Glossary

Acetate

The anion of acetic acid (CH3COO-). A common counter-ion in peptide salts, used as an alternative to trifluoroacetate. Read more.

Acetylation (N-terminal)

Addition of an acetyl group (CH3CO-) to the N-terminal amine, written Ac- at the start of a sequence. It removes the terminal positive charge and adds 42.01 Da. Read more.

Aliquot

A measured portion of a larger quantity, set aside so that the remainder is not repeatedly exposed to air or temperature changes. Read more.

Alpha carbon (Cα)

The central carbon of an amino acid, bonded to the amine group, the carboxyl group, a hydrogen atom and the side chain. Read more.

Amidation (C-terminal)

Conversion of the C-terminal carboxylic acid to a carboxamide, written -NH2 at the end of a sequence. It removes the terminal negative charge and lowers the mass by 0.98 Da. Read more.

Amide bond

The covalent link between the carboxyl group of one amino acid and the amine of the next. In peptides it is called a peptide bond.

Amino acid analysis (AAA)

Hydrolysing a peptide to its free amino acids and quantifying them, giving the composition and the peptide content of a sample. Read more.

Aspartimide

A five-membered ring formed when an aspartic acid side chain cyclises with the next backbone nitrogen, losing water (-18.01 Da). Most common before glycine. Read more.

Average mass

Molecular mass calculated using the natural-abundance average of each element's isotopes. This is the value usually given as molecular weight. Read more.

Bacteriostatic

Slowing or stopping the growth of bacteria without necessarily killing them. Distinct from bactericidal. Read more.

Batch number

An identifier for material made in one production run. Used interchangeably with lot number. Read more.

Beer–Lambert law

The relationship A = εcl between absorbance, molar extinction coefficient, concentration and path length, used to measure concentration by UV absorbance. Read more.

Benzyl alcohol

An aromatic alcohol (CAS 100-51-6) used as a preservative, typically at 0.9% in bacteriostatic water. Read more.

Borosilicate glass

Glass made mainly from silica and boron trioxide. It has low thermal expansion and high chemical resistance, and is the usual material for laboratory glassware and Type I vials. Read more.

Bulking agent

An inert solid, such as mannitol, added to a freeze-dried formulation to give the cake mass and structure. Read more.

C-terminus

The end of a peptide chain that carries a free carboxyl group, or an amide where the peptide is C-terminally amidated.

C18 column

A reversed-phase HPLC column packed with silica carrying 18-carbon hydrocarbon chains. The standard column for peptide analysis. Read more.

Cake

The solid plug or film left in a vial after freeze-drying. Its appearance varies with fill weight, formulation and the drying cycle. Read more.

CAS check digit

The last digit of a CAS registry number, calculated from the other digits. It catches most typing errors. Read more.

CAS number

A unique numerical identifier assigned to a chemical substance by the Chemical Abstracts Service, used to look up a compound unambiguously.

Certificate of analysis (COA)

A document issued for one production lot, listing the tests run, the method for each and the results. Read more.

Charge-state envelope

The series of electrospray peaks produced by one molecule carrying different numbers of protons. Read more.

Chromatogram

The trace produced by a chromatography detector, showing signal against time. Each separated component appears as a peak. Read more.

Co-elution

Two or more compounds leaving a chromatography column at the same time, so they appear as a single peak. Read more.

Collapse temperature

The temperature above which a freeze-dried product softens during drying and loses its porous structure. Read more.

Coordination complex

A compound in which a metal ion is bound by surrounding donor atoms, as copper(II) is by nitrogen atoms in GHK-Cu. Read more.

Counter-ion

An ion that balances the charge of another. In a peptide salt, anions such as trifluoroacetate, acetate or chloride balance the positive charges on the peptide. Read more.

Crimp seal

An aluminium cap crimped over a vial's stopper and neck flange to hold the stopper in place, often with a plastic flip-off disc on top. Read more.

D-amino acid

The mirror-image form of a chiral amino acid, marked with a D- prefix in a sequence. It has the same mass as the L-form, so mass spectrometry cannot tell them apart. Read more.

Deamidation

Conversion of an asparagine or glutamine side chain to the corresponding acid, a common degradation pathway for peptides. Read more.

