LC-MS/MS means “Liquid Chromatography coupled to tandem Mass Spectrometry”.

In a first step, the peptides resulting from the enzymatic hydrolysis of the proteins are separated by reverse phase liquid chromatography according to their hydrophobicity and arrive sequentially in the source of the mass spectrometer (nanospray) where they are ionized.

In a second step, the peptides are analyzed in the mass spectrometer. This instrument allows to measure the peptide masses and also, if necessary, to fragment the peptides in the gas phase to obtain elements of primary structure (their sequence).

Example of an annotated MS2 spectra resulting from the fragmentation of a peptide