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Literature DB >> 18563730

OMSSAGUI: An open-source user interface component to configure and run the OMSSA search engine.

Ravi Tharakan¹, Lennart Martens, Jennifer E Van Eyk, David R Graham.

Abstract

We here present a user-friendly and extremely lightweight tool that can serve as a stand-alone front-end for the Open MS Search Algorithm (OMSSA) search engine, or that can directly be used as part of an informatics processing pipeline for MS driven proteomics. The OMSSA graphical user interface (OMSSAGUI) tool is written in Java, and is supported on Windows, Linux, and OSX platforms. It is an open source under the Apache 2 license and can be downloaded from http://code.google.com/p/mass-spec-gui/.

Mesh：

Year: 2008 PMID： 18563730 PMCID： PMC2905866 DOI： 10.1002/pmic.200701126

Source DB: PubMed Journal: Proteomics ISSN： 1615-9853 Impact factor: 3.984

12 in total

1. Probability-based protein identification by searching sequence databases using mass spectrometry data.

Authors: D N Perkins; D J Pappin; D M Creasy; J S Cottrell
Journal: Electrophoresis Date: 1999-12 Impact factor: 3.535

2. Rapid identification of proteins by peptide-mass fingerprinting.

Authors: D J Pappin; P Hojrup; A J Bleasby
Journal: Curr Biol Date: 1993-06-01 Impact factor: 10.834

3. TANDEM: matching proteins with tandem mass spectra.

Authors: Robertson Craig; Ronald C Beavis
Journal: Bioinformatics Date: 2004-02-19 Impact factor: 6.937

4. Open mass spectrometry search algorithm.

Authors: Lewis Y Geer; Sanford P Markey; Jeffrey A Kowalak; Lukas Wagner; Ming Xu; Dawn M Maynard; Xiaoyu Yang; Wenyao Shi; Stephen H Bryant
Journal: J Proteome Res Date: 2004 Sep-Oct Impact factor: 4.466

5. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry.

Authors: Joshua E Elias; Steven P Gygi
Journal: Nat Methods Date: 2007-03 Impact factor: 28.547

6. Comparative evaluation of tandem MS search algorithms using a target-decoy search strategy.

Authors: Brian M Balgley; Tom Laudeman; Li Yang; Tao Song; Cheng S Lee
Journal: Mol Cell Proteomics Date: 2007-05-28 Impact factor: 5.911

Review 7. Is proteomics the new genomics?

Authors: Jürgen Cox; Matthias Mann
Journal: Cell Date: 2007-08-10 Impact factor: 41.582

OMSSAGUI: An open-source user interface component to configure and run the OMSSA search engine.

1. Probability-based protein identification by searching sequence databases using mass spectrometry data.

2. Rapid identification of proteins by peptide-mass fingerprinting.

3. TANDEM: matching proteins with tandem mass spectra.

4. Open mass spectrometry search algorithm.

5. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry.

6. Comparative evaluation of tandem MS search algorithms using a target-decoy search strategy.

Review 7. Is proteomics the new genomics?

8. Implementation and application of a versatile clustering tool for tandem mass spectrometry data.

9. A uniform proteomics MS/MS analysis platform utilizing open XML file formats.

10. MASPECTRAS: a platform for management and analysis of proteomics LC-MS/MS data.

1. A graphical user interface for RAId, a knowledge integrated proteomics analysis suite with accurate statistics.