Peptide , fragmentation methods

Figure 1 The SILAC method for comparative proteomics. A real experiment requires collection of thousands of mass spectra corresponding to different peptides. In the case portrayed, the drug has lowered the abundance of the affected protein in the treated cells compared to the control cells. Multiple peptide fragments of the affected protein would show this effect, supporting the conclusion that the protein was affected.

No tandem MS experiment can be successful if the precursor ions fail to fragment (at the right time and place). The ion activation step is crucial to the experiment and ultimately defines what types of products result. Hence, the ion activation method that is appropriate for a specific application depends on the MS instrument configuration as well as on the analyzed compounds and the structural information that is wanted. Various, more or less complementary, ion activation methods have been developed during the history of tandem MS. Below we give brief descriptions of several of these approaches. A more detailed description of peptide fragmentation mles and nomenclature is provided in Chapter 2. An excellent review of ion activation methods for tandem mass spectrometry is written by Sleno and Volmer, see Reference 12, and for a more detailed review on slow heating methods in tandem MS, see Reference 13. 

K. Biemann, Nomenclature for Peptide Fragment Ions. In Methods in Enzymology, Vol. 193, J. A. McCloskey (ed.), Elsevier Science and Technology, Orlando, FL, 1990, 886-888. 

Two major synthetic strategies have been applied for the synthesis of S-prenylated peptides as shown in Scheme 1. In the first approach (method A), S-alkylation is performed on the final peptide in a protected or unprotected form.13641 In method B, which has produced better results in terms of overall yield, thiol alkylation is carried out on the cysteine residue or on a small peptide fragment and then the S-prenylated synthons are coupled to the remaining peptide fragment to produce the final products.[45 501 Most of the procedures reported for the synthesis of farnesylated peptide derivatives, can also be applied to the synthesis of geranylgeranylated peptides. 

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