N-terminal Protein Sequencing, also known as Edman degradation, involves the sequential cleavage of amino acids from the N-terminal end of a protein, and identification of individual amino acids using microbore HPLC. A single cycle will identify a single amino acid, and sequential cleavage will determine the amino acid sequence.
Improvements in this field have allowed minute quantities of purified protein/peptides to be easily sequenced, assuming the protein is pure, not blocked and 100% sequenceable. If the protein is already in one of the many databases, sequencing about 12 residues can be sufficient for protein identification. Cysteine residue is not detectable under normal sample preparation conditions and its presence is inferred by a gap in the sequence, reported as X.
However, post-translational modifications to the peptide molecules may cause protein samples to be blocked at the N-terminal. This is a biological process that occurs in the cell and is not typically caused by sample preparation. Common N-terminal blocking groups include pyroglutamate, N-acetyl groups such as acetyl-serine or acetyl-threonine and N-formylated amino acids. As a result, more than 50% of eukaryote proteins are blocked at N-terminal.
If the ultimate objective is to identify the protein, mass spectrometry using either MALDI-ToF/ToF or LC-MS/MS is the best alternative method to be used in Protein Identification.
If confirming the sequences at the N-terminal of the protein remains the ultimate objective of the experiment, we can offer mass spectrometry services for the protein by comparing its provided theoretical peptide sequences. Please contact us for more details.
Samples should be submitted with our Service Order Form.