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Strategies for the enrichment and identification of basic proteins in proteome projects
Author(s) -
Bae SooHan,
Harris Andrew G.,
Hains Peter G.,
Chen Hong,
Garfin David E.,
Hazell Stuart L.,
Paik YoungKi,
Walsh Bradley J.,
Cordwell Stuart J.
Publication year - 2003
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/pmic.200300392
Subject(s) - proteome , isoelectric focusing , chromatography , isoelectric point , bottom up proteomics , chemistry , gel electrophoresis , two dimensional gel electrophoresis , mass spectrometry , proteomics , matrix assisted laser desorption/ionization , immobilized ph gradient , electrophoresis , protein mass spectrometry , tandem mass spectrometry , biochemistry , protein purification , desorption , enzyme , gene , organic chemistry , adsorption
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 (p I ) 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 p I of greater than 10.23. A second approach to examine extremely alkaline proteins (p I > 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 p I > 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.