Reference
Peptide Glossary
Last reviewed
The terms that appear on peptide labels, product pages and Certificates of Analysis, defined in plain language and in alphabetical order. Where British and American spellings differ, both are given: lyophilised and lyophilized are the same word. Each definition is short on purpose, and where a term needs more room it links to the page that gives it.
The short version
- Purity is how much of the peptide material is the target sequence, measured by HPLC.
- Net peptide content is how much of the powder is peptide at all, by weight.
- Mass spectrometry confirms identity by matching the measured mass to the sequence.
- Batch number ties a COA to a vial. If the numbers do not match, the COA is not evidence about that vial.
- Endotoxin is a bacterial contaminant, tested separately from purity.
A to Z
Terms, in alphabetical order
From acetate salt to vial strength.
Acetate salt
A peptide whose positive charges are balanced by acetate ions rather than trifluoroacetate. Many peptides are exchanged into acetate after purification because acetate is less likely to interfere with cell-based experiments 3. See also counter-ion and TFA salt.
Amino acid
The unit a peptide is built from. Twenty standard amino acids are encoded in the genetic code, each with the same backbone and a different side chain. The full list, with the one-letter codes used to write sequences, is on What are peptides?
Amino acid analysis (AAA)
A method that breaks a peptide down into its individual amino acids and measures how much of each is present. It is the standard way to determine net peptide content, and the ratio of amino acids it finds is also a check on composition.
Bacteriostatic water
Sterile water containing 0.9% benzyl alcohol, which inhibits bacterial growth after a vial has been opened. Sterile water contains no preservative. The difference is covered in Bacteriostatic water vs sterile water.
Batch number (lot number)
The identifier for one production run. It should appear on the vial, the box and the Certificate of Analysis, and a COA only describes a vial when the two numbers match.
CAS number
A unique identifier assigned to a chemical substance by the Chemical Abstracts Service. It lets a compound be looked up unambiguously whatever name a supplier uses, and our product pages list it where one exists.
Certificate of Analysis (COA)
A document from an analytical laboratory reporting what it found when it tested a sample from a specific batch, typically identity by mass spectrometry and purity by HPLC. What a good one contains is set out on Quality and COAs.
Chromatogram
The trace an HPLC run produces. Time runs along the horizontal axis and detector response up the vertical one. Each compound that reaches the detector appears as a peak, and purity is calculated from the area of the main peak as a share of all the peaks.
Counter-ion
An ion of opposite charge that balances the charges on a peptide in its solid form. Counter-ions add weight to the powder without adding peptide, which is one reason net peptide content is always below 100% 3.
Deletion sequence
An impurity that is the target peptide with one amino acid missing, caused by a coupling step during synthesis that did not go to completion. Because it is so close to the target in size and behaviour, it is among the hardest impurities for purification to remove 2.
Endotoxin
A lipopolysaccharide from the outer membrane of certain bacteria, measured in endotoxin units (EU), usually by the Limulus amebocyte lysate (LAL) test. It survives ordinary heat sterilisation and passes through standard sterilising filters, which is why it is tested for separately from sterility.
Freeze-thaw cycle
One round of freezing and thawing a solution. Each cycle can damage a peptide in solution through ice-crystal formation and local concentration changes, which is why solutions are usually split into single-use portions before freezing. More on Handling and storage.
GMP (Good Manufacturing Practice)
The quality system medicines must legally be made under, covering facilities, processes, records and batch release, with regulators inspecting compliance. Research peptides are not normally made under GMP. See What research grade actually means.
HPLC
High-performance liquid chromatography. A sample is pushed through a packed column, and different compounds leave it at different times, so each can be detected separately. On a COA, HPLC is what produces the purity figure.
Hygroscopic
Readily absorbs moisture from the air. Lyophilised peptides are hygroscopic, which is why a cold vial is left to reach room temperature before it is opened: opening it cold draws condensation onto the powder.
Lyophilised (lyophilized)
Freeze-dried. The peptide solution is frozen and the ice is removed under vacuum, leaving a dry powder or cake. With the water gone, most of the reactions that degrade a peptide in solution slow dramatically, which is why lyophilised material keeps far longer than a solution 4. Our guide to how long reconstituted peptides last covers the solution side.
Mass spectrometry (MS)
A method that measures the mass of molecules. On a COA it confirms identity: the measured mass is compared with the mass calculated from the sequence, and a match shows the main component is the peptide it is claimed to be. Combined with chromatography it is called LC-MS.
Molecular weight
The mass of one molecule, the sum of the masses of its atoms, given in grams per mole or daltons (Da). Our product pages list the calculated value, and the mass spectrometry result on a COA should agree with it.
