Mass spectrometry based proteomics is a technology driven possibility of analysing the proteome of cell cultures, organelles or tissues. For mass spectrometry based proteomics, proteins samples are first digested by an appropriate protease, e,g, Trypsin to yield a complex peptide mixture that can be separated in a reversed phase C18 liquid chromatography system according to hydrophobicity and size. With the analytes eluting from the reversed phase column being introduced into the coupled mass spectrometer via the gas phase, ions are formed that can be analysed therein. In the mass spectrometer, the exact masses of peptide ions are detected and fragment spectra are acquired for later identification of peptides according to database searches yielding peptide to spectrum matches.
Mass spectrometry based proteomics is very versatile technique that is allowing for in depth analyses of proteome samples. Besides identification of peptides and therefore proteins in a sample, quantification can be performed wither by label- free techniques or by using stable isotope labelling.