Proteins are digested with multiple enzymes and the resulting peptides are analyzed by high resolution nano-Liquid Chromatography Mass Spec (nLC-MS/MS). The peptides are fragmented inside the mass spectrometer to produce patterns which are then matched to protein sequence databases using computer software.
Simple sample buffers such as water or volatile compounds are compatible with direct in-solution digestion. However, more complex buffers such as salts, detergent, salts or glycerol may require an additional clean-up step prior to sample analysis. The sensitivity of this technique is 1ng or less starting material for a given protein.