Identification involves the usual Proteomic routines of digest your protein, do MS-MS in the fragments, identify them, identify the full sequence of amino-acids (primary structure) of the protein and them identify the protein by comparing with the existing sequences in a data base. Characterization is a not so well defined term. It depends on what you need. Maybe the m/z of the protein is all that you need and that is your characterization. People use the term usually meaning to obtain all possible information about the primary, secondary, tertiary and quaternary structures of the protein. For that, other techniques besides mass spectrometry are necessary. For instance to obtain info about the three dimensional structure of the protein (tertiary structure) crystallography is needed, for secondary structure far ultraviolet circular dichroism is used.

What I think could be a good example is the case of caspases; these proteins have to be cutted in order to be active, when you find in your extract or whatever peptides belonging to a caspase you can clearly identify the protein based on the peptide that you find that are sufficient for the identification, but could be that you don't find any of the specific peptide/peptides that differ between active and inactive form... so you identify but not characterize your protein...

Identification involves the usual Proteomic routines of digest your protein, do MS-MS in the fragments, identify them, identify the full sequence of amino-acids (primary structure) of the protein and them identify the protein by comparing with the existing sequences in a data base. Characterization is a not so well defined term. It depends on what you need. Maybe the m/z of the protein is all that you need and that is your characterization. People use the term usually meaning to obtain all possible information about the primary, secondary, tertiary and quaternary structures of the protein. For that, other techniques besides mass spectrometry are necessary. For instance to obtain info about the three dimensional structure of the protein (tertiary structure) crystallography is needed, for secondary structure far ultraviolet circular dichroism is used.

Identification---to confirm what protein it is(as said above, by Mass spec!)

Characterization--after identifying a protein, we can study the protein in various aspects according to our interest and the currenk knowledge available on the protein's function/activity.

All useful answers i got until now. As a conclusion can i say that, in proteomics first one should identify the protein then can go for characterization based on further questions.

All identifications in proteomics are probablistic - there is very rarely a 'confirmed' true identification, as part of the protein is nearly always unseen. You have the most likely answer, and it will sometimes not be right. Also, it requires that there be a high quality protein DB sitting behind it. The alternative is to completely sequence a protein de novo by MS (we've done this, for example, look up roborovskin).

We work on species for which there is no genome/proteome data at all. That makes for an interesting experience!

Oh thats awesome!!

Identification- eager to know exactly what kind of proteins you dealing with, either by checking their masses( MS, MALDI-TOF etc) or retention time.

Characterization- determining the properties of that protein (Chemical or physical) ..e.g structure determination, water solubility(hydrophobic/hydrophillic) , Ph, functions etc.

Supporting the previous answers.

i support Isaya John Bususu