Deconvolution

Calculating a single neutral mass from a series of multiply charged m/z peaks. Read more.

Delamination (glass)

Thin flakes of glass detaching from the inner surface of a container, most often after long contact with high-pH or some buffered solutions. Read more.

Deletion sequence

A synthesis by-product in which one residue is missing because a coupling step failed. Read more.

Deliquescent

Absorbing so much water from the air that the solid dissolves into a liquid solution. A stronger form of hygroscopic behaviour. Read more.

Depyrogenation

Removing or destroying endotoxin on a material, for glassware usually by dry heat at around 250 °C. Read more.

Desiccator

A sealed container holding a drying agent such as silica gel, used to keep materials dry. Read more.

Dilution factor

The ratio of the starting concentration to the final concentration in a dilution, or of the final volume to the volume transferred. Read more.

Dinucleotide

A molecule made of two nucleotides joined through their phosphate groups. NAD+ is a dinucleotide, not a peptide. Read more.

Drug affinity complex (DAC)

In CJC-1295, a C-terminal lysine carrying a 3-maleimidopropionyl group on its side-chain amine. Read more.

Electrospray ionisation (ESI)

A mass spectrometry ionisation method in which a sample is sprayed from solution. Peptides usually appear at several charge states. Read more.

Endotoxin

Lipopolysaccharide from the outer membrane of Gram-negative bacteria. It is measured in laboratory materials by methods such as the limulus amebocyte lysate (LAL) assay. Read more.

Endotoxin unit (EU)

The unit endotoxin is reported in, defined against a reference endotoxin standard. Results are given as EU/mL or EU/mg. Read more.

Excipient

An ingredient other than the substance of interest, added to help processing, stability or form. Bulking agents such as mannitol are excipients. Read more.

Extinction coefficient

How strongly a compound absorbs light at a given wavelength, per unit concentration and path length. For peptides at 280 nm it is calculated from the tryptophan, tyrosine and cystine content. Read more.

Fill weight

The amount of material put into a vial, usually stated in milligrams. It can refer to the peptide, to the whole powder, or to a calculated amount from the solution that was filled. Read more.

Fmoc

9-Fluorenylmethyloxycarbonyl, a protecting group on the N-terminus of an amino acid, removed with a base during solid-phase synthesis. Read more.

Fragment

A peptide made of a contiguous stretch of a longer peptide or protein, written with its residue range, such as Tβ4(17–23). It is a different molecule from the parent, with its own mass and formula. Read more.

FTIR

Fourier-transform infrared spectroscopy: measures which infrared wavelengths a sample absorbs, revealing its chemical bonds. In peptides the amide I band reflects backbone structure. Read more.

Gradient

A change in mobile phase composition over the course of a chromatography run, for example from mostly water to mostly acetonitrile. Read more.

Halobutyl rubber

Bromobutyl or chlorobutyl rubber, used for vial stoppers because very little moisture or oxygen passes through it. Read more.

Henderson–Hasselbalch equation

The relationship between pH, pKa and the ratio of protonated to deprotonated forms of a group, used to calculate a peptide's net charge. Read more.

High-performance liquid chromatography (HPLC)

A method that separates the components of a sample by passing it through a packed column under pressure. Used to measure peptide purity. Read more.

Hydrolytic resistance

How little alkali a glass releases into water under a standard test. Used to classify glass containers as Type I, II or III. Read more.

Hygroscopic

Readily taking up water from the surrounding air. Lyophilised peptides are typically hygroscopic. Read more.

InChIKey

A fixed-length identifier derived from a chemical structure by a standard algorithm, so each distinct structure has its own key. Read more.

Ion-pairing agent

A mobile-phase additive, such as TFA, that pairs with charged groups on an analyte to sharpen peaks in reversed-phase HPLC. Read more.

ISO/IEC 17025

The international standard for the competence of testing and calibration laboratories. Accreditation covers the specific methods listed in a lab's scope. Read more.

Isobaric

Having the same nominal or exact mass. Leucine and isoleucine are isobaric, so mass alone cannot distinguish them. Read more.

Isoelectric point (pI)

The pH at which a peptide has no net charge. Solubility is usually lowest near this pH. Read more.

