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Protein identification – which method to choose?

Protein identification is important in all stages of drug development; from discovery / development
up to and including final API drug characterization and quality control.
In principle, two different methods exists for protein identification; one based on Edman degradation,
also known as Protein sequence analysis or amino acid sequence analysis, and one based on mass spectrometric techniques, often referred to as peptide mass fingerprinting.

The first technique unambiguously identifies the protein by determination of its N-terminal amino
acid sequence, and is often the method of choice for batch release testing of biopharmaceuticals. However, since there are quite some eukaryotic proteins that might be N-terminally blocked for
Edman degradation by N-acetylation, and internal sequence analysis is more costly to perform, it
might be advisable to use the peptide mass fingerprinting approach.

The latter method is based on the identification of a protein by comparing the peptide masses found
after tryptic digestion of the protein, with theoretical masses in a data base comprising all known
DNA and protein sequences. The latter also explains the limitations of this method, viz.: if not all
proteins or their DNA sequences are know of the organism from which the protein originates,
identification is likely to fail. Also, certain chemical or post-translational modifications which change
the masses of the peptides, might hamper proper identification. Yet, since the method is very sensitive and wide applicable (also on protein bands present in a piece of SDS-PAGE gel) it could be the best solution in your case. See for more information, the individual technical / background information of
these methods.     

Summarizing, if the exact N-terminal sequence is not important for you to know, and you only wish
to identify a protein, please consider also the peptide mass fingerprinting as option instead of
N-terminal sequencing.