We have developed a highly efficient method for the site-specific attachment of biophysical probes to unprotected peptides after chemical synthesis. This methodology takes advantage of the selective reactivity of an N-methylaminooxy amino acid that is appropriately protected for direct incorporation during solid-phase peptide synthesis. The functional N-methylaminooxy group is unmasked using normal peptide cleavage conditions and is capable of selective reaction with activated N-hydroxysuccinimide esters ia the presence of cysteine, lysine and the amino terminus, as demonstrated in model peptides and test proteins. Selective labeling can be accomplished after synthesis using commercially available or chemically sensitive probes. This technology is compatible with the synthesis of Cu-thioester-containing peptides and amide-forming ligations, required steps for the synthesis of proteins by either total chemical synthesis or expressed protein ligation. The N-methylaminooxy amino acid can be introduced into different sites by parallel peptide synthesis to generate a polypeptide analogue family with each member possessing a single specifically labeled site. This enables the synthesis of optimized biosensors through combinatorial screening of different attachment sites for maximal response and minimal perturbation of biological activity.