Proteomics has largely been practiced through the separation of proteins in two dimensional gel electrophoresis. One one axis, the proteins are separated by molecular weight, and in the other, they are separated by isoelectric point. The gel is dyed with Coomasie staining or silver to highlight the proteins. Spots on the gel are proteins that have migrated to specific locations.
The mass spectrometer has augmented proteomics. Mass mapping identifies a protein by cleaving it into short peptides and then deduces the protein's identity by matching the observed peptide masses against a sequence database. Tandem mass spectrometry, on the other hand, can get sequence information from individual peptides by isolating them, colliding them with a nonreactive gas, and then cataloging the fragment ions produced.