Identification of membrane proteins by tandem mass spectrometry of protein ions.

TitleIdentification of membrane proteins by tandem mass spectrometry of protein ions.
Publication TypeJournal Article
Year of Publication2007
AuthorsCarroll, J, Altman, MC, Fearnley, IM, Walker, JE
JournalProc Natl Acad Sci U S A
Date Published2007 Sep 04
KeywordsAmino Acid Sequence, Animals, Dogs, Escherichia coli, Ions, Membrane Proteins, Molecular Sequence Data, Tandem Mass Spectrometry

The most common way of identifying proteins in proteomic analyses is to use short segments of sequence ("tags") determined by mass spectrometric analysis of proteolytic fragments. The approach is effective with globular proteins and with membrane proteins with significant polar segments between membrane-spanning alpha-helices, but it is ineffective with other hydrophobic proteins where protease cleavage sites are either infrequent or absent. By developing methods to purify hydrophobic proteins in organic solvents and by fragmenting ions of these proteins by collision induced dissociation with argon, we have shown that partial sequences of many membrane proteins can be deduced easily by manual inspection. The spectra from small proteolipids (1-4 transmembrane alpha-helices) are dominated usually by fragment ions arising from internal amide cleavages, from which internal sequences can be obtained, whereas the spectra from larger membrane proteins (5-18 transmembrane alpha-helices) often contain fragment ions from N- and/or C-terminal parts yielding sequences in those regions. With these techniques, we have, for example, identified an abundant protein of unknown function from inner membranes of mitochondria that to our knowledge has escaped detection in proteomic studies, and we have produced sequences from 10 of 13 proteins encoded in mitochondrial DNA. They include the ND6 subunit of complex I, the last of its 45 subunits to be analyzed. The procedures have the potential to be developed further, for example by using newly introduced methods for protein ion dissociation to induce fragmentation of internal regions of large membrane proteins, which may remain partially folded in the gas phase.

Alternate JournalProc. Natl. Acad. Sci. U.S.A.
Citation Key10.1073/pnas.0706817104
PubMed ID17720804
PubMed Central IDPMC1952138
Grant ListMC_U105663148 / / Medical Research Council / United Kingdom