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Originally published In Press as doi:10.1074/mcp.M700415-MCP200 on October 15, 2007.
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Molecular & Cellular Proteomics 7:308-314, 2008.
© 2008 by The American Society for Biochemistry and Molecular Biology, Inc.

Research

Analysis of Electroblotted Proteins by Mass Spectrometry: Protein Identification after Western Blotting*,S

Jose L. Luque-Garcia{ddagger}, Ge Zhou§, Daniel S. Spellman{ddagger}, Tung-Tien Sun§ and Thomas A. Neubert{ddagger},¶

From the {ddagger} Kimmel Center for Biology and Medicine, Skirball Institute and Department of Pharmacology, and § Epithelial Biology Unit, Departments of Cell Biology, Dermatology, Pharmacology, and Urology, New York University School of Medicine, New York, New York 10016

We describe a new approach for the identification and characterization by mass spectrometry of proteins that have been electroblotted onto nitrocellulose. Using this method (Blotting and Removal of Nitrocellulose (BARN)), proteins can be analyzed either as intact proteins for molecular weight determination or as peptides generated by on-membrane proteolysis. Acetone is used to dissolve the nitrocellulose and to precipitate the adsorbed proteins/peptides, thus removing the nitrocellulose which can interfere with MS analysis. This method offers improved protein coverage, especially for membrane proteins, such as uroplakins, because the extraction step after in-gel digestion is avoided. Moreover, removal of nitrocellulose from the sample solution allows sample analysis by both MALDI- and (LC) ESI-based mass spectrometers. Finally, we demonstrate the utility of BARN for the direct identification of soluble and membrane proteins after Western blotting, obtaining comparable or better results than with in-gel digestion.

To whom correspondence should be addressed. Tel.: 212-263-7265; Fax: 212-263-8214; E-mail: neubert{at}saturn.med.nyu.edu


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