The invention provides intermediates and methods that allow for site-specific modification of peptides after synthesis. Accordingly, functional molecules can be selectively linked to a peptide to provide a peptide conjugate having altered biological, chemical, or physical properties. For example, functional molecules (e.g. biophysical probes, peptides, polynucleotides, and therapeutic agents) can be linked to a peptide to provide a peptide conjugate having differing and useful properties. The invention also provides a compound of formula (III): ##STR00001## wherein: R.sup.6 is a peptide; X is a direct bond or a linking group; R.sup.7 is hydrogen, (C.sub.1-C.sub.6)alkyl, an amino protecting group, or a radical comprising one or more aminooxy groups; Y is a direct bond or a linking group; and D is a functional molecule.