Pharmaceutical Sciences Faculty Publications

Multidimensional Separation of Peptides for Effective Proteomic Analysis

Document Type

Article

Publication Date

3-5-2005

Journal Title

Journal of Chromatography B

ISSN

1570-0232

Volume

817

Issue

1

First Page

35

Last Page

47

PubMed ID

15680787

Abstract

Current solution based proteomic analysis methods are generally based on enzymatic digestion of a protein mixture followed by separation using multidimensional liquid chromatography and/or electrophoresis where peptide identification is typically accomplished by tandem mass spectrometry (MS/MS). It is generally accepted that no single chromatographic or electrophoretic procedure is capable of resolving the complex mixture of peptides that results from a global proteolytic digest of a proteome. Therefore, combining two or more orthogonal (multimodal) separation procedures dramatically improves the overall resolution and results in a larger number of peptides being identified from complex proteome digests. Separation of a proteome digest is a particularly challenging analytical problem due to the large number of peptides and the wide concentration dynamic range. While it has been demonstrated that increasing the number of dimensions of separation prior to MS analysis increases the number of peptides that may be identified, a balance between the time invested and the overall results obtained must be carefully considered. This manuscript provides a review of two- and three-dimensional peptide separation strategies combined with MS for the analysis of complex peptide mixtures.

Keywords

Chromatography, liquid, peptides, proteomics

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