The information presented in this article is for educational and research purposes only, intended for laboratory professionals, researchers and collaborators. This content does not constitute medical or clinical advice.
This alphabetical peptide glossary provides essential terminology for peptide synthesis researchers, covering key terms and concepts from basic amino acid chemistry to advanced synthetic methodologies and analytical techniques.
A
Acetamidomethyl (Acm) – A thiol protecting group commonly used in peptide synthesis for orthogonal protection of cysteine residues during disulfide bond formation.
Active Ester – Reactive amino acid derivatives such as pentafluorophenyl (OPfp) and hydroxysuccinimido (OSu or NHS) esters that find broad application in peptide synthesis.
Aggregation – The tendency of growing peptide chains to associate with each other during synthesis, often leading to reduced coupling efficiency and impaired synthesis quality. The main cause of failure for peptide chemosynthesis.
Alpha-amino Acid – The building blocks from which peptides are constructed, containing both amine and carboxyl functional groups.
Amino Acid – Any molecule that contains both amine and carboxyl functional groups. The fundamental building blocks of peptides and proteins.
Antimicrobial Peptides (AMPs) – Peptides that possess antimicrobial activity, frequently cationic and associate with anionic LPS located on the outer membranes of Gram-negative bacteria.
Aspartimide Formation – A side reaction where aspartic acid residues can form cyclic imide structures during peptide synthesis, particularly problematic when DBU is used for Fmoc deprotection.
B
Benzotriazole (HOBt) – A coupling additive used to reduce racemization and improve coupling efficiency in peptide synthesis, though it has safety concerns due to explosive properties when anhydrous.
Boc (tert-Butyloxycarbonyl) – One of the most common carbamate protecting groups for amino acids, removable with strong acid (trifluoroacetic acid) or heat. Introduced in the late fifties and rapidly applied in peptide synthesis.
Boc/Benzyl Strategy – A protection scheme where Boc protecting groups are used to temporarily protect the Nα nitrogen groups and benzyl-based protecting groups provide permanent protection of side chains.
BOP (Benzotriazol-1-yloxytris(dimethylamino)phosphonium hexafluorophosphate) – A HOBt-based phosphorus positive ion peptide coupling reagent widely used in solid-phase and liquid-phase synthesis of peptides.
C
C-terminus – The carboxy-terminal end of a peptide chain. Chemical peptide synthesis most commonly starts at the carboxyl end of the peptide and proceeds toward the amino-terminus.
Capping – An optional process where the N-terminal amino group is blocked to prevent the obtained peptide from further reaction.
Carbodiimides – Coupling reagents including DCC, DIC, and EDC·HCl commonly used to prepare amides, esters and acid anhydrides from carboxylic acids.
CBz (Carboxybenzyl) – A protecting group with a benzyl group that can be removed using catalytic hydrogenation (Pd-C, H₂).
Cell-Penetrating Peptides (CPPs) – Short chains of 5–30 amino acid residues widely used for effective intracellular transportation of biologically active drug molecules.
COMU – A safer and more efficient coupling reagent than benzotriazole-based reagents, requiring only one equivalent of base rather than two equivalents needed for HATU and HBTU.
Coupling Reagents – Chemical compounds used to facilitate the formation of amide bonds between amino acids in peptide synthesis. Examples include HATU, HBTU, HCTU, DIC, and PyBOP.
Cyclic Peptides – Peptides in which the amino acid sequence forms a ring structure rather than a straight chain, such as the antibiotics tyrocidin and gramicidin.
D
D-Amino Acids – Mirror image isomers of natural L-amino acids that have wide applications due to increased resistance against degradation enzymes, making peptides containing D-amino acids more stable.
DBU (1,8-Diazabicyclo[5.4.0]undec-7-ene) – A base that removes the Fmoc protecting group much faster than piperidine, but should not be used when aspartic acid residues are present due to aspartimide formation.
DCC (Dicyclohexylcarbodiimide) – A popular condensation reagent applied in peptide coupling since 1955, routinely used in solution and solid-phase peptide synthesis, mostly in combination with additives such as HOBt.
