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Peptide chemistry glossary

Short definitions of the terms used on our product pages, certificates of analysis and guides. Each entry says what a term means in peptide chemistry and analysis.

For research use only. Not for human or veterinary use. Sold strictly for in-vitro laboratory research; not for diagnosis or treatment.

A

Acetate salt

Analytical

An acetate salt is a peptide whose positive charges are balanced by acetate ions rather than trifluoroacetate. It is produced by an ion-exchange step after purification, which replaces the trifluoroacetate left from synthesis. Acetate is lighter than trifluoroacetate, so the same peptide has a different gross mass per mole in each salt form, which matters when net peptide content is compared between materials.

Amino acid residue

Structure

An amino acid residue is what remains of an amino acid once it is joined into a peptide chain. Each peptide bond forms with the loss of one water molecule, so a residue is the amino acid minus the atoms of that water. Peptide length is counted in residues, and residue masses, rather than free amino acid masses, are summed to calculate a peptide's molecular mass.

B

Batch / lot number

Documentation

A batch or lot number identifies material produced together in one manufacturing run and documented under one set of records. Material from the same batch shares the number, so a certificate of analysis that names a batch can be matched to the material it describes. A certificate that states no batch number cannot be tied to a specific batch.

C

CAS Registry Number (CAS number)

Structure

A CAS Registry Number is the unique numeric identifier that CAS, a division of the American Chemical Society, assigns to a chemical substance. It is written as three groups of digits separated by hyphens, the last being a single check digit. Because each number refers to one defined substance, it is a dependable way to match a product to reference records, although a salt form may carry its own number.

Certificate of analysis (COA)

Documentation

A certificate of analysis is a document from the analysing laboratory that reports the tests carried out on a sample of a material and their results. For a peptide it typically covers HPLC purity and identity by mass spectrometry, with the method, the analysis date, the laboratory, the client it was issued to and, where one is stated, the batch or lot number. It relates only to the batch it names.

Guides: How to Read a Peptide Certificate of Analysis

Chelate

Structure

A chelate is a metal complex in which a single ligand binds one metal ion through two or more donor atoms, forming a ring that includes the metal. Peptides can act as chelating ligands through backbone nitrogen atoms and side chains such as the imidazole of histidine. In GHK-Cu, the tripeptide glycyl-histidyl-lysine binds a copper(II) ion through nitrogen atoms of the glycine amine, a backbone amide and the histidine imidazole.

Guides: What Is GHK-Cu? Chemistry of the GHK Copper Peptide

Chromatogram

Analytical

A chromatogram is the plot an HPLC or LC-MS run produces: detector signal on the vertical axis against time on the horizontal axis. Each separated component appears as a peak at its retention time. For a synthetic peptide, the chromatogram typically shows one main peak for the target sequence and smaller peaks for related impurities, and it is often reproduced on a certificate of analysis.

Guides: How to Read a Peptide Certificate of Analysis

Counter-ion

Analytical

A counter-ion is an ion of opposite charge that balances the charged groups of a peptide in its solid form. Basic residues such as lysine and arginine, and a free N-terminus, carry positive charges that are paired with anions left from synthesis and purification, most often trifluoroacetate or acetate. Counter-ions add to the gross mass of the material but are not part of the peptide sequence.

Guides: Peptide Purity vs Net Peptide Content

Crimp cap

Manufacturing & material

A crimp cap is the aluminium seal pressed around the neck of a glass vial to hold its stopper in place. It is applied with a crimping tool after the vial has been filled and stoppered, and it is often topped with a plastic flip-off disc. Together with the stopper, the crimp cap closes the vial against air and moisture until the seal is broken.

D

D-amino acid

Structure

A D-amino acid is the mirror-image form of an amino acid. Apart from glycine, which is not chiral, the amino acids that make up natural proteins have the L-configuration at their alpha carbon; the D-form has the same formula and mass but the opposite spatial arrangement. Synthetic peptides may include D-residues at chosen positions, written with a D- prefix, such as D-Phe or D-Arg.

Guides: What Is SS-31? The Aromatic-Cationic Tetrapeptide

Deconvolution

Analytical

Deconvolution, in mass spectrometry, is the calculation that turns a series of peaks from one molecule carrying different numbers of charges into a single neutral mass. Electrospray ionisation gives a peptide several charge states, each at its own m/z; software recognises the series from the spacing between its peaks and reports the neutral mass, which is the value compared with the expected mass.

