| Abstract
| - Current methodologies for protein quantitation include2-dimensional gel electrophoresis techniques, metaboliclabeling, and stable isotope labeling methods to name onlya few. The current literature illustrates both pros and consfor each of the previously mentioned methodologies.Keeping with the teachings of William of Ockham, “withall things being equal the simplest solution tends tobe correct”, a simple LC/MS based methodology ispresented that allows relative changes in abundance ofproteins in highly complex mixtures to be determined.Utilizing a reproducible chromatographic separationssystem along with the high mass resolution and massaccuracy of an orthogonal time-of-flight mass spectrometer, the quantitative comparison of tens of thousands ofions emanating from identically prepared control andexperimental samples can be made. Using this configuration, we can determine the change in relative abundanceof a small number of ions between the two conditionssolely by accurate mass and retention time. Employingstandard operating procedures for both sample preparation and ESI-mass spectrometry, one typically obtainsunder 5 ppm mass precision and quantitative variationsbetween 10 and 15%. The principal focus of this paperwill demonstrate the quantitative aspects of the methodology and continue with a discussion of the associated,complementary qualitative capabilities.
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