Deprotection – The process of removing protecting groups from amino acids during peptide synthesis to expose reactive sites for the next coupling reaction.
Depsipeptides – Special peptide units used to circumvent side reactions and development of automated synthesis techniques for difficult sequences.
DIC (Diisopropylcarbodiimide) – A carbodiimide coupling reagent that generates more soluble reaction by-products compared to DCC, making it preferred for solid-phase synthesis.
Difficult Sequences – Peptide sequences that are challenging to synthesize using standard protocols, often requiring special techniques to reduce aggregation of the growing peptide chain.
Dipeptide – The shortest peptide, composed of just two amino acids.
Disulfide Bond Formation – The formation of covalent bonds between cysteine residues, achieved on solid-phase by air, K₃Fe(CN)₆, or other oxidizing agents.
E
EDC (1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide) – A water-soluble carbodiimide coupling reagent used in peptide synthesis.
Epimerization – The unwanted conversion of L-amino acids to D-amino acids during coupling reactions, which can be minimized by using appropriate coupling reagents and additives.
F
Fmoc (9-Fluorenylmethoxycarbonyl) – A base-labile protecting group for amines, typically removed with 20% piperidine in DMF. Introduced by Carpino in 1972 and rapidly adopted in modern peptide chemistry.
Fmoc/tBu Strategy – A protection scheme that combines base-sensitive Fmoc protection with acid-sensitive tert-butyl side-chain protecting groups, offering true orthogonal protection.
FRET (Förster Resonance Energy Transfer) – A spectroscopic technique used in peptide analysis and characterization, often involving fluorescently labeled peptides.
G
Glycopeptides – Peptides containing carbohydrate modifications, whose synthesis has developed rapidly using the mild conditions of Fmoc chemistry.
H
Handle – The product formed when a C-terminal Fmoc amino acid is coupled to a linker, which can be purified before loading the polymer.
HATU (2-(7-Aza-1H-benzotriazol-1-yl)-N,N,N’,N’-tetramethylaminium hexafluorophosphate) – A highly efficient coupling reagent for solid- and solution-phase reactions, preferred to HBTU in most rapid coupling protocols.
HBTU (2-(1H-Benzotriazol-1-yl)-1,1,3,3-tetramethylaminium hexafluorophosphate) – A HOBt-based uronium coupling reagent successfully used in peptide synthesis since 1978.
HCTU (O-(6-Chlorobenzotriazol-1-yl)-N,N,N’,N’-tetramethyluronium hexafluorophosphate) – A coupling reagent that remains colorless through long synthesis sequences and has greater stability, reported to be less allergenic than other coupling reagents.
HPLC (High-Performance Liquid Chromatography) – The primary method for peptide purification and analysis, typically using C18 reverse phase columns with acetonitrile-water gradients and TFA as ion pairing reagent.
Hydrazine – A reagent used to remove Dde and ivDde protecting groups, typically as 2% hydrazine in DMF.
I
Ion-Exchange Chromatography – A separation method that separates peptides based on charge using resins with opposite charge to capture peptides.
L
Linker – Bifunctional molecules anchoring the growing peptide to the insoluble carrier, determining the properties of the final product and the chemistry that can be used.
Liquid-Phase Peptide Synthesis (LPPS) – A classical approach to peptide synthesis that is slow and labor-intensive because the product must be manually removed from reaction solution after each step.
M
MALDI-TOF MS (Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry) – A mass spectrometer used to determine the molecular weight of peptides.
Mass Spectrometry – An analytical technique providing detailed information on peptides’ mass-to-charge ratios, used to reconstruct protein sequences and detect post-translational modifications.
Microwave-Assisted Peptide Synthesis – A technique that has been used to complete long peptide sequences with high degrees of yield and low degrees of racemization.
N
N-terminus – The amino-terminal end of a peptide chain. Peptides are biologically synthesized from N-terminus to C-terminus, opposite to chemical synthesis.
Native Chemical Ligation – A ligation approach where two shorter fully deprotected synthetic peptides can be joined in solution to access longer peptide lengths.
