Glossary
60 terms used in peptide chemistry, analytical testing and regulation.
- 503A
- Section 503A of the US Federal Food, Drug, and Cosmetic Act, covering compounding by licensed pharmacists or physicians for individual patients based on prescriptions. Bulk substances must meet specific criteria, such as appearing on FDA's 503A bulks list.
- 503B
- Section 503B of the US Federal Food, Drug, and Cosmetic Act, covering registered outsourcing facilities that compound drugs under current good manufacturing practice and FDA inspection, with their own bulk drug substance lists.
A
- Acetate
- The anion of acetic acid, a common alternative counter-ion to trifluoroacetate for peptides intended for biological work. Acetate salts are usually obtained by an exchange step. More
- Acetylation
- Addition of an acetyl group, most often to the N-terminal amine. N-terminal acetylation removes a positive charge and can reduce cleavage by aminopeptidases. More
- Aggregation
- Self-association of peptide molecules into oligomers, gels or fibrils. It is favored by hydrophobicity, high concentration, pH near the isoelectric point and freeze-thaw cycles. More
- Agonist
- A molecule that binds a receptor and activates it, producing a response. Partial agonists produce less than the maximal response, and antagonists bind without activating.
- Aliquot
- A measured portion of a stock solution divided off for single use. Aliquoting avoids repeated freeze-thaw cycles and contamination of the whole stock. More
- Amino acid
- An organic molecule with an amino group, a carboxyl group and a side chain attached to a central carbon. Twenty standard amino acids are the building blocks of peptides and proteins. More
- Analogue
- A molecule derived from a parent peptide by substituting, adding or modifying residues to change properties such as stability or receptor selectivity.
- Average mass
- The mass of a molecule calculated from natural isotope abundances of each element. For larger peptides it can exceed the monoisotopic mass by several daltons. More
B
- Bioburden
- The number of viable microorganisms present on or in a material before sterilization. It is a quantitative measure, distinct from a pass/fail sterility test. More
- BLA
- Biologics License Application, the submission requesting FDA approval to market a biological product. Some larger peptides and proteins are regulated as biologics.
- Bulk drug substance
- In US compounding regulation, an active pharmaceutical ingredient used in compounding a drug. Whether a substance may be used depends on its status under the relevant 503A or 503B provisions.
C
- C-terminal amidation
- Replacement of the C-terminal carboxylic acid with a carboxamide. It removes a negative charge, is common in natural peptide hormones, and changes the expected mass by about −1 Da relative to the free acid. More
- C-terminus
- The end of a peptide chain bearing a free alpha-carboxyl group, or a modified form of it such as an amide. More
- Cake collapse
- Loss of the porous structure of a freeze-dried product, which shrinks into a dense or glassy mass when it warms above its collapse temperature during drying or absorbs moisture afterward. More
- Category 1 / Category 2
- Categories FDA uses in its interim lists of bulk drug substances nominated for compounding. Category 1 substances are under evaluation and may be used under interim policy, while Category 2 substances have been identified as raising significant safety concerns; current listings should be checked directly.
- COA (certificate of analysis)
- A document reporting test results for a specific production lot, typically covering identity, purity, content and contaminants, with methods and the testing laboratory. More
- Counter-ion
- An oppositely charged ion that balances the charges on a peptide in the solid state. Synthetic peptides usually carry anions bound to their protonated amine and guanidine groups. More
- Cyclization
- Formation of a ring within a peptide, by joining the termini, linking side chains or connecting a side chain to a terminus. Cyclic peptides are usually more conformationally constrained and protease-resistant than linear ones.
D
- D-amino acid
- The mirror-image form of an amino acid; natural peptides are built mainly from L-amino acids. D-amino acid substitutions are used in synthetic peptides to reduce enzymatic degradation.
- Deamidation
- Conversion of an asparagine or glutamine side-chain amide to a carboxylic acid, adding about 1 Da and a negative charge. It is fastest at Asn-Gly sequences and at neutral to alkaline pH. More
- Deletion sequence
- A synthetic impurity missing one or more residues because a coupling step was incomplete. It differs from the target by the mass of the missing residue. More
- Disulfide bond
- A covalent sulfur–sulfur bond between the thiol groups of two cysteine residues. It can link parts of one chain into a ring, as in oxytocin, or join separate chains. More
E
- Endotoxin
- Lipopolysaccharide from the outer membrane of Gram-negative bacteria. It is a potent activator of innate immune signaling and can confound cell-based and animal experiments. More
- ESI (electrospray ionization)
- An ionization method that sprays a solution through a charged needle to produce gas-phase ions, typically multiply charged for peptides. It is commonly coupled to liquid chromatography. More
- EU (endotoxin unit)
- A unit of endotoxin biological activity defined against a reference standard endotoxin. Results for solids are reported in EU/mg and for solutions in EU/mL. More
- Extinction coefficient
- A measure of how strongly a molecule absorbs light at a given wavelength. For peptides it is usually estimated at 280 nm from Trp, Tyr and cystine content and used to determine concentration by UV absorbance. More
F
- Fmoc
- 9-Fluorenylmethoxycarbonyl, a base-labile protecting group for the alpha-amino group, used in the most common SPPS strategy. It is removed with piperidine at each cycle. More
- Fragment
- A peptide corresponding to part of a longer peptide or protein sequence. TB-500 is commonly described as a fragment-based peptide related to thymosin β4. More
G
- GMP
- Good manufacturing practice, the regulatory quality standards governing production of medicines and their ingredients. Research-grade materials are generally not produced under GMP.
