Multidimensional protein identification technology for direct-tissue proteomics of heart

Multidimensional protein identification technology (MudPIT) is an invaluable approach to identify proteins at large-scale level. Here, we describe a procedure of investigation to functional characterize the proteomic profile of complex samples such as those from cardiac tissues. In particular, we focus on the main steps concerning sample preparation, MudPIT analysis, tandem mass spectra processing, and biomarker discovery using label-free approaches. Finally, we report a data-derived systems biology approach to identify groups of proteins of over-, under-, and normal expression.