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Title

A collection of open source applications for mass spectrometry data mining

AuthorsGallardo, Oscar ; Ovelleiro, David; Gay, Marina ; Carrascal, Montserrat ; Abián, Joaquín
KeywordsBioinformatics
Data analysis
Data handling
Phosphoproteomics
Search engine
Issue Date5-Sep-2014
PublisherJohn Wiley & Sons
CitationProteomics 14(20): 2275-2279 (2014)
Abstract© 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. We present several bioinformatics applications for the identification and quantification of phosphoproteome components by MS. These applications include a front-end graphical user interface that combines several Thermo RAW formats to MASCOT™ Generic Format extractors (EasierMgf), two graphical user interfaces for search engines OMSSA and SEQUEST (OmssaGui and SequestGui), and three applications, one for the management of databases in FASTA format (FastaTools), another for the integration of search results from up to three search engines (Integrator), and another one for the visualization of mass spectra and their corresponding database search results (JsonVisor). These applications were developed to solve some of the common problems found in proteomic and phosphoproteomic data analysis and were integrated in the workflow for data processing and feeding on our LymPHOS database. Applications were designed modularly and can be used standalone. These tools are written in Perl and Python programming languages and are supported on Windows platforms. They are all released under an Open Source Software license and can be freely downloaded from our software repository hosted at GoogleCode.
Publisher version (URL)http://dx.doi.org/10.1002/pmic.201400124
URIhttp://hdl.handle.net/10261/124779
DOI10.1002/pmic.201400124
Identifiersdoi: 10.1002/pmic.201400124
issn: 1615-9861
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