A grid environment for high-throughput proteomics

IEEE Trans Nanobioscience. 2007 Jun;6(2):117-23. doi: 10.1109/tnb.2007.897495.

Abstract

We connect in a grid-enabled pipeline an ontology-based environment for proteomics spectra management with a machine learning platform for unbiased predictive analysis. We exploit two existing software platforms (MS-Analyzer and BioDCV), the emerging proteomics standards, and the middleware and computing resources of the EGEE Biomed VO grid infrastructure. In the setup, BioDCV is accessed by the MS-Analyzer workflow as a Web service, thus providing a complete grid environment for proteomics data analysis. Predictive classification studies on MALDI-TOF data based on this environment are presented.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Artificial Intelligence
  • Database Management Systems*
  • Databases, Protein*
  • Information Storage and Retrieval / methods*
  • Internet*
  • Mass Spectrometry / methods
  • Proteome / chemistry*
  • Proteome / classification
  • Proteome / physiology*
  • Proteomics / methods*
  • Sequence Analysis, Protein
  • Software
  • Systems Integration
  • User-Computer Interface

Substances

  • Proteome