Figure 1.

“Bottom-up” and “top-down” Proteomic Strategies in clinical samples. In “bottom-up” proteomics approaches, proteins are processed with an exogenous protease (e.g., trypsin), producing internal peptides that have adequate properties for LC MS/MS and database searches, including length, ionization, and fragmentation parameters. These peptides can be analyzed by shotgun proteomics methods to identify the parent protein based on the endogenous cleavage site, and thereby identify the protein itself. By contrast, top-down proteomics permits both strategies: protein cleavage with proteases and direct protein identification without cleavage.