Proteins and peptides can be sequenced from the carboxy terminus with isothiocyanate reagents to produce amino acid thiohydantoin derivatives. Previous studies in our laboratory indicated that the use of trimethylsilyl isothiocyanate (TMS-ITC) as a coupling reagent significantly improved the yields and reaction conditions and reduced the number of complicating side products [Hawke et al. (1987) Anal. Biochem. 166, 298]. The present study further explores the conditions for formation of the peptidylthiohydantoins by TMS-ITC and examines the cleavage of these peptidylthiohydantoin derivatives into a shortened peptide and thiohydantoin amino acid derivative. Schizophrenia-related peptide (Thr-Val-Leu) was used as a model peptide and was treated with acetic anhydride and TMS-ITC at 50 degrees C for 30 min, and the peptidylthiohydantoin derivatives were isolated by reverse-phase HPLC and characterized by FAB-MS. The purified derivatives were subjected to a variety of cleavage conditions, and rate constants for hydrolysis were determined. Hydrolysis with acetohydroxamate as reported originally by Stark [(1968) Biochemistry 7, 1796] was found to give excellent cleavage of the terminal thiohydantoin amino acid, but also led to the formation of stable hydroxamate esters of the shortened peptide which are poorly suited for subsequent rounds of degradation. Hydrolysis with 2% aqueous triethylamine under mild conditions (1-5 min at 50 degrees C) was found to be more suitable for carboxy-terminal sequence analysis by the thiocyanate method. The shortened peptide, which could be isolated and subjected to a second round of degradation, and the released thiohydantoin amino acid are formed in good yield (90-100%). Several other small peptides containing 15 different C-terminal amino acid side chains were also investigated in order to examine any interfering reactions that might occur when these side chains are encountered in a stepwise degradation using the thiocyanate chemistry. Quantitative yields of peptidylthiohydantoins were obtained for all the amino acids examined with the following exceptions: low yields were obtained for C-terminal Glu or Thr, and no peptidylthiohydantoins were obtained for C-terminal Pro or Asp. Asparagine was found to form cyclic imides (64%) at the penultimate position (C-2) during hydrolysis of the peptidylthiohydantoins by 2% aqueous triethylamine. Cleavage of C-terminal Asn under these conditions led to the formation of the expected shortened peptide (69%), but also to the formation of a shortened peptide (31%) with a C-terminal amide. Problems with Glu and Thr could be solved by minimizing the reaction time with acetic anhydride.(ABSTRACT TRUNCATED AT 400 WORDS)