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Chromatographic isolation of methionine-containing peptides for gel-free proteome analysis: identification of more than 800 Escherichia coli proteins

Kris Gevaert (UGent) , Jozef Van Damme (UGent) , Marc Goethals (UGent) , Grégoire Thomas, Bart Hoorelbeke, Hans Demol (UGent) , Lennart Martens (UGent) , Magda Puype (UGent) , An Staes (UGent) and Joël Vandekerckhove (UGent)
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Abstract
A novel gel-free proteomic technology was used to identify more than 800 proteins from 50 million Escherichia coli K12 cells in a single analysis. A peptide mixture is first obtained from a total unfractionated cell lysate, and only the methionine-containing peptides are isolated and identified by mass spectrometry and database searching. The sorting procedure is based on the concept of diagonal chromatography but adapted for highly complex mixtures. Statistical analysis predicts that we have identified more than 40% of the expressed proteome, including soluble and membrane-bound proteins. Next to highly abundant proteins, we also detected low copy number components such as the E. coli lactose operon repressor, illustrating the high dynamic range. The method is about 100 times more sensitive than two-dimensional gel-based methods and is fully automated. The strongest point, however, is the flexibility in the peptide sorting chemistry, which may target the technique toward quantitative proteomics of virtually every class of peptides containing modifiable amino acids, such as phosphopeptides, amino-terminal peptides, etc., adding a new dimension to future proteome research.
Keywords
SEQUENCE, DESORPTION/IONIZATION MASS-SPECTROMETRY, CODED AFFINITY TAGS, MIXTURES, PHOSPHOPROTEOME, ELECTROSPRAY

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Chicago
Gevaert, Kris, Jozef Van Damme, Marc Goethals, Grégoire Thomas, Bart Hoorelbeke, Hans Demol, Lennart Martens, Magda Puype, An Staes, and Joël Vandekerckhove. 2002. “Chromatographic Isolation of Methionine-containing Peptides for Gel-free Proteome Analysis: Identification of More Than 800 Escherichia Coli Proteins.” Molecular & Cellular Proteomics 1 (11): 896–903.
APA
Gevaert, K., Van Damme, J., Goethals, M., Thomas, G., Hoorelbeke, B., Demol, H., Martens, L., et al. (2002). Chromatographic isolation of methionine-containing peptides for gel-free proteome analysis: identification of more than 800 Escherichia coli proteins. MOLECULAR & CELLULAR PROTEOMICS, 1(11), 896–903.
Vancouver
1.
Gevaert K, Van Damme J, Goethals M, Thomas G, Hoorelbeke B, Demol H, et al. Chromatographic isolation of methionine-containing peptides for gel-free proteome analysis: identification of more than 800 Escherichia coli proteins. MOLECULAR & CELLULAR PROTEOMICS. 2002;1(11):896–903.
MLA
Gevaert, Kris, Jozef Van Damme, Marc Goethals, et al. “Chromatographic Isolation of Methionine-containing Peptides for Gel-free Proteome Analysis: Identification of More Than 800 Escherichia Coli Proteins.” MOLECULAR & CELLULAR PROTEOMICS 1.11 (2002): 896–903. Print.
@article{208762,
  abstract     = {A novel gel-free proteomic technology was used to identify more than 800 proteins from 50 million Escherichia coli K12 cells in a single analysis. A peptide mixture is first obtained from a total unfractionated cell lysate, and only the methionine-containing peptides are isolated and identified by mass spectrometry and database searching. The sorting procedure is based on the concept of diagonal chromatography but adapted for highly complex mixtures. Statistical analysis predicts that we have identified more than 40\% of the expressed proteome, including soluble and membrane-bound proteins. Next to highly abundant proteins, we also detected low copy number components such as the E. coli lactose operon repressor, illustrating the high dynamic range. The method is about 100 times more sensitive than two-dimensional gel-based methods and is fully automated. The strongest point, however, is the flexibility in the peptide sorting chemistry, which may target the technique toward quantitative proteomics of virtually every class of peptides containing modifiable amino acids, such as phosphopeptides, amino-terminal peptides, etc., adding a new dimension to future proteome research.},
  author       = {Gevaert, Kris and Van Damme, Jozef and Goethals, Marc and Thomas, Gr{\'e}goire and Hoorelbeke, Bart and Demol, Hans and Martens, Lennart and Puype, Magda and Staes, An and Vandekerckhove, Jo{\"e}l},
  issn         = {1535-9476},
  journal      = {MOLECULAR \& CELLULAR PROTEOMICS},
  keyword      = {SEQUENCE,DESORPTION/IONIZATION MASS-SPECTROMETRY,CODED AFFINITY TAGS,MIXTURES,PHOSPHOPROTEOME,ELECTROSPRAY},
  language     = {eng},
  number       = {11},
  pages        = {896--903},
  title        = {Chromatographic isolation of methionine-containing peptides for gel-free proteome analysis: identification of more than 800 Escherichia coli proteins},
  url          = {http://dx.doi.org/10.1074/mcp.M200061-MCP200},
  volume       = {1},
  year         = {2002},
}

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