How to Read a Peptide COA: HPLC Purity, Mass Spec and Endotoxin Testing Explained

A peptide certificate of analysis (COA) should answer three separate questions: is it the right molecule (mass spectrometry), how clean is it (HPLC purity), and how much is actually in the vial (peptide content). Safety tests such as endotoxin, sterility and heavy metals are additional, and many supplier COAs leave them out.

Research peptides are sold for laboratory use only. A COA is a quality document for a batch of material, not evidence that a compound is safe or effective in people. Research-grade products are not FDA-approved medicines, even when the molecule, such as semaglutide, is the active ingredient of an approved drug. Our explainer on what research use only actually means covers the legal side.

This guide walks through each section of a typical COA, explains what the numbers can and cannot tell you, and summarises what independent testing of online peptides has found.

At a glance: what each test on a peptide COA tells you

Test	Question it answers	What a useful result shows	Red flag
HPLC purity	What share of detected material is the target peptide?	Chromatogram, peak table, % area, method and wavelength	A single percentage with no chromatogram
Mass spectrometry	Is it the right molecule?	Expected and observed mass, with the spectrum	“Conforms” with no numbers
Peptide content (assay)	How much peptide is in the vial?	Milligrams measured against the label claim	Missing entirely
Counter-ion	Which salt form, such as TFA or acetate?	Named salt, ideally quantified	Not stated
Endotoxin	Are bacterial toxins present?	Result in EU/mg with the method used	No endotoxin test
Sterility and bioburden	Are live microbes present?	Method, result and date	Not tested
Elemental impurities	Are toxic metals present?	ICP-MS results for lead, cadmium, arsenic, mercury	Not tested
Batch and lab details	Does this report belong to my vial?	Lot number, dates, named lab, signatory, contact	Generic or reused report

What a peptide COA is, and who should produce it

A COA is a report of laboratory results for one manufacturing batch, identified by a lot or batch number. It may come from the manufacturer’s own quality lab or from an independent third-party lab. Third-party reports are more useful when the lab is named, can be contacted, and holds accreditation to ISO/IEC 17025, the international standard that “enables laboratories to demonstrate that they operate competently and generate valid results”.¹

Ask whether the accreditation covers the specific tests on the report, not just the lab in general. Our article on the signs a brand is genuinely third-party tested sets out how to check a lab’s credentials, and the same logic applies to peptides as to supplements.

HPLC purity: what 98% or 99% really means

High-performance liquid chromatography (HPLC) separates the contents of a sample, and a detector draws each component as a peak. Purity is usually reported as the main peak’s share of the total detected peak area. One large dataset analysis defined it in exactly those terms: the tested peptide as a percentage of all detected substances.²

Two limits follow. First, the figure only counts what the detector sees, so anything that does not separate from the main peak or does not register at that wavelength is invisible. Second, “99%” says nothing about what the other 1% is. Peptides made by solid-phase synthesis carry characteristic impurities: deletion sequences where an amino acid is missing, insertions where one is added, diastereomers from racemisation, leftover protecting groups, oxidised forms and dimers.³ Some of these are close cousins of the target peptide with their own biological activity.

Regulated medicines set a much finer standard. For generic synthetic versions of certain peptide drugs, FDA guidance requires that any new impurity is no more than 0.5% of the drug substance,⁴ and new impurities between 0.10% and 0.5% must be identified and justified.⁵ A research-grade “98% pure” result does not identify impurities at all.

When an independent analysis applied thresholds to thousands of submitted samples, it used 98.0% HPLC purity as an approximation of compounding standards and 99.5% as a stricter manufactured-drug benchmark, while stressing that these were chosen benchmarks rather than codified rules.²

What to look for: the actual chromatogram, the retention time of the main peak, a peak table, the column and detection wavelength, and a test date that matches the batch.

