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What are peptides?

Peptides are short chains of amino acids joined by peptide bonds. Chemically they sit between single amino acids and proteins: a peptide has a defined sequence and a defined molar mass, and in the lab it usually comes as a freeze-dried (lyophilised) powder. This page explains what peptides are, how research peptides are made and analysed in general, and how lyophilised material is handled in the laboratory.

Last reviewed: 3 November 2026

Amino acids and the peptide bond

An amino acid carries an amino group (–NH2) and a carboxyl group (–COOH) on the same carbon atom, plus a side chain that differs from one amino acid to the next. Twenty amino acids are the standard building blocks of proteins; they differ in size, charge and in how strongly they attract water.

When the carboxyl group of one amino acid reacts with the amino group of the next, water is released and an amide bond forms – the peptide bond. Its C–N bond has partial double-bond character, so the group is flat and rigid; this planarity was a key assumption of the helix models of protein structure that Pauling and colleagues proposed in 1951 [1]. Each amino acid built into a chain is called a residue.

A peptide chain has a direction. One end carries a free amino group (N-terminus), the other a free carboxyl group (C-terminus). Sequences are written from the N-terminus to the C-terminus, using the three-letter or one-letter codes of the IUPAC-IUB nomenclature [2]. The molar mass of a linear, unmodified peptide is the sum of its residues plus one molecule of water.

Peptide, polypeptide, protein – where the line is

There is no sharp chemical boundary. Chains of a few residues are often called oligopeptides, longer ones polypeptides. A widely used rule of thumb calls chains of up to about 50 amino acids peptides, and longer chains, which usually fold into a stable three-dimensional shape, proteins. The terms describe length and structure, not how a molecule behaves.

Structure and modifications

Besides the sequence itself, many peptides carry defined chemical modifications. They are part of the identity of a compound and show up in its name or sequence:

  • C-terminal amidation: the chain ends in an amide (–CONH2) instead of a free acid, often written as “-NH2” at the end of a sequence. Many naturally occurring peptides are amidated [3].
  • N-terminal acetylation: an acetyl group (“Ac-”) caps the N-terminus. In nature it is one of the most common modifications of proteins [4].
  • Cyclisation: the chain is closed into a ring – head to tail, through side chains or through a disulfide bridge between two cysteines [5].

How research peptides are made

Research peptides are made by chemical synthesis, mostly by solid-phase peptide synthesis (SPPS). R. B. Merrifield introduced the method in 1963: the first amino acid is anchored to an insoluble resin and the chain is built step by step from the C-terminus towards the N-terminus [6]. Because the growing chain stays attached to the solid support, excess reagents can simply be washed away after each step.

Today the Fmoc strategy is the standard [7]. Every amino acid is added in the same order of steps:

  1. The temporary Fmoc protecting group is removed from the N-terminus of the chain.
  2. The next amino acid, itself Fmoc-protected, is activated and coupled.
  3. Excess reagents are washed off.

Reactive side chains carry permanent protecting groups during the build-up [8]. At the end, a strongly acidic mixture based on trifluoroacetic acid cleaves the peptide from the resin and removes these groups at the same time [7].

Purification and analysis in general

No synthesis step works perfectly. Besides the target peptide, the crude product therefore contains related by-products: chains with a missing residue (deletion sequences), chains that stopped early, or chains with protecting groups left on. The standard method to separate them is reversed-phase high-performance liquid chromatography (RP-HPLC), which separates molecules by how strongly they bind to a water-repellent column material. Used analytically, the same technique shows what share of the detected peptide material is the target peptide [9].

Mass spectrometry (MS) measures the mass of a molecule very precisely and so shows whether it matches the mass calculated from the expected sequence; tandem mass spectrometry can also read out the sequence itself [10]. This section describes the methods of peptide chemistry in general; it makes no statement about individual products.

Lyophilised form: what freeze-dried means

After purification the peptide is dissolved in water. To obtain a stable solid, it is freeze-dried (lyophilised): the solution is frozen, then the ice is removed under vacuum by sublimation, passing straight from solid to vapour (primary drying). A secondary drying step removes the remaining bound water [11].

The reason is stability. In the presence of water, peptides and proteins can change chemically, for example through hydrolysis of the chain, deamidation of asparagine and glutamine, or oxidation of methionine and cysteine [12]. A dry solid slows these reactions down and is easier to store and ship [11].

Lyophilised peptide usually looks like a white powder or a compact “cake”. Milligram amounts take up very little space and can also sit as a thin film on the glass, so a vial may look almost empty.

