Mass spectrometry, peptide sequence determination

Mass spectrometry sequencing of oligonucleotides is not as common a practice as it is for proteins and peptides. However, the following mass spectrometry-based sequence determination strategies have gained acceptance ... 

Mass spectral fragmentation patterns of alkyl and phenyl hydantoins have been investigated by means of labeling techniques (28—30), and similar studies have also been carried out for thiohydantoins (31,32). In all cases, breakdown of the hydantoin ring occurs by a-ftssion at C-4 with concomitant loss of carbon monoxide and an isocyanate molecule. In the case of aryl derivatives, the ease of formation of Ar—NCO is related to the electronic properties of the aryl ring substituents (33). Mass spectrometry has been used for identification of the phenylthiohydantoin derivatives formed from amino acids during peptide sequence determination by the Edman method (34). 

As each resin bead contains only a single molecule the beads can be screened individually for bioactivity by either screening for activity of bound peptide in the biological assay or by cleaving the resultant peptide from the bead before undertaking the bioanalysis. The identity of any active compounds can then be determined by using mass spectrometry to sequence the active peptide. 

Part 2. Mass spectrometry in amino-acid and peptide analysis and in peptide sequence determination... 

Peptide Sequence Determination Using Mass Spectrometry... 

See also Capillary Electrophoresis Overview. Chir-optical Analysis. Liquid Chromatography Column Technology Mobile Phase Selection Reversed Phase Instrumentation Amino Acids. Mass Spectrometry Peptides and Proteins. Nuclear Magnetic Resonance Spectroscopy Techniques Nuclear Overhauser Effect. Proteins Traditional Methods of Sequence Determination Foods. 

However, interpretation of, or even obtaining, the mass spectrum of a peptide can be difficult, and many techniques have been introduced to overcome such difficulties. These techniques include modifying the side chains in the peptide and protecting the N- and C-terminals by special groups. Despite many advances made by these approaches, it is not always easy to read the sequence from the mass spectrum because some amide bond cleavages are less easy than others and give little information. To overcome this problem, tandem mass spectrometry has been applied to this dry approach to peptide sequencing with considerable success. Further, electrospray ionization has been used to determine the molecular masses of proteins and peptides with unprecedented accuracy. 

Complex peptide mixmres can now be analyzed without prior purification by tandem mass spectrometry, which employs the equivalent of two mass spectrometers linked in series. The first spectrometer separates individual peptides based upon their differences in mass. By adjusting the field strength of the first magnet, a single peptide can be directed into the second mass spectrometer, where fragments are generated and their masses determined. As the sensitivity and versatility of mass spectrometry continue to increase, it is displacing Edman sequencers for the direct analysis of protein primary strucmre. 

The major advantage of the tandem mass spectrometry approach compared to MALDI peptide fingerprinting, is that the sequence information obtained from the peptides is more specific for the identification of a protein than simply determining the mass of the peptides. This permits a search of expressed sequence tag nucleotide databases to discover new human genes based upon identification of the protein. This is a useful approach because, by definition, the genes identified actually express a protein. 

Figure 5.11. Generic approaches to identify interacting proteins within complexes. The complex is isolated from cells by affinity purification using a tag sequence attached to a protein known to be in the complex. Alternatively, the complex can be immunprecipitated with an antibody to one of the proteins in the complex. The proteins are resolved by polyacrylamide gel electrophoresis, proteolyzed, and the mass of the resulting peptides is determined by mass spectrometry. Alternatively, the proteins can be proteolyzed and the resulting peptides resolved by liquid chromatography. The peptide masses are then determined by mass spectrometry and used for database searching to identify the component proteins.

Tandem mass spectrometry has become an important tool for determining the sequence of amino acids in protonated peptides98 and the sequence of bases in deprotonated nucleic acids such as DNA.99 Despite the importance and widespread use of CID-MS to sequence peptides and nucleic acids, the mechanistic details of the dissociation processes are poorly understood. A better understanding of the... 

Ermer, for example, utilized LCQ to monitor impurity profiles of various batches of ramorelix used in toxicological studies, clinical stndies and scale-up. Ramorelix is a synthetic glycosylated decapeptide with monoisotopic of 1530.7. The toxicological batch served as the benchmark against which all other batches were compared. Molecnlar weights of impurities were determined by ESI mass spectrometry, and nsed in conjunction with UV peak area % to gauge impurities in batches nsed in clinical trials. These impurity profiles were compared to those of batches used in the toxicologically qualified batch. Eour impurities were detected with the same value. They were believed to be diastereoisomers of ramorelix, i.e., a peptide sequence with one of the amino acids in the opposite enantiomeric form. 

When air oxidation of the reduced p-conotoxin GIIIB (18) was carried out in 0.1 M NHtOAc buffer (pH 7.5) at 0.01 mM peptide concentration and at 10 °C, three major products, isomers 15,16, and 17 were produced after 40 hours in a ratio of 1 4 3 (Figure 2). 86 The disulfide structures of each isomer were determined by enzymatic digestion followed by amino acid analyses, mass spectrometry, sequence analyses, as well as by the synthetic approach (Scheme 10). 

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