Sequencing, mass spectrometric approaches

Mass Spectrometric Approaches to Sequencing and Compositional Characterization... 

The second approach is the tandem mass spectrometric method (Wilm et ah, 1996 Link et ah, 1999 Yates, 2000). This method relies on fragmentation of individual peptides in the tryptic peptide mixture to gain sequence information. Its main advantage is that sequence information derived from several peptides is much more specific for the identification of a protein than a list of peptide masses. The sequence data can be used to search not only protein sequence databases but also nucleotide databases such as expressed sequence tag (EST) databases and, more recently, even... 

For routine analysis, it is suggested that mass determination of an HPLC purified product is sufficient to be relatively assured that the correct product has been made. Of course, this approach will neither determine if the correct amino acids have been incorporated into an incorrect sequence nor determine if a substitution of amino acids of identical mass has occurred. However, the numerous checkpoints for automated peptide synthesis (bar codes, printouts, etc.) should greatly reduce the probability of this occurring. Should access to mass spectrometric analysis not be available, amino acid analysis is preferable. 

It is evident from the discussions above that mass spectrometric method in combination with enzymatic digestion offers a convenient approach to the characterization of GM-CSF and its variants. ESI-MS method demonstrated a mass accuracy of better than 0.01% for a recombinant protein. The mass spectral data of the enzymatic digest of GM-CSF and its variants allow the precise determination of the molecular weights of the peptides, leading to the identification of sites of covalent modifications, the disulfide bonding pattern, and confirmation of the cDNA-derived sequence of the protein. 

We have gained an appreciation for the ionization bias observed between MALDI and LSIMS. The utilization of PSD to identify known peptides and provide sequence information has been investigated for conotoxins. This approach to obtaining sequence information on novel peptides is attractive because of the low amount of material required. A number of mass spectrometric based derivatizations have been used to scan fractions of venoms in order to characterize peptides of interest. For closely related components (based on HPLC retention time and mass), the small scale derivatization schemes can be used to test hypotheses about peptides with otherwise novel masses (i.e. which may be homologs). The mass accuracy of the TOF technique, with a gridless reflector, was important for identifying and calling these substitutions. 

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