. For such an upload one needs proteomics data in a standardized format. Therefore, it is desirable, that the proprietary vendor's software will integrate in the future such an export functionality using the standard formats for proteomics results defined by the HUPO-PSI group. Currently not all search engines and analysis tools support these standard formats. In the meantime there is a need to provide user-friendly free-to-use conversion tools that can convert the data into such standard formats in order to support wet-lab scientists in creating proteomics data files ready for upload into the public repositories. ProCon is such a conversion tool written in Java for conversion of proteomics identification data into standard formats mzIdentML and Pride XML. It allows the conversion of Sequest™/Comet .out files, of search results from the popular and often used ProteomeDiscoverer® 1.x (x=versions 1.1 to1.4) software and search results stored in the LIMS systems ProteinScape® 1.3 and 2.1 into mzIdentML and PRIDE XML. This article is part of a Special Issue entitled: Computational Proteomics.
authors.affiliation: Medizinisches Proteom Center (MPC), Ruhr-Universität Bochum, D-44801 Bochum, Germany.
authors.forename: Gerhard
authors.initials: G
authors.lastname: Mayer
authors.affiliation: Medizinisches Proteom Center (MPC), Ruhr-Universität Bochum, D-44801 Bochum, Germany; Kairos GmbH, Universitätsstraße 136, D-44799 Bochum, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Stephan
authors.affiliation: Medizinisches Proteom Center (MPC), Ruhr-Universität Bochum, D-44801 Bochum, Germany; Leibniz-Institut für Analytische Wissenschaften, ISAS, e.V., D-44139 Dortmund, Germany.
authors.forename: Helmut E
authors.initials: HE
authors.lastname: Meyer
authors.affiliation: Medizinisches Proteom Center (MPC), Ruhr-Universität Bochum, D-44801 Bochum, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Kohl
authors.affiliation: Medizinisches Proteom Center (MPC), Ruhr-Universität Bochum, D-44801 Bochum, Germany.
authors.forename: Katrin
authors.initials: K
authors.lastname: Marcus
authors.affiliation: Medizinisches Proteom Center (MPC), Ruhr-Universität Bochum, D-44801 Bochum, Germany. Electronic address: martin.eisenacher@rub.de.
authors.forename: Martin
authors.initials: M
authors.lastname: Eisenacher
mesh_terms: D000465:Algorithms; D003628:Database Management Systems; D030562:Databases, Protein; D016247:Information Storage and Retrieval / Q000379:methods; D009323:Natural Language Processing; D020543:Proteome / Q000737:chemistry* / Q000145:classification; D040901:Proteomics / Q000379:methods; D012984:Software; D012985:Software Design; D018875:Vocabulary, Controlled
chemical_list: D020543:Proteome
keywords: Conversion tool; PRIDE; ProCon; ProteomeXchange; Proteomics; mzIdentML