One of the commonly used techniques is Peptide
Mass Fingerprinting. This utilises the AXIMA CFR and MASCOT. It
is especially useful and quick if the protein is pure and you are
looking for a final confirmation.
When using the LC-MS-IT-ToF system, the added
dimension of chromatographic separation gives more information to
be used for the database search. This is enhanced further by the
collection of MSn data in both positive and negative modes.
For complex mixtures, it is always best to
run the sample down a size exclusion column to separate out the
components of the mixture.