Proteomic profiling of heart tissue might help to discover the molecular events related to or even causing cardiovascular diseases in human. However, this material is rare and only available from biopsies taken for diagnostics, e.g., assessment of inflammatory events or virus persistence. Within this chapter, we describe a workflow for the quantitative proteome analysis of heart biopsies. Starting with 1-2 mg of tissue material, crude protein extracts were prepared, digested with LysC and trypsin, and then analyzed by LC-ESI-tandem mass spectrometry. Due to the low technical variance, the method can be used for label-free quantitation of disease-specific alterations in the human heart. Methods discussed include homogenization of biopsy tissue, sample preparation, proteolytic digestion, as well as data analysis for label-free quantitation.
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