Mass Spectrometry will be much more beneficial to you than N terminal sequencing as it is faster and more accurate method than the later.... Go for Either Peptide mass Finger printing or for Tandem mass spectrophotometry. The former is useful if you have an idea of the your protein having similarity with the existing protein. However if the protein reported is entirely new one you should opt for Tandem.... Gud luck:)

I would also recommend tandem mass spectrometry due to high resolution (depending upon type of mass analyzer). We use LC/MS/MS (Nanoelectrospray -linear ion trap and nanoelectrospray-QTOF) in conjunction with SEQUEST database to analyze model proteins and cell surface proteins.

Thank you Deepti and Ujwal!

I have another question, if in mass spectrometry method, we use endoprotease to digest the protein before we proceed to HPLC, but what if my sample is protease itself? would it still work?

It depends what kind of endoprotease you are using. The pH and the temperature conditions do play a critical role for the protease activity. It may work if you know that at what pH your protease works optimally and you can choose an endoprotease whose pH range differs from the protease you have isolated... Wishing you good luck. Best regards, Deepti

Thank you Deepti!