Protein fragments after a protease (for example trypsine) will be separated and sequenced. Let us assume that the following two peptide sequences are obtained.

Gly-Gly -Phe -Ala -Lys

Thr- Phe- Gly-Lys

Now, a second method is used to cleave protein at other site. For example if we use chymotrypsin. Following sequence is found for one peptide sequence.

Gly-Lys-Gly-Gly-Phe

Now data from tyrosine cleavage fragment sequence and chymotrypsin cleavage fragment sequence can be analyze to get larger sequence information (Fig. 5)

 

Figure 5: Sequences of smaller fragments may be overlapped and analyzed for complete sequence as explained above