Guides: Mass Spectrometry and Peptide Identity

Deletion sequence

Manufacturing & material

A deletion sequence is a peptide impurity missing one or more residues from inside the intended sequence. It arises in solid-phase synthesis when a coupling step does not go to completion and the chain carries on growing at the next step without that residue. Deletion sequences are close in structure to the target, so they are separated by reversed-phase HPLC and recognised by LC-MS from their lower mass.

Guides: Solid-Phase Peptide Synthesis (SPPS) Explained

Disulfide bridge (disulphide bridge)

Structure

A disulfide bridge is a covalent sulfur–sulfur bond between the thiol groups of two cysteine residues, formed by oxidation. It closes a ring within a single chain or joins two separate chains. Forming one lowers the molecular mass by 2.02 Da, the two hydrogen atoms lost. Its position is written as a note to the sequence, giving the two cysteine residues it connects.

E

Expected and observed mass

Analytical

Expected mass is the molecular mass calculated from a peptide's molecular formula; observed mass is the value a mass spectrometer measures for the sample. A certificate of analysis often reports both. Agreement within the instrument's stated tolerance is evidence that the main component is the intended sequence, while a consistent offset, such as 18 Da or the mass of one residue, points to a specific modification or impurity.

Guides: Mass Spectrometry and Peptide Identity

F

Fmoc (fluorenylmethyloxycarbonyl)

Manufacturing & material

Fmoc, the fluorenylmethyloxycarbonyl group, is the temporary protecting group placed on the amino group of each incoming amino acid in most solid-phase peptide synthesis. It is stable to acid and removed with a mild base, usually piperidine, before the next coupling. Side chains carry acid-labile protecting groups instead, so they stay protected until the final cleavage with trifluoroacetic acid.

H

HPLC (high-performance liquid chromatography)

Analytical

High-performance liquid chromatography is an analytical separation technique. A liquid sample is carried by a pumped mobile phase through a column packed with fine particles, and its components leave the column at different times according to how strongly they interact with the packing. A detector, usually measuring UV absorbance for peptides, records each component as a peak. HPLC is the standard method for stating the purity of a synthetic peptide.

Guides: HPLC and Peptide Purity: How It Is Measured

Hygroscopic

Manufacturing & material

A hygroscopic material takes up water vapour from the surrounding air. Many lyophilised peptides are hygroscopic, particularly those with several charged residues or counter-ions, so the dry solid can gain moisture and mass when it is exposed to room air. This moisture uptake is one reason storage statements for lyophilised peptides call for cold, dry storage in the sealed vial.

Guides: How to Store Lyophilised Peptides

I

In vitro

Documentation

In vitro, Latin for 'in glass', describes work carried out with molecules or cells outside a living organism, in test tubes, plates, columns and other laboratory vessels. Chemical analysis by HPLC or mass spectrometry is in vitro work. Our products are sold strictly for in-vitro laboratory research, under the research-use notice shown on every product page.

K

Karl Fischer titration

Analytical

Karl Fischer titration is the standard method for measuring the water content of a solid, based on the reaction of iodine with water in the presence of sulfur dioxide and a base. Lyophilised peptides retain some residual moisture and can take up more from the air, so a water figure from Karl Fischer titration helps explain the gap between the gross mass of a material and its net peptide content.

L

Lactam bridge

Structure

A lactam bridge is an amide bond formed between two amino acid side chains, typically the carboxyl group of an aspartic or glutamic acid residue and the amino group of a lysine or ornithine residue. It closes a ring within the peptide with the loss of one water molecule, 18.02 Da. The cyclic heptapeptides in the melanocortin research area carry a lactam bridge between aspartic acid and lysine.

LC-MS (liquid chromatography–mass spectrometry)

Analytical

Liquid chromatography–mass spectrometry couples an HPLC separation to a mass spectrometer, so each peak leaving the column is also measured by mass. For peptides it is usually run with electrospray ionisation, which produces multiply charged ions. LC-MS is used to confirm the identity of the main component against its expected mass and to characterise impurities, such as deletion or truncated sequences, by their mass differences.

Guides: Mass Spectrometry and Peptide Identity

Lipidation

Structure

Lipidation is the covalent attachment of a lipid, typically a fatty acid or fatty diacid, to a peptide, usually through the side chain of a lysine residue and often by way of a hydrophilic linker. It changes the molecule's formula, mass and chromatographic behaviour. Semaglutide and tirzepatide each carry a fatty diacid chain attached through a linker to a lysine side chain; cagrilintide carries one on its N-terminal amine instead.

