Combinatorial use of mRNA and two-dimensional electrophoresis expression data to choose relevant features for mass spectrometric identification

Ketan Patel, Rob Stein, Silvia Benvenuti, Marketa J. Zvelebil

Research output: Contribution to journalArticlepeer-review

Abstract

It is only recently that quantitative studies of differential proteome analysis (DPA) have become possible. In this paper the issues involved in quantitative DPA are discussed and novel tools to select features for identification by mass spectrometry (MS) are described. The problem of comparing two sets of gels on a global level is explored as well as how to find specific protein features that differentiate two sets of two-dimensional electrophoresis gels. The concept of a 'virtual' gel, derived from gene expression data, is introduced. The virtual gel enables the co-analysis of data from gene and protein expression. We discuss the value of such an approach, and consider what new information can be gained by using gene and protein expression together. These tools are illustrated by analysis of data from tandem gene and protein expression experiments. Features that are highlighted by the above methods are putative candidates for MS identification. Tools are described that integrate the process of feature selection, cutting, and MS analysis.

Original languageEnglish
Pages (from-to)1464-1473
Number of pages10
JournalProteomics
Volume2
Issue number10
DOIs
Publication statusPublished - Oct 1 2002

Keywords

  • Differential gene expression
  • Differential protein expression
  • Regulons
  • Stimulons

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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