To make more practical the total chemical synthesis of proteins by the ligation of unprotected peptide building blocks, we have developed a method to facilitate the isolation and handling of intermediate products. The synthetic technique makes use of a His6 tag at the C terminus of the target polypeptide chain, introduced during the synthesis of the C-terminal peptide segment building block. The presence of a His6 tag enables the isolation of peptide or protein products directly from ligation reaction mixtures by Ni-NTA affinity column purification. This simple approach enables facile buffer exchange to alternate reaction conditions and is compatible with direct analytical control by protein MS of the multiple ligation steps involved in protein synthesis. We used syntheses of crambin and a modular tetratricopeptide repeat protein of 17 kDa as models to examine the utility of this affinity purification approach. The results show that His6 tag-assisted chemical protein synthesis is a useful method that substantially reduces handling losses and provides for rapid chemical protein syntheses. (16). Synthetic access to protein molecules has been used to elucidate the molecular basis of protein folding and stability (17), to elucidate the molecular basis of protein function (18), to design and build proteins of novel structure (19), and to determine the molecular structure of proteins by both NMR (20) and x-ray crystallography (21). Chemical protein synthesis has also been used to develop candidate protein therapeutic molecules with improved properties (21,22).Thus far, most research on chemically synthesized protein molecules (16) has been focused on relatively small proteins in the size range of 50 to Ϸ150 aa (i.e., made from two or three peptide segments). This size limitation is the result of two phenomena: (i) practical constraints on the size of the unprotected peptide segment building blocks (23) and (ii) technical challenges in the chemical ligation of more than two or three peptide segments. Even highly optimized stepwise solid-phase peptide synthetic procedures are limited to Ϸ50 amino acid residues for the practical preparation of high-purity unprotected peptides (24). Thus, the chemical synthesis of a protein of typical size (Ϸ300 aa) (25) would require the use of at least six synthetic peptide segments as building blocks.The most effective way of covalently joining unprotected peptide segments to form a protein molecule is native chemical ligation (3,26). Native chemical ligation involves the reaction of a peptide-␣ thioester with a Cys-peptide; reversible thioesterthiol exchange with the N-terminal Cys residue gives a thioesterlinked intermediate that undergoes an irreversible intramolecular rearrangement to give a near-quantitative yield of a single product linked by a native peptide bond at the ligation site. The native chemical ligation reaction is both practical and highly effective. ¶ Each ligation product can be purified by reverse-phase HPLC and characterized with great precision by electrospray M...