Peptide Basics
How Are Peptides Made? Synthesis, Purification and Why the Powder Is a Salt
Most peptides are made by chemical synthesis: the chain is built one amino acid at a time on resin beads, cut free, purified by HPLC and freeze-dried. Some are made by microorganisms instead, and some by both. This page explains the three routes in plain terms, where the impurities on a certificate of analysis come from, and why a peptide powder is usually a salt rather than the peptide alone. Explanation only — no manufacturing procedure.
The short answer
- Chemical synthesis is the main route. A 2014 review of peptide medicines states that most peptides today are manufactured by solid-phase peptide synthesis (SPPS).
- Living cells are the other route. Teriparatide is made by genetically modified bacteria; the liraglutide and semaglutide labels describe a yeast-made backbone that is modified chemically afterwards.
- Every route ends in purification. The crude peptide is purified by chromatography — HPLC for synthetic peptides — and freeze-dried when the product is a powder.
- Synthesis leaves characteristic impurities. Chains with a missing or extra amino acid, mirror-image forms, leftover protecting groups, oxidised forms and counter-ions are the ones a purity test is looking for.
- The powder is usually a salt. Trifluoroacetic acid used in cleavage and purification leaves TFA salts, which are often exchanged for acetate. Approved peptides such as cetrorelix and octreotide are acetate salts.
The three ways peptides are made
In the body, peptides are assembled on ribosomes from a genetic template. Manufactured peptides come from one of three routes, and approved U.S. labels say which route a product uses.
| Route | What happens | Labelled example |
|---|---|---|
| Chemical synthesis (solid phase) | The chain is built one amino acid at a time on tiny resin beads, then cut free and purified. | Cetrorelix — its U.S. label calls it “a synthetic decapeptide”. |
| Recombinant production | A microorganism carrying the gene makes the chain; it is then isolated and purified. | Teriparatide — made in a strain of E. coli (FORTEO) or Pseudomonas fluorescens (another U.S. teriparatide label). |
| Recombinant backbone + chemical modification | Yeast makes the peptide chain; a fatty-acid side chain is attached afterwards. | Liraglutide (VICTOZA) and semaglutide (OZEMPIC) — both labels describe a yeast-made backbone with a modified lysine 26. |
Sources: U.S. labels for cetrorelix acetate, FORTEO, teriparatide injection, VICTOZA and OZEMPIC, read through openFDA on 15 October 2026 (label versions effective February 2023 to August 2026).
Solid-phase peptide synthesis, in plain terms
Bruce Merrifield received the 1984 Nobel Prize in Chemistry for this idea: instead of building a peptide in solution and isolating it after every step, anchor the first amino acid to an insoluble resin bead and grow the chain on the bead. Each new amino acid arrives with its reactive groups temporarily blocked by protecting groups, so it can only join at the intended place. After each coupling, the excess reagents are washed away while the chain stays attached, and the next protecting group is removed so the cycle can repeat.
When the sequence is complete, the chain is cut from the resin and its remaining protecting groups come off, usually with trifluoroacetic acid. What comes out is a crude mixture: the intended peptide plus every chain that went slightly wrong along the way. It is purified by preparative HPLC, and the purified solution is freeze-dried into a powder — the step our lyophilized peptide page describes.
The reason this matters to anyone reading a certificate: each coupling step is a chance for a small error, and a long chain has many steps. Purification removes most of the wrong chains, but not all of them.
Where synthesis impurities come from
A 2014 review of related impurities in peptide medicines (D’Hondt et al., Ghent University) groups the impurities that come from synthesis itself. They are the “rest” behind a purity figure such as 98%.
| Impurity | How it arises |
|---|---|
| Deletion sequences | A deprotection step did not go to completion, so the next amino acid could not attach and the chain is missing one. |
| Insertion sequences | Excess amino-acid reagent added a residue twice, so the chain carries an extra one. |
| Diastereomers | An amino acid converted to its mirror-image form during synthesis — same mass, different shape. |
| Protection adducts | A temporary protecting group was not fully removed and is still attached. |
| Oxidised and aggregated forms | Side chains oxidised, or chains joined into dimers and larger clusters. |
| Counter-ions | Trifluoroacetate (TFA) left from cleavage and purification, bound to the peptide as a salt. |
| Unrelated peptides | Another product's peptide carried over — which the review attributes to a lack of appropriate GMP. |
A second group appears later, as the finished peptide degrades in storage. The review also notes that these impurities can distort early laboratory studies and lead to wrong conclusions. For approved medicines the bar is explicit: when a generic version of one of five synthetic peptides seeks FDA approval, FDA asks that any new impurity at 0.10% or more be identified and characterised, and treats a new one above 0.5% as not acceptable. Our certificate of analysis guide explains how purity testing measures them and why one headline percentage is not an impurity profile.
Why the powder is a salt
Trifluoroacetic acid (TFA) does two jobs in solid-phase synthesis: it cuts the finished chain from the resin, and it is the ion-pairing reagent in the HPLC purification. Peptides that carry positive charges therefore come out bound to trifluoroacetate, as TFA salts. Studies in the Journal of Peptide Science describe exchanging it for a different counter-ion — by repeated freeze-drying from hydrochloric or acetic acid, by ion-exchange resin, or by a further HPLC step.
