Peptide Glossary

Last reviewed: August 2, 2026

The vocabulary around research peptides is drawn from three different fields — synthetic organic chemistry, analytical chemistry, and regulatory classification — which is why a certificate of analysis can be hard to read even for someone comfortable with two of the three. These are the terms that actually appear on peptide paperwork, defined plainly, with links to the guides that cover each subject in full.

A – C

Aggregation — irreversible association of peptide molecules with one another, usually driven by hydrophobic surfaces or beta-sheet formation. Accelerated by high concentration, air-liquid interfaces, vigorous mixing and repeated freezing.
Aliquot — a single-use portion of a prepared solution, divided out so the remainder is never thawed twice. See peptide storage and handling.
Amide bond — the covalent linkage between the carboxyl group of one amino acid and the amino group of the next. In a peptide it is called a peptide bond.
Amino acid analysis (AAA) — complete acid hydrolysis of a sample followed by quantification of the released amino acids. The reference method for net peptide content; it cannot be done by HPLC.
Area-percent — the definition of chromatographic purity: the area under the main peak as a percentage of total integrated peak area. Blind to anything that does not absorb UV at the detection wavelength.
Aspartimide — a five-membered cyclic intermediate formed at an aspartate residue. It reopens to a mixture of the original aspartate and iso-aspartate, changing the backbone without changing the mass.
Batch / lot — one production run of material, identified by a number that should appear on both the container and the certificate of analysis. The unit that analytical data actually describes.
Boc chemistry — solid-phase synthesis using the acid-labile tert-butyloxycarbonyl protecting group. Largely superseded by Fmoc for routine work.
CAS Registry Number — a unique numeric identifier assigned to a chemical substance by the Chemical Abstracts Service. Useful for unambiguous identification across catalogues.
Certificate of analysis (COA) — a record of which tests were run on which lot, by whom, on what date, with what results. Not a warranty. Read one field by field.
Chaotrope — a reagent such as guanidine hydrochloride or urea that disrupts non-covalent structure, used to break up aggregated material.
Chromatogram — the detector trace from a chromatographic run: absorbance against time. More informative than the purity number derived from it.
Co-elution — two different molecules emerging from the column at the same retention time and integrating as one peak. The principal blind spot of HPLC purity.
Counter-ion — the ion that balances a peptide's charge in the solid state, typically trifluoroacetate or acetate. It contributes mass to the vial but nothing to the chromatogram.
C-terminus — the end of the chain bearing a free carboxyl group, unless modified. Written on the right in conventional sequence notation.

D – H

Deamidation — loss of the side-chain amide from asparagine or glutamine, converting it to the corresponding acid. Sequence-dependent and fastest at Asn-Gly.
Deletion sequence — a synthesis by-product missing one or more residues, caused by an incomplete coupling step. Often co-elutes with the target, which is why mass spectrometry is needed alongside HPLC.
Deprotection — removal of a temporary protecting group, exposing the amino group so the next residue can be coupled. One half of each synthesis cycle.
DMSO — dimethyl sulfoxide, a strong aprotic solvent used for hydrophobic sequences. Not suitable for peptides containing cysteine or methionine, which it oxidises.
Electrospray ionisation (ESI) — the standard soft ionisation method for peptide mass spectrometry. Produces multiply charged ions rather than a single peak.
Fmoc chemistry — solid-phase synthesis using the base-labile fluorenylmethyloxycarbonyl protecting group. The usual modern approach because its conditions are milder than Boc.
Free acid — an unmodified C-terminus. Distinguished in notation from a C-terminal amide, written -NH2, which differs by roughly one mass unit.
Gradient — the programmed change in mobile phase composition during a chromatographic run. Its slope and duration materially affect the purity figure reported.
HPLC — high-performance liquid chromatography. Separates a mixture by partitioning between a stationary and a mobile phase, and answers how much of a sample is one substance. Compared with mass spectrometry here.
Hygroscopic — readily absorbing water from the air. Lyophilised peptide is, which is why a cold vial should reach room temperature before it is opened.

