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Submitted on November 29, 2002
Revised on January 21, 2003
Accepted on January 21, 2003

Proteome analysis of intact proteins in complex mixtures

Julia R. Hayter, Duncan H.L. Robertson, Simon J. Gaskell, and Robert J. Beynon

Vet Preclinical Sciences, University of Liverpool, Liverpool, Merseyside L697ZJ

Corresponding Author: r.beynon{at}liv.ac.uk

Analysis of intact protein mixtures by electrospray ionisation mass spectrometry requires the resolution of a complex, overlapping set of multiply charged envelopes. To ascertain the ability of a moderate resolution mass spectrometer to resolve such mixtures, we have analysed the soluble proteins of adult chick skeletal muscle. This is a highly specialised tissue, showing a marked bias in expression of glycolytic enzymes in the soluble fraction. SDS-PAGE resolved proteins were first identified by a combination of MALDI-TOF and tandem mass spectrometry. Then, the mixture of intact proteins was introduced into the electrospray source of a Q-TOF mass spectrometer either by direct infusion or via a C4 desalting trap. In both instances, the complex pattern of peaks could be resolved into true mass spectra, and these masses could in many instances be reconciled with the masses predicted from the known protein sequences, when qualified by expected co- and post-translational modifications. These included loss of the N-terminal initiator methionine residue and N-terminal acetylation. The ability to resolve such a complex mixture of proteins with a routine instrument is of considerable value in analyses of protein expression, and in the confirmation of post-translational changes in mature proteins.


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