Karl Fischer titration

A water-specific method in which iodine reacts with water one-to-one in the presence of sulfur dioxide, a base and an alcohol. Read more.

LC-MS

Liquid chromatography coupled directly to a mass spectrometer, so each peak in the chromatogram is given a mass. Read more.

Limit of detection (LOD)

The smallest amount of a substance that a method can reliably distinguish from a blank. The limit of quantitation is the smallest amount it can measure with acceptable accuracy.

Limulus amebocyte lysate (LAL)

An extract of horseshoe crab blood cells that clots in the presence of endotoxin. Used in gel-clot, turbidimetric and chromogenic endotoxin tests. Read more.

Lipopolysaccharide (LPS)

The large lipid-and-sugar molecule of the Gram-negative bacterial outer membrane, made of lipid A, a core oligosaccharide and an O-antigen. It is the chemical form of endotoxin. Read more.

Loss on drying

The mass a sample loses when heated. It counts all volatile material, not only water. Read more.

Lot

A quantity of material made in one production run and treated as a single batch for testing and documentation. Read more.

Lyophilisation

Freeze-drying: removing water from a frozen sample by sublimation under vacuum, leaving a dry solid. Read more.

MALDI

Matrix-assisted laser desorption/ionisation, a mass spectrometry method in which a sample dried with a matrix is ionised by a laser. Read more.

Maleimide

A five-membered imide ring whose carbon–carbon double bond reacts selectively with thiols by Michael addition, forming a thioether. Read more.

Mannitol

A sugar alcohol commonly used as a bulking agent in freeze-dried formulations. Read more.

Marketing authorisation

The licence a medicinal product needs before it can be sold or supplied in the UK. Read more.

Mass shift

The difference between the measured mass of an impurity and that of the main compound, used to identify what the impurity is. Read more.

Mass spectrometry (MS)

A method that measures the mass-to-charge ratio of ions. Used to confirm the molecular weight of a peptide. Read more.

Medicinal product

The legal category defined in regulation 2 of the Human Medicines Regulations 2012. A product is medicinal by presentation or by function, and needs a licence to be sold or supplied. Read more.

Method validation

Showing by experiment that an analytical method is fit for its purpose, for example in accuracy, precision, specificity, linearity and range.

MHRA

The Medicines and Healthcare products Regulatory Agency, which regulates medicines and medical devices in the UK. Read more.

Michael addition

The addition of a nucleophile, such as a thiol, across a carbon–carbon double bond next to a carbonyl group. Read more.

Mobile phase

The liquid or gas that moves through the stationary phase and carries the sample's components with it. Read more.

Molar mass

The mass of one mole of a substance in g/mol, numerically equal to its molecular weight. Read more.

Molarity (M)

The amount of a solute in moles per litre of final solution. Read more.

Molecular weight

The mass of one mole of a substance in g/mol, normally the average mass. Calculated from the sequence or molecular formula.

Monoisotopic mass

Molecular mass calculated from the most abundant isotope of each element. It is the first peak in an isotope cluster. Read more.

N-terminus

The end of a peptide chain that carries a free amine group, or a blocking group such as an acetyl where the peptide is N-terminally acetylated.

Net peptide content (NPC)

The proportion of a powder, by weight, that is peptide. The remainder is water, counter-ions and any other residual material. Read more.

NMR spectroscopy

Nuclear magnetic resonance spectroscopy: a method that probes atomic nuclei such as 1H, 13C or 19F in a magnetic field to give information on structure and composition. Read more.

Non-proteinogenic amino acid

An amino acid not encoded by the genetic code, such as ornithine, Aib or 2′,6′-dimethyltyrosine (Dmt). Common in synthetic peptides. Read more.

Oligopeptide

A short peptide, usually up to about 20 residues. Read more.

One-letter code

The single-letter abbreviation for an amino acid, such as G for glycine or W for tryptophan, used to write sequences compactly. Read more.

Oxidation

A degradation pathway in which residues such as methionine, cysteine and tryptophan are chemically oxidised, accelerated by oxygen, light and trace metals. Read more.