Two things follow. First, the salt form is part of the product: approved peptides state it, as the U.S. labels for cetrorelix acetate and octreotide acetate do. A 2025 ETH Zurich study notes that numerous studies report effects of TFA salts in biological assays, and recommends that the counter-ion content be quantified and specified. Second, the counter-ion is weighed together with the peptide, so a salt form weighs more than the peptide alone — one reason why purity and peptide content are separate figures on a certificate of analysis.
What this means when you read research material
An approved peptide comes with a label that names its manufacturing route and its salt form, and it was released against a specification. Research-market peptides usually carry none of that. The questions this page makes possible are the ones a certificate of analysis should answer: was identity confirmed by mass spectrometry, what does the purity figure leave out, is the counter-ion stated (TFA, acetate or chloride), and is the peptide content reported separately from purity? A document that cannot answer them describes less than its headline number suggests.
Medibact does not manufacture or sell peptides. We supply USP-grade bacteriostatic water, made in the USA, for research use only, and publish reference material like this page.
Where this sits in the rest of the reference
FAQ
How are peptides made?
Three ways. Most are made by chemical synthesis, building the chain one amino acid at a time on resin beads (solid-phase peptide synthesis). Some are made by microorganisms carrying the gene, as teriparatide is in E. coli. And some combine the two: the U.S. labels for liraglutide and semaglutide describe a peptide backbone made in yeast with a fatty-acid side chain attached afterwards. Whatever the route, the crude peptide is then purified by chromatography and, for a powder product, freeze-dried.
What is solid-phase peptide synthesis (SPPS)?
It is the method Bruce Merrifield developed, for which he received the 1984 Nobel Prize in Chemistry. The first amino acid is anchored to an insoluble resin bead; each following amino acid is added with its reactive groups temporarily protected, and after each step the excess reagents are simply washed away while the growing chain stays on the bead. At the end the chain is cut from the resin, the protecting groups come off, and the crude product is purified.
Are peptides synthetic or natural?
The body makes peptides naturally, on ribosomes. Peptides sold or supplied as products are manufactured, either by chemical synthesis or by recombinant microorganisms. A peptide with the same sequence as a natural one is chemically the same molecule whichever way it was made; what differs between routes is the set of impurities each one leaves behind.
Is semaglutide synthetic?
The approved product is not purely synthetic. The OZEMPIC label states that the peptide backbone is produced by yeast fermentation, and that lysine 26 is modified with a spacer and a C18 fatty di-acid. In other words, a hybrid of the recombinant and chemical routes.
Why are peptides supplied as acetate or TFA salts?
Because of how they are made. Trifluoroacetic acid (TFA) is used to cut the finished chain from the resin and again during HPLC purification, so a peptide carrying positive charges comes out as a trifluoroacetate salt. Manufacturers can exchange it for acetate or chloride, for example by repeated freeze-drying from hydrochloric or acetic acid, or by ion exchange. Approved peptides such as cetrorelix and octreotide are labelled as acetate salts.
What impurities come from peptide synthesis?
A 2014 review of peptide medicines lists chains missing an amino acid (deletions) or carrying an extra one (insertions), amino acids flipped to their mirror-image form, leftover protecting groups, oxidised and aggregated forms, trifluoroacetate counter-ions, and in poorly controlled production even other, unrelated peptides. Storage then adds degradation products on top. A purity percentage on a certificate is the share of the main peak; it does not say which of these make up the rest.
Does the salt form change how much peptide is in a vial?
It changes what the powder weighs. A counter-ion is weighed together with the peptide, so a salt form weighs more than the peptide alone. That is one reason why purity and peptide content are different figures on a certificate of analysis; our certificate of analysis guide explains how to read both.
Is this a guide to making peptides?
No. This page explains in general terms how peptides are manufactured so that a certificate of analysis or a label can be read with understanding. It contains no synthesis procedure, reagent amounts or equipment list, and no dosing information. Medibact does not manufacture, sell or test peptides, and is not affiliated with Pfizer, Eli Lilly, Novo Nordisk or any manufacturer named here.
References: Nobel Prize in Chemistry 1984 (Merrifield); Merrifield, Adv Enzymol 1969 (PMID 4307033); D’Hondt et al., J Pharm Biomed Anal 2014 (PMID 25044089); Roux et al., J Pept Sci 2008 (PMID 18035848); Mrozik et al., J Pept Sci 2012 (PMID 22252914); Erckes et al., Pharmaceuticals 2025 (PMID 40872554); U.S. labels via openFDA; FDA SBIA, synthetic peptide ANDAs. All read 15 October 2026.
Educational use only — not medical advice. This guide summarizes information reported in published research and community practice for educational purposes. It is not medical advice and not a recommendation to use any compound. Any doses, schedules, or combinations shown are examples of what has been reported, not instructions for you. Many peptides described here are research compounds that are not FDA-approved for the uses discussed and may be investigational or restricted. Effects, risks, and legal status vary; individual needs and results vary. Consult a qualified, licensed healthcare professional before making any decision. Do not use this content to diagnose, treat, or dose yourself.