Methods for Protein Analysis Protein Separation Methods Western Blotting Protein Identification Methods 3A. Edman degradation 3B. Mass spectrometry However, and perhaps remarkably, if as shown above we digest samples of ourprotein with as few as two or three different endoproteases with different specificities, we can usually use the resulting digestion patterns (again, analyzedby mass spectrometry to provide highly accurate determination of the fragmentmolecular weights) to produce a unique identification of our unknown protein:Again, mass spectrometry is uniquely well-suited for such analyses because itcan yield very accurate determinations of molecular weights from very even verysmall amounts of fragments resulting from the digestion of a particular protein.Techniques have now been developed by which proteins separated in two-dimensional gels can be digested within the gels and then injected directly into amass spectrometer for analysis of the resulting fragments.