Determining protein concentrations of the human ventricular proteome

Proteomics is mostly used for measurements of relative differences in protein concentrations. Although such analyses are meaningful for comparing differences between two and more conditions, they do not directly provide details on the absolute protein concentrations within a system. Now, proteomics is heading more towards absolute quantitative strategies with results being expressed in copies/cell or ng/mg tissue. In the cardiac context, such quantitative information is crucial for (1) evaluating the feasibility of selecting a certain protein as potential novel drug target, (2) the expected concentration excreted into the circulation when selecting a biomarker, and (3) to build a model of cardiac function at the molecular level. At the same time, by mass spectrometry-based proteomics, a wealth of spectral information is gathered that can be used to evaluate protein levels of a select set of novel disease-altered proteins using, for instance, single reaction monitoring. Here we describe how to build a quantitative map of the human left ventricular proteome using a simple yet effective mass spectrometry-based spectral count method.