Protein ladder sequencing

Sequence information can also be obtained using Edman degradation to remove amino-terminal residues from a peptide, to produce a collection of peptides. MALDI-TOF can then be used to obtain the peptides masses, and the sequence determined by mass difference between consecutive peptides. This methodology is called protein ladder sequencing, and allows information to be obtained for up to 30 residues. This method is useful for the identification of posttranslational modifications, such as phosphorylated amino acid residues.24... 

BT Chait, R Wong, RC Beavis, SBH Kent. Protein ladder sequencing. Science... 

Many structural biology and biochemistry studies rely on the precise identification of the N-/C-terminal sequence of a protein (e.g., signal peptide identification, determining the cleavage site and specificity of a novel protease, etc.). Digestion of proteins in arrays of carboxypeptidase Y at different concentrations with MALDl-MS-based readout can be employed to derive C-terminal sequence information for proteins. The amino-terminus of a protein can be derived by wet chemistries similar to Edman degradation coupled to MS-readout. This method of protein ladder sequencing, reported first by Kent and... 

Figure 18.5. MALDI-TOF mass spectrum from protein ladder sequencing of the N-terminal peptide of cofilin (G-S-R-S-G-V-A-...). A stepwise degradation was carried out in the presence of 5% phenylisocyanate/95% phenylisothiocyanate. The peptide was subjected to two cycles of ladder generating chemistry. ...

Footprinting. A technique that results in a DNA sequence ladder in which part of the ladder is missing due to the binding of protein to the DNA before processing. 

The same approach has been applied to proteins. This protein sequencing technique, which is termed mass analysis of polypeptide ladders (MAP), allows rapid determination of protein sequences and characterization of protein modifications [121], Indeed, proteins... 

Zhong, H.Y., Zhang, Y., Wen, Z.H. and Li, L. (2004) Protein sequencing by mass analysis of polypeptide ladders after controlled protein hydrolysis. Nat. Biotechnol., 22, 1291-6. 

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