title: The OMSSAPercolator: an automated tool to validate OMSSA results.
abstract: Protein identification by MS/MS is an important technique in proteome studies. The Open Mass Spectrometry Search Algorithm (OMSSA) is an open-source search engine that can be used to identify MS/MS spectra acquired in these experiments. Here, we present a software tool, termed OMSSAPercolator, which interfaces OMSSA with Percolator, a post-search machine learning method for rescoring database search results. We demonstrate that it outperforms the standard OMSSA scoring scheme, and provides reliable significant measurements. OMSSAPercolator is programmed using JAVA and can be readily used as a standalone tool or integrated into existing data analysis pipelines. OMSSAPercolator is freely available and can be downloaded at http://sourceforge.net/projects/omssapercolator/.
authors: BGI-Shenzhen, Shenzhen, P. R. China.
authors: Bo
authors: B
authors: Wen
authors: Guilin
authors: G
authors: Li
authors: James C
authors: JC
authors: Wright
authors: Chaoqin
authors: C
authors: Du
authors: Qiang
authors: Q
authors: Feng
authors: Xun
authors: X
authors: Xu
authors: Jyoti S
authors: JS
authors: Choudhary
authors: Jun
authors: J
authors: Wang
mesh_terms: D000465:Algorithms; D010449:Peptide Mapping; D011506:Proteins / Q000032:analysis / Q000737:chemistry; D020543:Proteome / Q000032:analysis* / Q000737:chemistry; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D020539:Sequence Analysis, Protein; D012984:Software
chemical_list: D011506:Proteins; D020543:Proteome
keywords: Bioinformatics; MS; Peptide identification; Shotgun proteomics