, the most commonly used resin for peptides with C-terminal carboxylic acids. Protecting groups schemes As described above, the use of N-terminal and side chain protecting groups is essential during peptide synthesis to avoid undesirable side reactions, such as self-coupling of the activated amino acid leading to (polymerization). This would compete with the intended peptide coupling reaction, resulting in low yield or even complete failure to synthesize the desired peptide. Two principal protecting group schemes are typically used in solid phase peptide synthesis: so-called Boc/benzyl and Fmoc/tert.butyl approaches. The Boc/Bzl strategy utilizes TFA-labile N-terminal Boc protection alongside side chain protection that is removed using anhydrous hydrogen fluoride during the final cleavage step (with simultaneous cleavage of the peptide from the solid support). Fmoc/tBu SPPS uses base-labile Fmoc N-terminal protection, with side chain protection and a resin linkage that are acid-labile (final acidic cleavage is carried out via TFA treatment). Both approaches, including the advantages and disadvantages of each, are outlined in more detail below. Boc/Bzl SPPS Before the advent of SPPS, solution methods for chemical peptide synthesis relied on tert-butyloxycarbonyl (abbreviated 'Boc') as a temporary N-terminal α-amino protecting group. The Boc group is removed with acid, such as trifluoroacetic acid (TFA). This forms a positively charged amino group in the presence of excess TFA (note that the amino group is not protonated in the image on the right), which is neutralized and coupled to the incoming activated amino acid. Neutralization can either occur prior to coupling or in situ during the basic coupling reaction. The Boc/Bzl approach retains its usefulness in reducing peptide aggregation during synthesis. In addition, Boc/benzyl SPPS may be preferred over the Fmoc/tert.butyl approach when synthesizing peptides containing base-sensitive moieties (such as depsipeptides or thioester moeities), as treatment with base is required during the Fmoc deprotection step (see below). Permanent side-chain protecting groups used during Boc/benzyl SPPS are typically benzyl or benzyl-based groups. Final removal of the peptide from the solid support occurs simultaneously with side chain deprotection using anhydrous hydrogen fluoride via hydrolytic cleavage. The final product is a fluoride salt which is relatively easy to solubilize. Scavengers such as cresol must be added to the HF in order to prevent reactive cations from generating undesired byproducts. Fmoc/tBu SPPS The use of N-terminal Fmoc protection allows for a milder deprotection scheme than used for Boc/Bzl SPPS, and this protection scheme is truly orthogonal under SPPS conditions.