Ninhydrin Test – A qualitative test used to monitor coupling reactions during peptide synthesis by detecting free amino groups.
O
Oligopeptides – Shorter peptides made up of relatively small numbers of amino acids, generally less than ten.
Orthogonal Protection – A protection scheme where the Nα protecting group and side-chain protecting groups can be removed under completely different conditions.
Oxyma Pure – A coupling additive that is not based on potentially explosive triazole reagents, offering advantages over HOBt-based systems.
P
Peptide – Two or more amino acids chained together by peptide bonds, typically 2 to 50 amino acids. Longer chains (51 or more) are polypeptides.
Peptide Bond – A covalent chemical bond formed between two consecutive amino acid monomers when the carboxyl group of one molecule reacts with the amino group of another, releasing water.
Peptide Library – A systematic combination of different peptides in large numbers, providing a powerful tool for drug design, protein-protein interactions, and biochemical applications.
Peptide Mapping – An analytical technique used to identify and characterize proteins by breaking them down into smaller peptide fragments and analyzing their sequences and structures.
Peptide Synthesis – A biological or chemical process in which amino acids are added stepwise to a chain by formation of peptide bonds between carboxyl and amino groups.
Piperidine – A secondary amine commonly used at 20% concentration in DMF for Fmoc deprotection during peptide synthesis.
Polypeptides – Peptides typically composed of more than ten amino acids, with longer chains (40-50+ amino acids) generally referred to as proteins.
Post-Translational Modifications (PTMs) – Chemical modifications to amino acids that occur after protein synthesis, including phosphorylation, glycosylation, and oxidation.
Protecting Groups – Chemical groups used to prevent unintended reactions during peptide synthesis by temporarily blocking reactive sites on amino acids.
Pseudoprolines – Specialized units used in difficult peptide synthesis to reduce aggregation and improve coupling efficiency.
PyBOP (Benzotriazol-1-yl-oxytripyrrolidinophosphonium hexafluorophosphate) – A phosphonium-based coupling reagent that generates OBt esters and finds wide application in routine SPPS.
R
Racemization – The unwanted conversion of optically active amino acids to their racemic mixture during coupling reactions, minimized by appropriate reagent selection and reaction conditions.
Resin – The insoluble polymeric support used in solid-phase peptide synthesis, most commonly polystyrene crosslinked with 1% divinylbenzene.
Reversed-Phase HPLC (RP-HPLC) – The most popular method for peptide purification, combining high resolution and recovery with ease and speed of operation.
Rink Resin – A type of resin commonly used for peptide synthesis that allows cleavage under specific acidic conditions.
S
Side-Chain Protection – Protection of reactive side chains on amino acids during peptide synthesis using groups like tert-butyl ethers, trityl ethers, or benzyl ethers.
Solid-Phase Peptide Synthesis (SPPS) – The most common method of peptide synthesis where the peptide is anchored by its C-terminus to an insoluble polymer and assembled by successive addition of protected amino acids.
Solution-Phase Synthesis – Traditional peptide synthesis method conducted in solution, which retains usefulness in large-scale production despite being labor-intensive.
Stapled Peptides – Conformationally constrained peptides created using unnatural alkenyl amino acids for peptide ‘stapling’, forming a new generation of chemical and drug discovery tools.
T
TFA (Trifluoroacetic Acid) – An acid used for Boc deprotection and as an ion pairing reagent in HPLC to improve peak width and symmetry.
Trityl (Trt) – A protecting group commonly used for asparagine and glutamine side chains in Fmoc chemistry.
Tripeptide – A peptide composed of three amino acids.
U
Unnatural Amino Acids (UAAs) – Non-proteinogenic amino acids that either occur naturally or are chemically synthesized, important tools for drug discovery with unlimited structural diversity and functional versatility.
Uronium Salts – A class of coupling reagents including HATU, HBTU, and HCTU that convert protected amino acids to activated species in the presence of tertiary base.
W
Wang Resin – A commonly used resin for peptides with C-terminal carboxylic acids.
This glossary provides essential terminology for peptide synthesis researchers and professionals. Terms are continuously evolving as the field advances.