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Does 99% purity on a peptide COA mean 99% peptide by weight?
No. HPLC purity is a peak-area fraction; net peptide content is a mass fraction. Six sequences show what a TFA counterion alone can take from a 10 mg vial.
No. A 99% purity figure on a peptide certificate of analysis is an HPLC peak-area fraction: of the peptide-related material detected, 99% was the target sequence. It says nothing about how much of the vial’s mass is peptide. That is net peptide content, a separate mass-fraction figure that AmbioPharm’s explainer places between 70 and 90% for a typical lot.
The question keeps being asked because the market keeps answering it in the vendor’s favour. Two research-supplier guides to reading a COA appeared within seven weeks of each other: American Peptides on 16 May 2026 and Great Northern Peptides on 3 July 2026. A third, from Onyx Biolabs, carries 12 August 2026 in its URL but was not fetched for this piece. This desk read the American Peptides and Great Northern guides, plus the Bachem and AmbioPharm pages cited below, on 11 September 2026. Both concede the purity-versus-content distinction. Neither scales the counterion mass with the sequence in the vial, which is the arithmetic the question actually turns on. The chemistry below does not date; only the guides do.
Why 99% purity on a peptide COA is not 99% peptide by weight
Bachem’s knowledge-hub page puts it in two sentences. Purity, analysed by HPLC, is the percentage of target peptide relative to peptide-based impurities. Content, measured through amino acid analysis or UV spectrophotometry, is the total peptide mass fraction against non-peptide components such as salts and moisture. Bachem’s own illustration is two lots at 95% purity, one with 80% content and one with 95%, holding different amounts of target peptide despite identical purity figures.
AmbioPharm’s short explainer describes the same certificate from the manufacturer’s side: purity above 98% by HPLC or UPLC on one line, peptide content on another. The non-peptide remainder is water, acetate or trifluoroacetate, and residual solvent left after lyophilisation. Typical content is 70 to 90%. Peptides rich in arginine bind more salt and are more hygroscopic, so they sit lower.
The mechanism is not exotic. Reverse-phase purification runs in trifluoroacetic acid, and the peptide comes off the column as a trifluoroacetate salt unless the manufacturer exchanges it for acetate or hydrochloride. Every basic site on the chain carries one counterion, and that counterion is weighed when the vial is filled.
How much of a 10 mg vial can the TFA counterion take?
This is the figure none of the read guides supplies, so this desk computed it. The model is a ceiling, not a measurement: one trifluoroacetate (C2HF3O2, 114.02 g/mol) per basic site, with basic sites counted as arginine, lysine, histidine and a free N-terminus, and the peptide’s average molecular weight taken from the PubChem property record for each compound, read on 11 September 2026. Acylated lysines, an acetylated N-terminus and a lysine tied into a lactam bridge are not counted. The counterion share is n × 114.02 ÷ (MW + n × 114.02).
| Sequence | PubChem MW | Basic sites | TFA share of a fully salted solid | Max peptide in a 10 mg label mass, before water |
|---|---|---|---|---|
| Tirzepatide | 4813 | 2 | 4.5% | 9.55 mg |
| Semaglutide | 4114 | 4 | 10.0% | 9.00 mg |
| BPC-157 | 1419.5 | 2 | 13.8% | 8.62 mg |
| Sermorelin | 3357.9 | 6 | 16.9% | 8.31 mg |
| Bremelanotide | 1025.2 | 2 | 18.2% | 8.18 mg |
| Ipamorelin | 711.9 | 3 | 32.5% | 6.75 mg |
Basic-site counts come from each peptide’s published sequence as this desk reads it: BPC-157 (GEPPPGKPADDAGLV) has one lysine plus the N-terminus; ipamorelin (Aib-His-D-2-Nal-D-Phe-Lys-NH2) has histidine, lysine and the N-terminus; bremelanotide is N-acetylated and its lysine sits in the lactam bridge, leaving histidine and arginine; sermorelin (GRF 1-29 amide) carries three arginines, two lysines and the N-terminus; semaglutide has two arginines, a histidine and the N-terminus, with its single lysine acylated; tirzepatide has one free lysine and the N-terminus, no arginine and no histidine.
