If the protein has a blocked N-terminus no sequence will be determined.
Proteins can also become modified or blocked during electrophoretic separation.
In either case the option then is to obtain Internal Sequence analysis Amino acid sequencing has become a central tool in contemporary labs with separation of proteins by SDS PAGE and subsequent transfer to PVDF type membranes. These techniques have made possible the sequencing of proteins that don't lend themselves to purification by conventional means. Internal Sequence Analysis Useful Links and References N-terminal sequcnce analysis provides general information on the chemistry and Instrumentation maintained by the facility. Sample preparation describes the general conditions and methods for preparing a sample for N-terminal sequencing. Internal sequence analysis is a continuation of the information provided in the previous section with techniques for generating peptides for internal sequence analysis of proteins with blocked N-termini.