How are proteins identified using mass spectrometry?
Proteins are first broken into smaller fragments by subjecting them to an endoprotease digestion (trypsin is our protease of choice). The peptide mixture can then be analyzed either directly by using a MALDI-MS instrument or after performing an LC separation before introducing peptides into the instrument in the case of an electrospray ionization (ESI)-LC-MS analysis. The instrument will determine the mass of ions present in the mixture by doing an MS survey scan and subsequently select a certain number of these ions for further analysis but allowing individual ions to be transmitted through a collision cell where intact ions (precursor ions) will break up into smaller fragments (daughter ions). The daughter ion fragments are then scanned to generate an MS/MS spectrum. The data generated including the precursor and daughter ion information is then used to search against a database of protein sequences that is in-silico digested by the database search engine (e.g. Mascot). The peptide q