Peptide mapping

Cutting a protein or long peptide with an enzyme such as trypsin and analysing the fragments by LC-MS to confirm the sequence and locate modifications. Read more.

pKa

The pH at which an ionisable group is half protonated. Each charged group in a peptide has its own pKa. Read more.

Protecting group

A chemical group that blocks a reactive site during synthesis and is removed at the end. One left in place shows up as a characteristic mass shift. Read more.

PubChem CID

The compound identifier in PubChem, the free chemical database run by the US National Center for Biotechnology Information. Read more.

Purity (HPLC)

The area of the main peak as a percentage of the total peak area at a stated wavelength. It is a ratio of peaks, not a mass fraction. Read more.

Pyroglutamate

A cyclic residue formed when an N-terminal glutamine or glutamic acid cyclises, written pGlu or pE. Read more.

Recombinant factor C (rFC)

A recombinant version of the first enzyme in the LAL cascade, used to measure endotoxin without horseshoe crab blood (Ph. Eur. 2.6.32). Read more.

Reference standard

A well-characterised sample of known identity and purity, used to calibrate a method or confirm a result by comparison.

Research use only (RUO)

A description of a product supplied as a laboratory reagent. It is not a licence, and on its own does not decide whether a product is a medicine. Read more.

Residual moisture

Water left in a freeze-dried solid after drying, usually a few percent by weight. Read more.

Residue

A single amino acid unit within a peptide chain, after the loss of water on forming the peptide bond.

Retained sample

A sealed portion kept back from each lot so it can be re-analysed if questions arise later. Read more.

Retention time

The time a component takes to leave a chromatography column, measured from injection. Read more.

Retest date

The date by which a lot should be re-analysed to confirm it still meets its specification. Read more.

Reversed-phase HPLC (RP-HPLC)

HPLC with a non-polar stationary phase, usually C18, and a polar mobile phase. The standard method for peptide analysis and purification. Read more.

Rf value

In paper and thin-layer chromatography, the distance a substance travels divided by the distance the solvent front travels. Always between 0 and 1. Read more.

Salt exchange

Replacing a peptide's counter-ion, such as trifluoroacetate, with another, such as acetate or chloride. Read more.

Sequence

The order of amino acid residues in a peptide, written from the N-terminus to the C-terminus, often with one-letter codes.

Serial dilution

A series of equal dilution steps, each made from the previous solution, used to reach low concentrations or build a standard curve. Read more.

Side chain (R group)

The variable group on an amino acid's alpha carbon. It sets the residue's size, charge and polarity. Read more.

Solid-phase peptide synthesis (SPPS)

A method of building a peptide one residue at a time while the chain is anchored to an insoluble resin. Read more.

Stationary phase

The part of a chromatography system that stays fixed, such as paper, a silica layer or column packing, and holds sample components back to different extents. Read more.

Sterile water

Purified water that has been sterilised and sealed, with no added substances. Not sterile once opened. Read more.

Sublimation

The change from solid directly to vapour without passing through the liquid state. Ice sublimes during the primary drying stage of lyophilisation. Read more.

Thiosuccinimide

The ring formed when a thiol adds to a maleimide. It can hydrolyse (+18.01 Da) or slowly reverse. Read more.

Time-of-flight (TOF)

A mass analyser that measures m/z from how long ions take to travel the length of a flight tube. Read more.

Traceability

The ability to link an item, through its lot number, to its production and test records. Read more.

Trifluoroacetate

The anion of trifluoroacetic acid (CF3COO-, 113.02 g/mol). The usual counter-ion in HPLC-purified peptides. Read more.

Trifluoroacetic acid (TFA)

A strong acid used to cleave peptides from the synthesis resin and as an ion-pairing additive in HPLC. Its anion is often the counter-ion in a peptide powder. Read more.

Type I glass

The pharmacopoeial grade of glass with the highest hydrolytic resistance, made from borosilicate. The normal grade for vials of sensitive contents. Read more.

UKAS

The United Kingdom Accreditation Service, the national body that accredits laboratories against standards such as ISO/IEC 17025. Read more.

Zwitterion

A molecule carrying both a positive and a negative charge with no net charge overall, as free amino acids are in water near neutral pH. Read more.

These definitions describe laboratory chemistry. Amidae products are supplied for laboratory research use only, and are not for human or veterinary use.