Two things the table says, and one it does not. First, mass per basic site is the whole story: a two-site 4.8 kDa peptide loses 4.5% of its label mass to a full trifluoroacetate set, while a three-site 0.7 kDa peptide loses a third. Second, the counterion identity matters: swapping every trifluoroacetate for acetate (59.04 g/mol) cuts the share to 2.4% for tirzepatide and 19.9% for ipamorelin. What the table does not say is what any vendor’s vial contains. A real lot may be sub-stoichiometric in counterion, may be acetate rather than trifluoroacetate, and carries bound water on top, which American Peptides’ guide calls a few percent as measured by Karl Fischer. Add an arithmetical 6% water to the ipamorelin row and the 6.75 mg becomes 6.35 mg; that is arithmetic, not a sourced figure.
What the three vendor guides commit to
Both guides read for this piece list net content among the fields a report should carry; the American Peptides article of 16 May is the one that treats its absence as a gap and puts a figure on it. Its own worked example is a hypothetical 10 mg vial at 78% peptide, 12% counterion, 6% water and 4% residual salt, tied to no sequence. Great Northern’s guide describes the net-content field, states that 99.2% by HPLC does not mean 99.2% of the vial by mass, and gives no figure. A third guide, from Onyx Biolabs, was not read for this piece and is not scored here. That is the scope of the audit: two pages, each read within a 6 KB window; not what either prints on its actual certificates.
What a buyer does with the number
Treat the purity line and the content line as two assays with two methods, and ask for both. This desk has argued before that a vendor-published certificate is evidence only of what it documents, and net content is the field the guides read here treat as the one most likely to be missing. It sits beside endotoxin as a result a purity figure cannot supply. Where a supplier’s report names the laboratory that signed it, check whether that laboratory ran a quantitative method or only the purity HPLC; a chromatogram proves the second and not the first. And if the certificate names no counterion, the table above gives the range of what a missing line can hide.
Questions readers ask
What is the difference between peptide purity and peptide content?
Purity is a chromatographic figure: the target peak’s share of all peptide-related peaks on an HPLC run. Content is a mass figure: the share of the dried solid that is peptide at all, as opposed to counterion, water and residual solvent. Bachem’s knowledge page states the two are uniquely different measurements, and a lot can score high on the first while sitting at 80% on the second.
What is net peptide content on a certificate of analysis?
Net peptide content is the fraction of the lyophilised solid that is peptide, reported as a percentage or as milligrams per vial. It is determined by a quantitative method, most often amino acid analysis or UV spectrophotometry, and AmbioPharm’s explainer places typical values between 70 and 90%. Where a certificate omits it, the label mass has not been converted into peptide mass by anyone.
Why is the peptide content lower than the purity?
Because the two figures exclude different things. Purity ignores everything that is not a peptide peak, so counterion and water do not lower it. Content counts them. A peptide purified by reverse-phase HPLC is isolated as a salt, usually trifluoroacetate, and the salt is part of the weighed solid. Arg-rich sequences bind more salt and more water, so their content runs lower still.
What does TFA salt mean on a peptide COA?
It means the peptide was isolated with trifluoroacetate as the counterion to its basic sites: arginine, lysine, histidine and the free N-terminus. Each trifluoroacetate weighs 114.02 g/mol. At one per basic site, the counterion set alone is 4.5% of a fully salted tirzepatide solid and 32.5% of a fully salted ipamorelin solid, before any water is counted.
How is net peptide content measured?
Bachem’s page names amino acid analysis or UV spectrophotometry. American Peptides’ guide adds mass-balance accounting: counterion content, Karl Fischer water and residual salt subtracted from the whole. Each is a separate assay from the purity HPLC run, with its own method statement. A percentage without a named method is a number, not a result, and the same applies to net content as to purity.
Materials in this category are supplied for laboratory research use only, and nothing above concerns their use in humans. Six sequences appear in the table and this desk has kept to their molecular weights. What a certificate says a vial weighs, and what it says of that weight is peptide, are two lines of paperwork. This market prints the first far more reliably than the second.