Reference

A plain-English glossary: 60 terms from peptide paperwork

The shorthand that appears on specifications, certificates of analysis and supplier pages, defined in ordinary words.

By the editors· 30 June 2026· 7 min read

A magnifying glass resting on printed documents
Sixty terms that appear on peptide paperwork, each traced back to the standard it comes from. Illustration: Pexels

Peptide paperwork is full of shorthand. Most of it is ordinary chemistry vocabulary, not jargon designed to confuse. But nobody is born knowing it. Below are the terms that come up most often on a specification, a certificate of analysis, or a supplier's technical page.

Where a term has a full article behind it, there is a link.

A to C

Acetate. One of the two common counterions left on a peptide after purification. See counterion.

Acetonitrile. A solvent used in reversed-phase chromatography. Traces can remain in the finished powder.

Aggregation. Peptide molecules clumping together into pairs, clusters, or fibres. One of three degradation routes.

Amino acid. The building block of peptides. Twenty standard ones are used by living things.

Amino acid analysis (AAA). Breaks a peptide back into its amino acids and counts them. Tells you how much peptide the powder holds.

Area percent. The purity figure. The main peak divided by all the peaks added up. Not the same as how much peptide is there.

Bacteriostatic water. Water with a preservative in it that holds back bacteria. Used to dissolve dried powder.

Bioburden. How many living micro-organisms are in a sample. A different measurement from endotoxin.

Boc. A protecting group used to cap the reactive end of an amino acid during synthesis. Removed by acid.

C-terminal. The end of a peptide chain finishing in an acid group. Sequences are written N-terminal first, so this is the end you read last.

Certificate of analysis (COA). The lab report supplied with a batch. How to read one.

Chromatogram. The chart a chromatography run produces: detector signal plotted against time.

Chromophore. The part of a molecule that soaks up light. Without one, a substance is invisible to the detector, however much is there.

Cleavage. The step that cuts a finished peptide off the bead it was built on. Usually done with strong acid.

Concentration. Amount divided by volume. How to calculate it.

Counterion. A charged partner bound to the peptide, left from purification. Usually trifluoroacetate or acetate, and a real share of the powder's weight.

Coupling agent. The chemical that switches on an amino acid so it will join the chain.

D to I

Dalton (Da). The unit of molecular mass. Roughly the mass of one hydrogen atom.

Deamidation. A side chain loses part of itself, turning asparagine into aspartate. Adds about 1 Da.

Deletion sequence. A copy of your peptide missing one link, left behind when a coupling step fails. The main impurity in most batches.

Deprotection. Removing the cap from the end of the chain so the next amino acid can attach.

Diastereomer. A form mirrored in one part of a molecule rather than all of it. Often very hard to separate by chromatography.

DMF (dimethylformamide). A solvent used during synthesis. Traces can survive into the final powder.

Elemental analysis. Measures which elements are present. One use is working out peptide content.

Endotoxin. A piece of the outer wall of Gram-negative bacteria. It survives heat, causes fever, and does not show on a purity chart.

Enantiomer. A non-superimposable mirror image of a molecule. See mirror-image errors.

Fmoc. The other common protecting group, removed by base rather than acid. The basis of most modern synthesis.

Forced degradation. Stressing a sample on purpose with heat, light, acid, base and oxygen, to see what it turns into.

Gas chromatography (GC). The method used to measure residual solvents.

GPCR (G protein coupled receptor). The receptor family most peptide hormones act through. How the signal works.

Gradient. The liquid mix changes during a run. That controls what comes off the column, and when.

Gram-negative. A class of bacteria whose outer wall is the source of endotoxin.

HPLC. High-performance liquid chromatography. The separation method behind most purity figures.

Hydrolysis. Water breaking a chemical bond. One of the three degradation routes.

ICH. The International Council for Harmonisation, which publishes the guidelines used to set specifications.

Ion chromatography (IC). The method used to measure counterion content.

IU (International Unit). A measure of biological activity, defined separately for each substance. Cannot be converted between compounds.

K to R

Karl Fischer titration. The standard method for measuring water content in a powder.

LAL (Limulus amebocyte lysate). The reagent used to detect endotoxin, derived from horseshoe crab blood.

Lipopolysaccharide (LPS). The molecule that endotoxin testing looks for.

Lot number. The identifier tying a certificate of analysis to one specific batch. If it does not match the vial, the paperwork describes different material.

Lyophilisation. Freeze-drying. What it does and does not protect against.

Mass spectrometry (MS). Weighing the molecule to confirm identity. How to read the result.

Mobile phase. The liquid that carries a sample through a chromatography column.

Monograph. An entry in an official pharmacopoeia covering one named substance, listing required tests and limits.

Monoisotopic mass. Mass worked out using the lightest common form of each atom. The usual basis for identity checks.

N-terminal. The end of the chain finishing in an amine group. Sequences are written starting here.

Net peptide content. The share of the powder's weight that is actually the target peptide. Typically 70 to 85 percent.

Oxidation. Reaction with oxygen, most often at methionine, cysteine or tryptophan. Adds 16 Da per oxygen atom.

Peak. A bump on a chromatogram, representing something arriving at the detector.

Peptide bond. The link joining one amino acid to the next, formed with the loss of a water molecule.

Pharmacopoeia. An official handbook of drug standards. The main ones are the United States, European and Japanese pharmacopoeias.

Picogram. A trillionth of a gram. The scale endotoxin testing works at.

Protecting group. A cap that stops part of an amino acid reacting before you want it to.

Pyroglutamate. A ring formed at the N-terminal end. Costs 18 Da from glutamate, or 17 Da from glutamine.

Racemisation. Loss of stereochemistry, producing a mirror image of the intended amino acid.

Reconstitution. Dissolving a freeze-dried powder in liquid.

Reference standard. Material of known identity and purity, used to set up a test.

Residual solvent. Solvent left over from manufacturing. Measured by gas chromatography.

Resin. The insoluble bead a peptide is built on during solid-phase synthesis.

Retention time. How long something takes to travel through the column. A clue to identity, not proof of it.

Reversed-phase. The usual setup for peptides. It sorts things by how much they repel water.

RUO (research use only). A labelling status governing sale. Not a safety finding.

S to W

Second messenger. A molecule inside the cell that boosts a signal picked up at the surface. Cyclic AMP is the usual one.

Side chain. The part that differs from one amino acid to the next. It sets the charge and how the amino acid behaves in water.

Solid-phase peptide synthesis (SPPS). Building a peptide one amino acid at a time on a bead. The four-step cycle.

Specification. The list of tests a batch has to pass, and the limit for each. Where those numbers come from.

Spike recovery. Adding a known amount of something to a sample, to check the test can still find it. Needed for each sequence in endotoxin testing.

Sterility. Nothing alive in the sample. A separate question from endotoxin, and a separate test.

Sublimation. Ice turning straight to vapour without melting. The mechanism behind freeze-drying.

TFA (trifluoroacetic acid / trifluoroacetate). The acid used for cleavage, and the counterion it leaves behind.

Truncated sequence. A chain that stopped short of the full sequence.

USP. The United States Pharmacopeia.

Wavelength. The kind of light a detector uses. Peptide work is usually done at 214 nm, sometimes 280 nm.

Scope note

This article explains published research and the rules around it. It carries no dose, no protocol, and no claim that any compound treats, cures or prevents a condition in anyone. Where the evidence is thin we say so. See our editorial standards.