Protocol for quantitative proteomics of cellular membranes and membrane rafts

Methods Mol Biol. 2010:658:235-53. doi: 10.1007/978-1-60761-780-8_14.

Abstract

Proteomic analysis of membrane and membrane raft proteins is complicated by their inherent insolubility, which exacerbates difficulties with in-solution digestion of the proteins prior to ESI-LC-MS/MS. In-gel digestion yields more comprehensive proteomic and protein coverage of membrane/membrane raft samples, for example by LC-MS/MS of protein samples resolved by 1D SDS-polyacrylamide gel electrophoresis. Although this type of analysis can be performed quantitatively by labelling at the protein level, for instance by SILAC, the separation of proteins on a resolving gel complicates the application of other quantitative methods that employ post-digestion labelling techniques. This chapter describes an alternative protocol to prepare membrane or membrane raft protein samples to be isolated, but not separated, as unresolved bands in a gel. Focusing as a single band enables the confident excision of different samples in their entirety, to be digested, labelled, and fractionated for quantitative mass spectrometric analysis.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Biomarkers / metabolism
  • Blotting, Western
  • Cattle
  • Chromatography, Ion Exchange
  • Chromatography, Liquid
  • Electrophoresis, Polyacrylamide Gel
  • Membrane Microdomains / metabolism*
  • Membrane Proteins / isolation & purification
  • Membrane Proteins / metabolism
  • Proteomics / methods*
  • Staining and Labeling
  • Tandem Mass Spectrometry

Substances

  • Biomarkers
  • Membrane Proteins
  • flotillins