I – M

Isobaric — having the same mass. Sequence isomers and the leucine / isoleucine pair are isobaric and cannot be told apart by a simple mass measurement.
Isoelectric point (pI) — the pH at which a peptide carries no net charge, and therefore the pH at which it is least soluble. Solvent selection largely consists of moving away from it.
Lyophilisation — freeze-drying. The solution is frozen and dried under vacuum so ice sublimates directly to vapour, leaving an amorphous solid that is far more stable than the same peptide in solution.
MALDI — matrix-assisted laser desorption/ionisation, an alternative to ESI that typically produces singly charged ions.
Mass spectrometry (MS) — measurement of mass-to-charge ratio, used to confirm that a molecule's mass matches the value calculated from its sequence. An identity measurement, not a purity measurement.
Molecular formula — the atom count of the molecule, for example C62H98N16O22. Fully determined by the sequence, so it can be checked against it.
Molecular weight — the mass of one mole of the compound in grams. On peptide paperwork this is normally the average mass; mass spectrometry may report the monoisotopic mass instead, and the two differ measurably for larger chains.
m/z — mass-to-charge ratio, the quantity a mass spectrometer actually measures. For a multiply charged peptide ion, m/z is much lower than the molecular weight.

N – R

Net peptide content — the percentage of a vial's total mass that is peptide, the remainder being counter-ions, salts and residual water. Commonly 70–90%, and not the same thing as purity.
N-terminus — the end of the chain bearing a free amino group, unless modified. Written on the left. An acetylated N-terminus is denoted Ac-.
Peptide — a short chain of amino acids joined by peptide bonds, generally understood as two to fifty residues. Full definition here.
Primary structure — the amino acid sequence itself, as distinct from any folded conformation the chain adopts.
PubChem CID — the compound identifier in the NIH PubChem database, giving a stable public reference for structure and computed properties.
Purity — on peptide certificates, almost always chromatographic area-percent by HPLC. Meaningful only with the method, wavelength and lot attached.
Reconstitution — dissolving lyophilised solid in a solvent to make a solution. Procedure here.
Research use only (RUO) — a classification indicating material is supplied for laboratory research and is not manufactured, tested or labelled as a drug. What the classification does and does not cover.
Residue — one amino acid as incorporated into a chain, after the loss of water that forms the peptide bond. A residue mass is therefore lower than the free amino acid's mass by 18 Da.
Retention time — how long a component takes to travel through a chromatographic column. Reproducible under fixed conditions, so useful for comparing runs.
Reversed-phase — chromatography with a non-polar stationary phase (typically C18) and a polar mobile phase. The standard configuration for peptides.

S – Z

Salt form — which counter-ion the peptide was isolated as, usually trifluoroacetate or acetate. It changes the mass fraction that is peptide by ten points or more.
Sequence — the order of amino acids in the chain, written N-terminus to C-terminus in one-letter or three-letter code.
Solid-phase peptide synthesis (SPPS) — building a peptide one residue at a time on an insoluble polymer resin, alternating deprotection and coupling steps. How essentially all research peptides are made.
Theoretical mass — the mass calculated from the sequence. Not an estimate; it is arithmetic, and the observed mass is compared against it.
Trifluoroacetic acid (TFA) — used as the cleavage reagent that releases the finished chain from the resin, and as an ion-pairing modifier in reversed-phase mobile phases. Its anion, trifluoroacetate, has a formula mass of 113.02 and is the most common peptide counter-ion.
UV detection at 214 nm — the usual detection wavelength for peptide HPLC, chosen because the backbone amide bond absorbs there. Salts, water and counter-ions do not.
Vial headspace — the gas volume above the solid in a sealed container. Filling it with an inert, dry gas limits both oxidation and moisture uptake.

Terms you encounter on a listing that are not defined here — strengths, salt forms, purity figures and composition data for individual compounds — appear on the individual product pages in the research peptides catalogue.