The application of capillary columns to the determination of the amino acid sequence of proteins and polypeptides by gas chromatography-mass spectrometry (GC-MS) of partial hydrolysates is described and discussed for the case of the Napetrifluoroacetyl-N,O-permethyl derivatives. Retention indices are determined with the aid of a computer program. The mass spectra of methionine enkephalin obtained by GC-MS on a packed and on a capillary column are presented and a retention index calculated. Amounts of derivative corresponding to sub-nanomole amounts of peptides are sufficient to provide full amino acid sequence information. To assist in the assignment of retention indices above 4400, a mixture of n-alkanes from a commercial source was characterized by GC-MS up to n-C54H110 and was found to contain material up to an expected C72H146.