Strategies for the enrichment and identification of basic proteins in proteome projects

Article


Bae, Soo-Han, Harris, Andrew G., Hains, Peter G., Chen, Hong, Garfin, David E., Hazell, Stuart L., Paik, Young-Ki, Walsh, Bradley J. and Cordwell, Stuart J.. 2003. "Strategies for the enrichment and identification of basic proteins in proteome projects." Proteomics. 3 (5), pp. 569-579. https://doi.org/10.1002/pmic.200300392
Article Title

Strategies for the enrichment and identification of basic proteins in proteome projects

ERA Journal ID2283
Article CategoryArticle
AuthorsBae, Soo-Han (Author), Harris, Andrew G. (Author), Hains, Peter G. (Author), Chen, Hong (Author), Garfin, David E. (Author), Hazell, Stuart L. (Author), Paik, Young-Ki (Author), Walsh, Bradley J. (Author) and Cordwell, Stuart J. (Author)
Journal TitleProteomics
Journal Citation3 (5), pp. 569-579
Number of Pages11
Year2003
Place of PublicationGermany
ISSN1615-9853
1615-9861
Digital Object Identifier (DOI)https://doi.org/10.1002/pmic.200300392
Abstract

Two-dimensional gel electrophoresis (2-DE) is currently the method of choice for separating complex mixtures of proteins for visual comparison in proteome analysis.
This technology, however, is biased against certain classes of proteins including low abundance and hydrophobic proteins. Proteins with extremely alkaline isoelectric
points (pI) are often very poorly represented using 2-DE technology, even when complex mixtures are separated using commercially available pH 6–11 or pH 7–10 immobilized
pH gradients. The genome of the human gut pathogen, Helicobacter pylori, is dominated by genes encoding basic proteins, and is therefore a useful model for
examining methodology suitable for separating such proteins. H. pylori proteins were separated on pH 6–11 and novel pH 9–12 immobilized pH gradients and 65 protein
spots were subjected to matrix-assisted laser desorption/ionization-time of flight mass spectrometry, leading to the identification of 49 unique proteins. No proteins were characterized with a theoretical pI of greater than 10.23. A second approach to examine extremely alkaline proteins (pI ! 9.0) utilized a prefractionation isoelectric focusing. Proteins were separated into two fractions using Gradiflow technology, and the extremely basic fraction subjected to both sodium dodecyl sulphate-polyacrylamide gel electrophoresis and liquid chromatography (LC) – tandem mass spectrometry post-tryptic digest, allowing the identification of 17 and 13 proteins, respectively.
Gradiflow separations were highly specific for proteins with pI ! 9.0, however, a single LC separation only allowed the identification of peptides from highly abundant
proteins. These methods and those encompassing multiple LC ‘dimensions’ may be a useful complement to 2-DE for ‘near-to-total’ proteome coverage in the alkaline pH range.

Keywordshelicobacter pylori; iquid chromatography; mass spectrometry; refractionation; two-dimensional gel electrophoresis
ANZSRC Field of Research 2020310701. Bacteriology
310109. Proteomics and intermolecular interactions (excl. medical proteomics)
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Byline AffiliationsAustralian Proteome Analysis Facility, Australia
University of New South Wales
Bio-Rad Laboratories, United States
Faculty of Sciences
Yonsei University, Korea
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