A purity figure gives the main peak's share, not what the small peaks are

ON THIS PAGE

1. Key findings
2. What the small peaks are
3. Naming a peak takes a second method
4. The thresholds the FDA proposes for generic peptides
5. Why ICH's general thresholds stop short of peptides
6. What one purity number leaves out
7. What 126 supplier records show
8. Limitations and open questions
9. Sources

Beside the main peak on a peptide chromatogram there are often small ones. Each is a real substance with a structure. Most are near-copies of the peptide itself, made wrong during synthesis or changed in storage. The field calls them related substances.

A certificate that prints one HPLC purity number tells you how much of the trace those peaks took up together. It does not tell you what any of them is. Drug regulators ask for the names too, peak by peak. No certificate noted in this publication's ledger is recorded naming one.

What the small peaks are

Most of them are the peptide gone slightly wrong. A 2014 review in the Journal of Pharmaceutical and Biomedical Analysis (D'Hondt and colleagues, abstract read 2026-10-06) sorts them into groups.

The first group comes from synthesis. A chain is built one amino acid at a time, and a step can fail. A missed step leaves a deletion: the chain comes out short a residue. An extra coupling leaves an insertion, one residue too many. The review adds three more. Some residues flip to their mirror-image form, which makes an isomer with the same atoms in a different shape. Some keep a protecting group that should have come off. Some side chains are oxidised.

The second group forms later, as the peptide breaks down. The review names pyroglutamate and succinimide formation among the routes. Deamidation is another: an asparagine or glutamine residue loses its amide group. A 1994 review in the Journal of Chromatography B (Bischoff and Kolbe, abstract read 2026-10-06) describes it running through a ring-shaped intermediate, in both proteins and peptides.

So a related substance is not dirt in the vial. It is a cousin of the peptide that the column happened to pull apart from it.

Naming a peak takes a second method

A chromatogram shows where a peak sits and how big it is. It does not say what the peak is. The International Council for Harmonisation (ICH), in its Q3A(R2) impurities guideline dated 25 October 2006 (read 2026-10-06), calls an impurity "identified" once its structure has been worked out. It defines an impurity profile as a description of the identified and unidentified impurities in a substance.

That work usually takes mass spectrometry or another test beside the HPLC run. A deletion weighs less than the full chain by one residue. An oxidised form weighs more. An isomer can weigh exactly the same, so mass alone may not name it.

The thresholds the FDA proposes for generic peptides

For generic peptide drugs, the FDA's current draft says when a peak should be reported and when it should be named. Its July 2026 draft guidance on teriparatide, one of 17 such drafts published that month (read 2026-10-06), lists these steps for "active ingredient-related impurities":

• Report each one present "at a level above 0.1% of the drug substance."
• Identify each one present "at a level above 0.5% of the drug substance."
• For an impurity also found in the brand-name drug, keep it no higher than the brand's level "or 1.0% of the drug substance, whichever is greater."
• For a new impurity not in the brand-name drug, make efforts to bring it "below 1.0% of the drug substance."
• Keep the total no higher than the brand's, summing every impurity above the 0.1 percent reporting threshold.

An impurity above these levels does not end an application. The draft says the applicant should then explain why it would not be expected to affect the product's safety or its efficacy compared with the brand.

Three limits apply to these numbers. The document is marked "Draft - Not for Implementation" and calls itself nonbinding. It governs abbreviated new drug applications, the route for generic medicines. And it replaces an older text: on 28 July 2026 the FDA withdrew its May 2021 guidance on highly purified synthetic peptides, stating it "no longer reflects FDA's current scientific thinking" (FDA statement, read 2026-10-06).

None of this binds a supplier selling peptides for research. It is the drug-application standard.

Why ICH's general thresholds stop short of peptides

The better-known impurity thresholds come from ICH Q3A(R2), and they do not cover peptides. Its preamble says so by name: peptide drug substances "are not covered in this guideline."

Q3A adds a step the peptide drafts handle differently. It defines qualification as gathering data that establishes "the biological safety of an individual impurity" at the level found. The FDA's peptide draft has no qualification number of its own. It asks for a justification instead, case by case.

