Proteomic workflow. Proteomic experiments share a common workflow encompassing separation, mass analysis, and protein identification. The top-down approach uses image analysis of proteins separated by 2-dimensional gel electrophoresis to find differences between case and control samples. Protein spots of interest are then identified by comparing their peptide mass spectrometry data to protein databases. Conversely, bottom-up workflows first digest proteins extracted from cardiac samples into peptides. The peptides are separated by reverse-phase liquid chromatography, and mass spectrometry is used to identify and quantify the proteins. Common to each of these strategies is the philosophy that differential analysis is performed prior to protein identification. This purposeful “open” approach enables proteomic work to discover information that might not otherwise have been hypothesized.