Mass spectrometry: confirming identity

HPLC shows how much of a sample is one compound, but not which compound. Mass spectrometry (MS) confirms identity by measuring molecular mass. A good COA lists the expected (theoretical) mass, the observed mass and the spectrum itself.

For example, PubChem lists BPC-157 as C62H98N16O22 with an average molecular weight of 1,419.5 and a monoisotopic mass of 1,418.70.⁶ Semaglutide’s average molecular weight is about 4,114.⁷ Larger peptides are often detected as multiply charged ions, so a spectrum may show peaks at a fraction of the full mass. One study of online semaglutide used the four-charged ion near m/z 1,029 as its reference peak.⁸ A competent report explains which ion it is reading.

MS has limits too. It confirms that a molecule of the right mass is present, not how much, and it cannot tell apart diastereomers, which have identical mass.³ That is why identity and purity need separate tests.

Peptide purity vs peptide content: net peptide content and counter-ions

This is where many buyers are misled. Purity is a ratio of peaks. Content is a quantity: how many milligrams of peptide the vial holds. A powder can be 99% pure by HPLC yet hold more or less peptide than the label says.

Part of the gap is counter-ions. Peptides made by standard solid-phase synthesis and purified by reverse-phase HPLC end up as trifluoroacetate (TFA) salts, and TFA may also be adsorbed in the freeze-dried powder as a contaminant.⁹ Most approved peptide drugs are supplied as acetate salts, and TFA content is considered highly undesirable in material for clinical and preclinical work.⁹ The US Pharmacopeia has separate chapters for measuring acetic acid and TFA in peptides.⁵ So the weight of powder in a vial is not the same as the weight of peptide, unless the supplier reports net peptide content.

Testing of online products shows how far apart the numbers can be:

• In a 2024 study, three semaglutide vials bought from illegal online pharmacies held 28.6% to 38.7% more semaglutide than labelled, yet semaglutide made up only 7.7% to 14.4% of the powder’s mass, against vendor claims of at least 99% purity. The authors could not identify the rest of the material.⁸
• In a 2026 preprint analysing 6,285 samples submitted by consumers and companies, 58.8% of tirzepatide samples met the stricter purity benchmark but failed on measured amount versus label.²

What to look for: a separate assay or content result in milligrams per vial, the stated salt form, and how content was measured.

Endotoxin, sterility and heavy metals

Purity and identity say nothing about contamination. Three further tests matter for any material intended for injectable research models.

Endotoxin (LAL or recombinant tests)

Endotoxins are bacterial contaminants measured in endotoxin units (EU), and limits for injectable drugs are built around a threshold fever-causing (pyrogenic) dose.¹⁰ The FDA’s current guidance on the Limulus Amoebocyte Lysate (LAL) and related bacterial endotoxin tests was revised in March 2026 and points to the US Pharmacopeia’s chapter on bacterial endotoxins for methods and limits.¹¹ For parenteral drugs, limits are calculated as K/M, where K is 5 EU per kg of body weight (0.2 EU/kg for intrathecal products) and M is the maximum dose per kg.¹⁰ A COA should give a numeric result and the method.

Endotoxin is not predicted by purity. In the 2026 preprint, purity showed no relationship with endotoxin, and 15% of the 243 samples with endotoxin data had measurable levels.² All three semaglutide samples in the 2024 study had endotoxin results between about 2.2 and 9.0 EU/mg, two reported as upper limits.⁸

Sterility

A clean HPLC trace says nothing about sterility. Sterility or bioburden testing shows whether live microorganisms were found at the time of testing. In the semaglutide study, the powders contained no viable microorganisms when tested, even though endotoxin was present,⁸ a reminder that the two tests measure different things.

Heavy metals

Elemental impurities are now assessed against permitted daily exposure limits under USP chapter 232 and the ICH Q3D guideline. Class 1 elements, with significant toxicity, are cadmium, lead, arsenic and mercury, measured by methods such as ICP-MS.¹² Few research peptide COAs report them.