What one purity number leaves out

A single figure hides the shape of what is missing. Take a hypothetical certificate, not any real product, reporting HPLC purity of 98.0 percent. The other 2.0 percent could be twenty small peaks of 0.1 percent each. It could also be one peak of 2.0 percent. On the FDA draft's scale, that single peak would sit above the 0.5 percent line for identification. If it were a new impurity, it would also sit above the 1.0 percent line the draft asks makers to work below. The certificate reads the same either way.

Identity matters to the people who regulate peptides for a reason. A 2025 study in Frontiers in Immunology (Mattei and colleagues, abstract read 2026-10-06) tested impurities of teriparatide with computer models and lab cell assays. That is the in silico and in vitro lane: nobody received the impurities. In those tests, several impurities came out more immunogenic, meaning more likely to provoke an immune response, than teriparatide itself. That is one compound in one study. It shows why a regulator wants each peak named, not what any research vial holds.

What 126 supplier records show

This publication keeps dated notes on 126 suppliers and their certificates, in ledger/vendors.json. On 2026-10-06, a script searched each record, with its address and web-address fields removed, for nine terms that name an impurity class: related substance, impurity profile, deletion, truncation, deamidation, oxidation (or oxidised), isomer, diastereomer and racemisation. The count was recs.filter(r => terms.some(t => t.test(text(r)))).length, which returned 3.

Read in context, none of the three is about a certificate. Two quote storefront marketing copy that uses the word oxidation. The third uses truncation for IP addresses in a privacy policy. So none of the 126 records notes a certificate that names a related substance.

Two records come closest. A SideChain Analytics certificate in Luxara Labs' library, read 2026-08-25, says its chromatographic purity "bounds peptide-related impurities only." It names the category, not any member of it. An MZ Biolabs certificate for Evolve Peptides, read 2026-08-23, carries a ten-row peak list. The note on it names two peaks: the peptide at 66.99 percent of area and D-mannitol, a sugar, at 6.76 percent, summed into an "Overall Purity" of 73.75. Mannitol is an added ingredient, not a related substance. The note does not record what the other eight peaks were.

Limitations and open questions

The ledger holds notes written between 2026-08-17 and 2026-09-25, not copies of every certificate. A certificate that named an impurity the note left out would be missed. The count describes the ledger, not the market.

The FDA thresholds quoted here are from one draft product-specific guidance and may change before it is final. The withdrawn 2021 guidance could not be retrieved from the FDA site on 2026-10-06, so its thresholds are not quoted; the FDA has said it plans to revise it this year. Three of the papers used here were read as abstracts only. The mass differences between a peptide and its deleted, oxidised or isomeric forms are textbook chemistry, not sourced to a document here.

Where the small peaks exist, they are already on the trace. Until a certificate names them, nobody reading it can.

Sources

1. US Food and Drug Administration. "Draft Guidance on Teriparatide." July 2026 (recommended August 2024; revised December 2025, July 2026). Read 2026-10-06. PSG_021318
2. US Food and Drug Administration. "FDA Publishes Revised Draft Product-Specific Guidances for Certain Generic Peptide Products." 28 July 2026. Read 2026-10-06. FDA statement
3. International Council for Harmonisation. "Impurities in New Drug Substances Q3A(R2)." Step 4 version dated 25 October 2006, published at database.ich.org. Read 2026-10-06.
4. D'Hondt M, Bracke N, Taevernier L, Gevaert B, Verbeke F, Wynendaele E, De Spiegeleer B. "Related impurities in peptide medicines." Journal of Pharmaceutical and Biomedical Analysis, 2014;101:2-30. Abstract read 2026-10-06. PubMed 25044089
5. Bischoff R, Kolbe HV. "Deamidation of asparagine and glutamine residues in proteins and peptides: structural determinants and analytical methodology." Journal of Chromatography B, 1994;662(2):261-278. Abstract read 2026-10-06. PubMed 7719481
6. Mattei AE, Roberts BJ, Lelias S, et al. "Immunogenicity risk assessment of peptide-related impurities identified in generic teriparatide products." Frontiers in Immunology, 2025. Abstract read 2026-10-06. PMC12722964
7. This publication's vendor ledger, ledger/vendors.json: 126 supplier records, searched 2026-10-06. Each vendor observation above carries the date its note was written. Vendors are named here, never linked.