Tissue proteomics by one-dimensional gel electrophoresis combined with label-free protein quantification


Label-free methods streamline quantitative proteomics of tissues by alleviating the need for metabolic labeling of proteins with stable isotopes. Here we detail and implement solutions to common problems in label-free data processing geared toward tissue proteomics by one-dimensional gel electrophoresis followed by liquid chromatography tandem mass spectrometry (geLC MS/MS). Our quantification pipeline showed high levels of performance in terms of duplicate reproducibility, linear dynamic range, and number of proteins identified and quantified. When applied to the liver of an adenomatous polyposis coli (APC) knockout mouse, we demonstrated an 8-fold increase in the number of statistically significant changing proteins compared to alternative approaches, including many more previously unidentified hydrophobic proteins. Better proteome coverage and quantification accuracy revealed molecular details of the perturbed energy metabolism.


Projects: A: Cellular level

J. Proteome Res.
J. Proteome Res. 11(7): 3680-9
21st Jun 2012

Andrej Vasilj, Marc Gentzel, Elke Ueberham, Rolf Gebhardt, Andrej Shevchenko

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[Rolf Gebhardt] [Andrej Shevchenko]

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Views: 2261
  • Created: 20th Jul 2012 at 10:20
  • Last updated: 24th Oct 2013 at 16:16

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