Figure 2.

Bottom-up and top-down proteomics. In bottom-up proteomics, the protein mixtures are digested and the peptide mixtures are analyzed by LC-MS and LC-MS/MS (shotgun approach) or separated by electrophoresis and then individual proteins are digested and analyzed by MALDI-MS in a method called peptide mass fingerprinting. In top-down proteomics, the individual proteins (or a mixture of proteins) are analyzed for molecular mass in MS mode or fragmented to provide partial fragments in MS/MS mode. Using this approach, the target protein’s mass is identified and its amino acid sequence confirmed by MS/MS fragmentation.