• De novo sequencing of proteins that are unlikely to be in the database
• Mapping of post-translational modifications.

Advantages: 

• Ability to use the determined sequence for primer design, or database searching against known proteins (cross species matching)
• Provide internal amino acid sequence data
• Can be used for post-translational modification analysis

Disadvantages: 

• Leucine and Isoleucine cannot be differentiated. Most peptides will contain at least one Leu/Ile.
• There can be problems calling Phenylalanine and methionine sulphoxide as these amino acids only vary by 0.04Da. Methionine sulphoxide is a common artefact of 2D gel electrophoresis.
• There can also be problems calling Lysine and Glutamine as these amino acids also vary by only 0.04Da.
• Both of these problems can be overcome and are not routinely an issue.
• There is no way of controlling what peptides will be seen in a digest. ie. we cannot specifically target the N-terminus of a protein