C. C-terminal residues: Not many methods are developed for c-terminal amino acid analysis. The most common method is to treat the protein with a carboxypeptidase to release the c-terminal amino acid and test the solution in a time dependent manner.

Stage 4. Ordering the peptide fragments: The usage of different protein cleavage reagent produces over-lapping amino acid stretches and these stretches can be used to put the whole sequence.

Stage 5. Locating disulfide bonds: The protein cleavage by typsin is performed with or without breaking di-sulphide linkage. Amino acid sequence analysis of the fragments will provide the site of disulphide bond. The presence of one disulphide will reduce two peptide fragment and will appear as one large peptide fragment.   

Mass Spectrometry Method: In recent pass, mass spectroscopy in conjugation with proteomics information is also been popular tool to chacracterize each peptide fragment to deduce its amino acid sequence. The minor detail of this approach can be explored by following the article

[ Collisions or Electrons? Protein Sequence Analysis in the 21st Century". Anal. Chem. 81 (9): 3208–3215.]