SearchGUI: An open‐source graphical user interface for simultaneous OMSSA and X!Tandem searches

The identification of proteins by mass spectrometry is a standard technique in the field of proteomics, relying on search engines to perform the identifications of the acquired spectra. Here, we present a user‐friendly, lightweight and open‐source graphical user interface called SearchGUI (http://searchgui.googlecode.com), for configuring and running the freely available OMSSA (open mass spectrometry search algorithm) and X!Tandem search engines simultaneously. Freely available under the permissible Apache2 license, SearchGUI is supported on Windows, Linux and OSX.

[1]  Lennart Martens,et al.  OMSSAGUI: An open‐source user interface component to configure and run the OMSSA search engine , 2008, Proteomics.

[2]  Lennart Martens,et al.  OMSSA Parser: An open‐source library to parse and extract data from OMSSA MS/MS search results , 2009, Proteomics.

[3]  Lennart Martens,et al.  PRIDE: The proteomics identifications database , 2005, Proteomics.

[4]  R. Beavis,et al.  A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes. , 2003, Analytical chemistry.

[5]  Rune Matthiesen,et al.  Virtual Expert Mass Spectrometrist v3.0 , 2007 .

[6]  J. Yates,et al.  An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database , 1994, Journal of the American Society for Mass Spectrometry.

[7]  B. Searle,et al.  Improving sensitivity by probabilistically combining results from multiple MS/MS search methodologies. , 2008, Journal of proteome research.

[8]  S. Bryant,et al.  Open mass spectrometry search algorithm. , 2004, Journal of proteome research.

[9]  B. Balgley,et al.  Comparative Evaluation of Tandem MS Search Algorithms Using a Target-Decoy Search Strategy*S , 2007, Molecular & Cellular Proteomics.

[10]  R. Aebersold,et al.  Mass spectrometry-based proteomics , 2003, Nature.

[11]  Lennart Martens,et al.  PRIDE Converter: making proteomics data-sharing easy , 2009, Nature Biotechnology.

[12]  D. N. Perkins,et al.  Probability‐based protein identification by searching sequence databases using mass spectrometry data , 1999, Electrophoresis.

[13]  Rune Matthiesen.  Virtual Expert Mass Spectrometrist v3.0: an integrated tool for proteome analysis. , 2007, Methods in molecular biology.

[14]  Yi-Kuo Yu,et al.  Enhancing Peptide Identification Confidence by Combining Search Methods , 2008, Journal of proteome research.

[15]  Lennart Martens,et al.  XTandem Parser: An open‐source library to parse and analyse X!Tandem MS/MS search results , 2010, Proteomics.