Pharmaceutical Sciences Faculty Publications

Title

Identification of Membrane Proteins From Mammalian Cell/Tissue Using Methanol-Facilitated Solubilization and Tryptic Digestion Coupled with 2D-LC-MS/MS

Document Type

Article

Publication Date

1-1-2006

Journal Title

Nature Protocols

ISSN

1750-2799

Volume

1

Issue

6

First Page

2784

Last Page

2790

DOI

10.1038/nprot.2006.359

PubMed ID

17406535

Abstract

The core prerequisites for an efficient proteome-scale analysis of mammalian membrane proteins are effective isolation, solubilization, digestion and multidimensional liquid chromatography-tandem mass spectrometry (LC-MS/MS). This protocol is for analysis of the mammalian membrane proteome that relies on solubilization and tryptic digestion of membrane proteins in a buffer containing 60% (vol/vol) methanol. Tryptic digestion is followed by strong cation exchange (SCX) chromatography and reversed phase (RP) chromatography coupled online with MS/MS for protein identification. The use of a methanol-based buffer eliminates the need for reagents that interfere with chromatographic resolution and ionization of the peptides (e.g., detergents, chaotropes, inorganic salts). Sample losses are minimized because solubilization and digestion are carried out in a single tube avoiding any sample transfer or buffer exchange between these steps. This protocol is compatible with stable isotope labeling at the protein and peptide level, enabling identification and quantitation of integral membrane proteins. The entire procedure--beginning with isolated membrane fraction and finishing with MS data acquisition--takes 4-5 d.

Keywords

Chromatography, liquid, membrane proteins, proteomics, solubility, tandem mass spectrometry, trypsin

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