title: A collection of open source applications for mass spectrometry data mining.
abstract: 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.
authors: CSIC/UAB Proteomics Laboratory, Instituto de Investigaciones Biomédicas de Barcelona-Consejo Superior de Investigaciones Científicas, IDIBAPS, Barcelona, Spain.
authors: Óscar
authors: Ó
authors: Gallardo
authors: David
authors: D
authors: Ovelleiro
authors: Marina
authors: M
authors: Gay
authors: Montserrat
authors: M
authors: Carrascal
authors: Joaquin
authors: J
authors: Abian
mesh_terms: D000818:Animals; D057225:Data Mining / Q000379:methods*; D030562:Databases, Protein; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D010750:Phosphoproteins / Q000032:analysis; D020543:Proteome / Q000032:analysis; D040901:Proteomics / Q000379:methods*; D057386:Search Engine; D012984:Software; D014584:User-Computer Interface
chemical_list: D010750:Phosphoproteins; D020543:Proteome
keywords: Bioinformatics; Data analysis; Data handling; Phosphoproteomics; Search engine