Batch matching and lab accreditation

A COA only means something if it belongs to the vial in front of you. Check that:

• the lot or batch number on the COA matches the vial label exactly;
• the test date falls after the manufacturing date and is recent;
• the lab is named, has a physical address and a contact, and can confirm the report;
• the lab’s ISO/IEC 17025 accreditation scope includes the methods reported;¹
• a signatory and report number appear, so the document can be traced.

Red flags on a peptide COA

1. Templated reports. The same layout, purity figure and date across different peptides or batches.
2. No chromatogram or spectrum. A number without the underlying data cannot be checked.
3. Purity only. No identity test, no content result, no endotoxin.
4. Missing or mismatched lot numbers.
5. An unnamed or uncontactable lab, or a supplier that refuses to say which lab ran the tests.
6. Perfect results such as “100.00%”, which should prompt questions given how many related impurities synthetic peptides can carry.³
7. Therapeutic claims or dosing advice alongside a “research use only” label.

The same checks apply to other categories; our guide to red flags on a kratom COA shows the pattern in a different market.

What independent testing of online peptides has found

Two recent analyses give a sense of scale. The 2024 semaglutide study found that none of three prefilled pens ordered from illegal online pharmacies arrived, and the three vials that did were judged probable substandard or falsified products.⁸ The 2026 preprint drew on public reports from Finnrick Analytics, an independent testing platform, covering 14 peptides, including BPC-157, TB-500, retatrutide, semaglutide and tirzepatide, from 203 companies. Between 41.6% and 71.1% of samples failed basic quality criteria, depending on the benchmark. For BPC-157, 3.5% failed identity testing outright.²

The preprint’s authors note likely selection bias, since samples were submitted voluntarily, and that sterility, residual solvents and stability were not assessed.² It has not been peer reviewed. Even so, its headline finding is consistent with the semaglutide study: a high purity figure on its own is a weak guarantee.

The regulatory backdrop is also unsettled. In July 2026 an FDA advisory committee voted to recommend adding BPC-157, TB-500 and four other peptides to the 503A compounding bulks list, against FDA staff advice; the votes are non-binding and nothing has yet been added.¹³ Our coverage of the BPC-157 advisory vote and BPC-157 safety research explains what is and is not known.

Peptide purity testing: putting it together

A credible COA for a research peptide shows, for the same lot: an HPLC chromatogram with purity and method details, a mass spectrum with expected and observed mass, a content result in milligrams, the salt form, an endotoxin result, and ideally sterility and heavy metal data, all from a named, accredited lab. Our overview of research peptide types explains the compounds most often sold, and our 2026 research peptide suppliers guide applies these checks to specific suppliers.

Frequently asked questions

What should a peptide COA include?

At minimum, a batch-matched COA should show an HPLC chromatogram with percentage purity, a mass spectrometry result with expected and observed mass, and a measured peptide content in milligrams. For material used in injectable research models, endotoxin, sterility and heavy metal results matter too. The report should name the lab, the method and the lot number, and the lab should be contactable.

What does 99% HPLC purity mean for a peptide?

It usually means the main peak accounts for 99% of the detected peak area in that HPLC run. It does not say how much peptide is in the vial, whether the molecule is correct, or what the remaining 1% is. Synthetic peptides can contain deletion, insertion and oxidised sequences,³ and only identity and content tests answer those questions.

What is the difference between peptide purity and peptide content?

Purity is a ratio of chromatogram peaks; content is the actual mass of peptide present. A freeze-dried powder also holds counter-ions such as TFA or acetate.⁹ In one study of online semaglutide, vials held more semaglutide than labelled, yet the peptide was only 7.7% to 14.4% of the powder’s mass.⁸

Can a peptide COA be faked or reused?