N-terminus and C-terminus
The two ends of a peptide chain. The N-terminus carries a free amino group and the C-terminus a free carboxyl group, and sequences are written from N to C. Some peptides are modified at one end, for example amidated at the C-terminus, which changes the molecular weight.
Net peptide content
The share of the powder in a vial that is peptide, by weight. The rest is water, counter-ions and residual salts. It is measured separately from purity, usually by amino acid analysis, and it is always below 100%.
Oxidation
A chemical change, most often at methionine or cysteine residues, caused by exposure to oxygen. Oxidised forms show up as separate small peaks on a chromatogram, and they are one reason peptides are stored sealed, dry and cold.
Peptide bond
The amide bond that joins one amino acid to the next, formed when the carboxyl group of one reacts with the amino group of the other and a molecule of water is released. Explained in full on What are peptides?
Purity (HPLC purity)
The main peak's share of the total peak area on an HPLC chromatogram. It measures how much of the detected peptide material is the target rather than related impurities. It does not measure how much of the vial's contents is peptide: that is net peptide content.
Reconstitution
Dissolving a lyophilised powder in a liquid to make a solution. The concentration of the result depends only on the amount of peptide in the vial and the volume of liquid added.
Residue
An amino acid once it is part of a chain. Having lost water when the bond formed, it is no longer strictly a free amino acid, so chain lengths are counted in residues: BPC-157 is a 15-residue peptide.
Retention time
How long a compound takes to pass through an HPLC column. Under fixed conditions a given compound leaves the column at a consistent time, which is how the main peak is identified on a chromatogram.
RUO (research use only)
A statement of intended use: supplied for laboratory research, not for use in humans, animals or diagnostic procedures. It describes what a product is for, not its quality.
Sequence
The order of amino acids in a chain, written in one-letter or three-letter codes from N-terminus to C-terminus. The sequence is the identity of a peptide: the same amino acids in a different order make a different molecule.
Solid-phase peptide synthesis (SPPS)
The standard method for making peptides. The chain is built one amino acid at a time while anchored to an insoluble resin, most often using Fmoc chemistry, then cleaved from the resin and purified 1.
TFA salt
A peptide whose positive charges are balanced by trifluoroacetate, left over from the trifluoroacetic acid used to cleave and purify it. Many synthetic peptides are supplied as TFA salts unless exchanged to acetate or hydrochloride 3, and residual trifluoroacetate can affect some cell-culture experiments 5.
Vial strength
The stated amount of peptide in a vial, for example 10 mg. Whether that figure refers to the peptide itself or to the total powder including counter-ions is worth confirming with any supplier.
References
- 1Advances in Fmoc solid-phase peptide synthesis. J Pept Sci (2016). PMC4745034
- 2Related impurities in peptide medicines. J Pharm Biomed Anal (2014). PMID 25044089
- 3The Role of Counter-Ions in Peptides: An Overview. Pharmaceuticals (Basel) (2020). PMC7761850
- 4Lyophilization and development of solid protein pharmaceuticals. Int J Pharm (2000). PMID 10967427
- 5Trifluoroacetate, a contaminant in purified proteins, inhibits proliferation of osteoblasts and chondrocytes. Am J Physiol (1999). PMID 10567002
Links open the record on PubMed or PubMed Central. These are citations to published research, not claims about this product.
Common questions
What does lyophilised mean?
Freeze-dried. The peptide is frozen in solution and the ice is removed under vacuum, leaving a dry powder. Lyophilized is the American spelling of the same word.
What is net peptide content?
The percentage of the powder in a vial that is peptide by weight, with water, counter-ions and salts making up the rest. It is measured separately from purity and is always below 100%.
What is a TFA salt?
A peptide paired with trifluoroacetate counter-ions, left over from the trifluoroacetic acid used in synthesis and purification. Many are exchanged to acetate for cell-based research.
What is the difference between HPLC and mass spectrometry?
HPLC separates the components of a sample and reports purity. Mass spectrometry measures molecular mass and confirms identity. Some laboratories report both on every COA; others offer mass spectrometry as an extra test.
What is a deletion sequence?
An impurity that is the target peptide with one amino acid missing, caused by an incomplete coupling step during synthesis.
What is a CAS number?
A unique identifier for a chemical substance, assigned by the Chemical Abstracts Service, used to look a compound up unambiguously.
Related
- What a peptide is, from amino acid to polypeptide chain
- What research grade does and does not mean
- What a Certificate of Analysis reports, and how to read one
- How lyophilised peptides behave, and what changes in solution
- Bacteriostatic water and sterile water compared
- How to verify a Janoshik COA: task number, unique key and what it proves