- GRAVY
- Grand average of hydropathy, the mean hydropathy value of all residues in a sequence on the Kyte–Doolittle scale. Positive values indicate an overall hydrophobic sequence. More
H
- Half-life
- The time taken for the concentration or amount of a substance to fall by half, whether in a solution, a stability study or a biological system. Values depend strongly on the context in which they are measured.
- HPLC
- High-performance liquid chromatography, a technique that separates components of a mixture by pumping it through a packed column. It is the standard method for measuring peptide purity. More
I
- ISO/IEC 17025
- The international standard for the competence of testing and calibration laboratories. Accreditation to it indicates that a laboratory's methods and quality system have been independently assessed. More
- Isoelectric point (pI)
- The pH at which a peptide carries no net electrical charge. Solubility is typically lowest near the isoelectric point. More
L
- LAL (Limulus amebocyte lysate)
- A reagent prepared from horseshoe crab blood cells that clots in the presence of endotoxin. It is used in gel-clot, turbidimetric and chromogenic endotoxin assays. More
- LC-MS
- Liquid chromatography coupled to mass spectrometry, which separates components and measures the mass of each as it elutes. It is used to identify the main product and individual impurities. More
- Lipidation
- Covalent attachment of a fatty acid or other lipid to a peptide. In semaglutide and tirzepatide, a fatty diacid side chain promotes binding to serum albumin. More
- Lot number
- An identifier assigned to a batch of material produced under the same conditions. It links a container to its certificate of analysis and experimental records. More
- Lyophilization
- Freeze-drying: removal of water from a frozen material by sublimation under vacuum. Peptides are usually supplied lyophilized because the dry state slows degradation. More
M
- MALDI-TOF
- Matrix-assisted laser desorption/ionization with a time-of-flight analyzer. The sample is co-crystallized with a matrix and ionized by a laser, producing mainly singly charged ions. More
- Monoisotopic mass
- The mass of a molecule calculated using the most abundant isotope of each element. It corresponds to the first peak in a resolved isotope pattern. More
N
- N-terminus
- The end of a peptide chain bearing a free alpha-amino group. Sequences are conventionally written starting from the N-terminus. More
- NDA
- New Drug Application, the submission requesting FDA approval to market a new drug. Most synthetic peptide drugs have been approved through NDAs.
- Net peptide content (NPC)
- The percentage by weight of a powder that is peptide, with the remainder being counter-ions, water and residual solvent. It is measured by amino acid analysis or nitrogen analysis. More
O
- Oxidation
- Chemical modification by reactive oxygen species, most often affecting methionine, cysteine and tryptophan. Methionine oxidation adds 16 Da per oxygen. More
P
- PCAC
- The Pharmacy Compounding Advisory Committee, which advises FDA on compounding matters such as bulk substance lists. Its votes are advisory, and FDA acts through its own rulemaking.
- PEGylation
- Covalent attachment of polyethylene glycol chains to a peptide or protein. It increases hydrodynamic size and can alter solubility, clearance and immunogenicity.
- Peptide bond
- The amide bond linking the carboxyl group of one amino acid to the amino group of the next. It forms by condensation with loss of water. More
R
- Receptor
- A protein, often on the cell surface, that binds a specific signaling molecule and transmits a signal into the cell. Many peptide hormones act through G protein-coupled receptors.
- Recombinant factor C (rFC)
- A cloned version of the endotoxin-sensing enzyme in LAL, used with a fluorogenic substrate as an animal-free endotoxin assay that does not respond to beta-glucans. More
- Residue
- An amino acid unit as it exists within a peptide chain, after losing the elements of water in forming peptide bonds. Peptide length is counted in residues. More
- Retro-inverso peptide
- A peptide made of D-amino acids assembled in the reverse order of a parent L-peptide, so that side-chain orientation is broadly similar while the backbone is resistant to proteases. FOXO4-DRI is described as a D-retro-inverso peptide. More
- RP-HPLC
- Reversed-phase HPLC, in which a hydrophobic stationary phase such as C18 and an increasing gradient of organic solvent separate peptides by hydrophobicity. More
- RUO (research use only)
- A labeling category for materials intended solely for laboratory research and not for use in humans, diagnostics or therapy. It does not indicate any regulatory approval.
S
- Salt form
- The specific salt in which an ionizable peptide is isolated, defined by its counter-ion, such as a trifluoroacetate, acetate or hydrochloride salt. Salt form affects powder composition and net peptide content. More
- SPPS
- Solid-phase peptide synthesis, in which a peptide is assembled residue by residue on an insoluble resin support, with reagents removed by washing between steps. More
- Sterility test
- A test that determines whether viable microorganisms are present in a material, typically by incubating samples in growth media. Sterility does not imply absence of endotoxin. More
T
- TFA (trifluoroacetic acid)
- A strong acid used to cleave peptides from resin in Fmoc synthesis and as an ion-pairing agent in HPLC. Residual trifluoroacetate is the default counter-ion of many synthetic peptides. More