Storing lyophilised peptides in the lab

Where a product page or label states storage conditions, those apply. General laboratory practice for lyophilised peptides:

  • keep the vial closed, cool, dry and protected from light;
  • let a cold vial reach room temperature before opening it, so that no moisture condenses on the powder;
  • open vials only as long as necessary and close them tightly again;
  • avoid repeated freezing and thawing.

Moisture, oxygen and light drive the chemical changes described above [11, 12].

Reconstitution as a lab step

For work in solution, the lyophilised powder is dissolved in a suitable solvent; this is called reconstitution. Which solvent suits a peptide depends on its sequence, above all on its charge and its share of water-repellent residues. One option is bacteriostatic water, sterile water with 0.9 % benzyl alcohol.

The concentration follows from simple arithmetic: amount of peptide divided by volume of solvent. For example, 5 mg in 2 mL gives 2.5 mg/mL. The peptide calculator does this for any vial content and volume. In solution, peptides are generally less stable than as a dry powder [11].

Single peptides and blends

Most products contain one peptide per vial. Blends contain several peptides in one vial; their composition is listed on the product page. Besides peptides and blends, the shop offers capsules and tablets and lab supplies.

Research use only

For laboratory research only. Not for human use. All products from NADA-Labs are intended exclusively for laboratory research and must not be used in humans or animals. This page covers chemistry and laboratory handling only.

Common questions

What is a peptide, in one sentence?

A chain of amino acids linked by peptide bonds – shorter than a protein, with no fixed cut-off (rule of thumb: up to about 50 amino acids).

What does “lyophilised” mean?

Freeze-dried: the water was removed from the frozen solution under vacuum, leaving a dry solid.

Why does a vial sometimes look almost empty?

Milligram amounts of freeze-dried material take up very little space and can sit as a thin film on the glass.

What do “-NH2” and “Ac-” in a sequence mean?

“-NH2” marks an amidated C-terminus, “Ac-” an acetylated N-terminus (see “Structure and modifications”).

How do I work out the concentration after reconstitution?

Divide the amount of peptide by the volume of solvent, or use the peptide calculator.

Sources

  1. Pauling L, Corey RB, Branson HR. The structure of proteins; two hydrogen-bonded helical configurations of the polypeptide chain. Proc Natl Acad Sci U S A. 1951;37(4):205–211. doi:10.1073/pnas.37.4.205 · PubMed 14816373
  2. IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN). Nomenclature and symbolism for amino acids and peptides. Eur J Biochem. 1984;138(1):9–37. doi:10.1111/j.1432-1033.1984.tb07877.x · PubMed 6692818
  3. Eipper BA, Stoffers DA, Mains RE. The biosynthesis of neuropeptides: peptide alpha-amidation. Annu Rev Neurosci. 1992;15:57–85. doi:10.1146/annurev.ne.15.030192.000421 · PubMed 1575450
  4. Ree R, Varland S, Arnesen T. Spotlight on protein N-terminal acetylation. Exp Mol Med. 2018;50(7):1–13. doi:10.1038/s12276-018-0116-z · PubMed 30054468
  5. White CJ, Yudin AK. Contemporary strategies for peptide macrocyclization. Nat Chem. 2011;3(7):509–524. doi:10.1038/nchem.1062 · PubMed 21697871
  6. Merrifield RB. Solid phase peptide synthesis. I. The synthesis of a tetrapeptide. J Am Chem Soc. 1963;85(14):2149–2154. doi:10.1021/ja00897a025
  7. Behrendt R, White P, Offer J. Advances in Fmoc solid-phase peptide synthesis. J Pept Sci. 2016;22(1):4–27. doi:10.1002/psc.2836 · PubMed 26785684
  8. Isidro-Llobet A, Álvarez M, Albericio F. Amino acid-protecting groups. Chem Rev. 2009;109(6):2455–2504. doi:10.1021/cr800323s · PubMed 19364121
  9. Mant CT, Chen Y, Yan Z, et al. HPLC analysis and purification of peptides. Methods Mol Biol. 2007;386:3–55. doi:10.1007/978-1-59745-430-8_1 · PubMed 18604941
  10. Steen H, Mann M. The ABC’s (and XYZ’s) of peptide sequencing. Nat Rev Mol Cell Biol. 2004;5(9):699–711. doi:10.1038/nrm1468 · PubMed 15340378
  11. Wang W. Lyophilization and development of solid protein pharmaceuticals. Int J Pharm. 2000;203(1–2):1–60. doi:10.1016/S0378-5173(00)00423-3 · PubMed 10967427
  12. Manning MC, Chou DK, Murphy BM, et al. Stability of protein pharmaceuticals: an update. Pharm Res. 2010;27(4):544–575. doi:10.1007/s11095-009-0045-6 · PubMed 20143256