Yes, which is why batch matching matters. Warning signs include identical reports across different products or batches, missing chromatograms, perfect round numbers, and labs that cannot be named or contacted. Check that the lot number matches your vial, that the lab holds ISO/IEC 17025 accreditation for the reported methods,¹ and, where possible, confirm the report directly with the lab.

Why does endotoxin testing matter if a peptide is 99% pure?

Because purity does not measure contamination. Endotoxins are bacterial toxins that HPLC purity results do not capture. In a 2026 preprint analysing submitted samples, purity did not predict endotoxin and 15% of tested samples had measurable levels.² A useful COA reports an endotoxin result in EU per mg, along with the test method used.

Sources

1. International Organization for Standardization. ISO/IEC 17025:2017 General requirements for the competence of testing and calibration laboratories. iso.org
2. Mendias CL, Awan TM. Evaluation of Research Grade Peptides Marketed Directly to Consumers Reveals Extensive Variability in Purity and Measured Abundance. Preprint (not peer reviewed), Preprints.org. 24 April 2026. DOI: 10.20944/preprints202604.1748.v1. preprints.org
3. D’Hondt M, Bracke N, Taevernier L, Gevaert B, Verbeke F, Wynendaele E, De Spiegeleer B. Related impurities in peptide medicines. J Pharm Biomed Anal. 2014;101:2-30. DOI: 10.1016/j.jpba.2014.06.012. PMID: 25044089. pubmed.ncbi.nlm.nih.gov
4. Lachman Consultants. While not entirely new, guidance places stamp of approval on some synthetic peptides where the RLD is of rDNA origin (on FDA guidance “ANDAs for Certain Highly Purified Synthetic Peptide Drug Products That Refer to Listed Drugs of rDNA Origin”, May 2021). 20 May 2021. lachmanconsultants.com
5. Carrick K (US Pharmacopeia). USP Standards to Support Quality of Peptide and Oligonucleotide Therapies. USP Workshop on Therapeutic Peptides and Oligonucleotides, 9 April 2024. usp.org
6. National Center for Biotechnology Information. PubChem Compound Summary: BPC-157 (CID 9941957). Accessed 24 October 2026. pubchem.ncbi.nlm.nih.gov
7. National Center for Biotechnology Information. PubChem Compound Summary: Semaglutide (CID 56843331). Accessed 24 October 2026. pubchem.ncbi.nlm.nih.gov
8. Ashraf AR, Mackey TK, Vida RG, Kulcsár G, Schmidt J, Balázs O, et al. Multifactor Quality and Safety Analysis of Semaglutide Products Sold by Online Sellers Without a Prescription: Market Surveillance, Content Analysis, and Product Purchase Evaluation Study. J Med Internet Res. 2024;26:e65440. DOI: 10.2196/65440. PMID: 39509151. pubmed.ncbi.nlm.nih.gov
9. Sikora K, Jaśkiewicz M, Neubauer D, Migoń D, Kamysz W. The Role of Counter-Ions in Peptides: An Overview. Pharmaceuticals (Basel). 2020;13(12):442. DOI: 10.3390/ph13120442. PMID: 33287352. pubmed.ncbi.nlm.nih.gov
10. Dawson M. Endotoxin Limits for Parenteral Drug Products. BET White Paper 1(2). Associates of Cape Cod. April 2017. acciusa.com
11. US Food and Drug Administration. Guidance for Industry: Pyrogen and Endotoxins Testing: Questions and Answers (Edition 2). March 2026. fda.gov
12. Labcorp. Elemental impurities per USP and ICH Q3D guidelines. 29 July 2024. labcorp.com
13. AJMC. FDA panel backs 6 peptides for compounding. July 2026. ajmc.com

This article is for educational purposes only and is not medical or legal advice. Products discussed here are not intended to diagnose, treat, cure or prevent any disease. Laws vary by location and change often, so verify the rules that apply where you are. Always talk to a licensed healthcare provider before use, especially if you are under 21, pregnant or nursing, taking medication, or managing a health condition.