M

MALDI-TOF (matrix-assisted laser desorption/ionisation time-of-flight)

Analytical

MALDI-TOF is a mass spectrometry technique that pairs matrix-assisted laser desorption/ionisation with a time-of-flight analyser. The sample is co-crystallised with a light-absorbing matrix on a target plate and ionised by a laser pulse, mostly as singly charged ions. The time each ion takes to cross a field-free flight tube gives its mass-to-charge ratio. It is a quick way to confirm a peptide's molecular mass.

N

Net peptide content

Analytical

Net peptide content is the proportion of a peptide material's gross mass that is the peptide itself, as opposed to counter-ions, residual water and other non-peptide components. It is usually determined by amino acid analysis or by elemental nitrogen analysis. It is a different quantity from HPLC purity: a material can show a single clean peak and still contain a substantial share of counter-ions and water by mass.

Guides: Peptide Purity vs Net Peptide Content

N-terminal acetylation

Structure

N-terminal acetylation is the capping of a peptide's free N-terminal amino group with an acetyl group, CH3CO–. It is written as Ac- at the start of a sequence. The modification removes the positive charge of the free amine and adds 42.01 Da to the molecular mass. In solid-phase synthesis it is carried out on the resin, after the last residue is coupled and before cleavage.

Guides: Peptide Sequence Notation: Reading an Amino Acid Sequence

O

One-letter code

Structure

The one-letter code represents each standard amino acid residue by a single capital letter, such as G for glycine, K for lysine and W for tryptophan, written without separators. It is compact and suits long sequences and database searches, but it has no agreed letter for most non-standard residues and no single convention for D-configuration, so modified peptides are usually written in three-letter code instead.

P

Peak area

Analytical

Peak area is the integrated signal under a peak in a chromatogram, measured from its baseline. For components that absorb similarly at the detection wavelength, peak area is proportional to the amount of each one, which is why HPLC purity is calculated from peak areas rather than peak heights. Integration settings, such as where the baseline is drawn, form part of the analytical method.

Peptide

Structure

A peptide is a chain of amino acid residues joined by peptide bonds. Chains of up to about fifty residues are usually called peptides and longer ones proteins, although the boundary is a convention rather than a strict rule. A peptide is defined by its sequence and by any modifications to its ends or side chains, such as amidation, acetylation, lipidation or cyclisation.

Guides: What Are Peptides? A Chemistry Guide

Peptide bond

Structure

A peptide bond is the amide bond, –CO–NH–, that links the carboxyl group of one amino acid to the amino group of the next. It forms in a condensation reaction that releases one water molecule. The bond has partial double-bond character, which holds the atoms around it in a roughly planar arrangement and limits the ways a peptide backbone can fold.

R

Research use only (RUO)

Documentation

Research use only is a supply status for materials sold as laboratory reagents for research and nothing else. Materials supplied on these terms are not medicines, foods, food supplements, cosmetics or medical devices. Every product we sell carries the notice: For research use only. Not for human or veterinary use. Sold strictly for in-vitro laboratory research; not for diagnosis or treatment.

S

Safety Data Sheet (SDS)

Documentation

A Safety Data Sheet is the standardised document that describes a chemical product's hazards and how to handle, store, transport and dispose of it. In Great Britain its format is set by UK REACH: sixteen sections covering, among others, identification, hazards, composition, first-aid and fire-fighting measures, exposure controls, and physical and chemical properties.

T

TFA salt (trifluoroacetate salt)

Analytical

A TFA salt is a peptide whose positive charges are balanced by trifluoroacetate ions. Trifluoroacetic acid is used to cleave peptides from the resin in solid-phase synthesis and as a mobile-phase additive in reversed-phase HPLC purification, so peptides isolated this way are commonly TFA salts unless a salt-exchange step follows. A specification may state the salt form separately from the peptide's own molecular formula.

Three-letter code

Structure

The three-letter code abbreviates each amino acid residue to three letters, such as Gly for glycine, Pro for proline and Lys for lysine, with residues joined by hyphens. It is easier to read than the one-letter code and leaves room for modifications: a D-residue takes a D- prefix, and non-standard residues such as Aib or Nle keep their own abbreviations. Our product specifications write sequences this way.