Separation and sequence of dipeptides using gas chromatography and mass spectrometry of their trimethylsilylated derivatives.

Dipeptides containing all 20 common amino acids in the amino and carboxyl positions were trimethylsilylated under a variety of conditions. The dipeptides (about 200 of the possible 400) were synthesized by conventional means or derived from polypeptides digested with dipeptidyl aminopeptidase. Derivatives were prepared in high yield by reaction with N,O-bis(trimethylsilyl)trifluoroacetamide in acetonitrile. Reaction products were identified by mass spectrometry. Numerous stationary phases and supports were compared in the gas chromatographic analysis of the derivatives. Best results were obtained with a 0.2 X 60 cm column packed with Chromosorb 750 coated with a 1% solution of OV-1. All Me3Si dipeptides except those containing arginine eluted in less than 30 min when the column was temperature programmed from 100 to 280 degrees C. The typical mass spectrum of trimethylsilylated dipeptides contains two significant ions used for identification: the ion derived from the amino terminal residue by beta cleavage of the central CH-CO bond and the molecular ion minus a methyl group. Other useful ions also have been noted. A sufficient variety of samples have been examined to establish predictable fragmentations which should allow the identification of all 400 possible dipeptides.