In so-called "bottom-up" proteomics, protein extracts are digested with an enzyme (usually trypsin) into peptides, which are then analyzed by liquid chromatography coupled to mass spectrometry (LC-MS/MS). MS/MS spectra and intensities of peptides are then used for the identification and quantification of their corresponding proteins.
In LC-MS/MS analyses, peptides from protein digests are injected on reversed phase column for separation at a very low flow (200-300 nl/min) by liquid chromatography. Eluting peptides are analyzed first by MS for determining their mass, and then fragmented to get the mass of their fragments (MS/MS spectrum).
Protein identification with database search
MS/MS spectra of peptides are searched against a protein database for their identification and protein inference, i.e. determining the minimum list of proteins explaining all the identified peptides.