We report here the use of an intein-mediated protein ligation strategy for the synthesis of glycoproteins and proteins containing various molecular probes. Several simple cysteine derivatives are synthesized and used as nucleophiles for specific incorporation onto the C-terminus of proteins expressed as N-terminal intein fusions. Examples of C-terminal carbohydrate labeling, fluorescence labeling, incorporation of a metal chelator, and incorporation of a nucleotide are presented.