Impurity thresholds are the levels at which an impurity has to be reported, identified or held below a limit. In FDA’s 2026 draft guidance for generic peptide products, impurities above 0.1% are reported and impurities above 0.5% are identified.
A purity figure such as 98% says how much of the chromatogram is the main peak. It does not say what the other 2% is, how many peaks make it up, or whether any single one of them is large.
This study summary explains impurity thresholds from the laboratory side: what the terms mean, what the current FDA numbers are, where peptide impurities come from and how to read the impurity section of a certificate of analysis. It belongs to the study summaries in the article library, which report what a source says and the limits that apply to it.
It covers analytical chemistry and published guidance only and does not describe any use of any compound in people or animals.
What impurity thresholds mean
Every peptide sample contains small amounts of molecules other than the target. Thresholds turn that into a set of decisions: which peaks are counted, which have to be identified, and which levels are acceptable. They are applied to the impurity peaks in a chromatogram, each expressed as a percentage of the main substance.
Reporting threshold
The level above which an impurity must be listed on its own. Peaks below it may still exist but are not reported individually.
Identification threshold
The level above which an impurity must be identified, meaning its structure is established rather than just its size.
Related impurity
An impurity that comes from the peptide itself, such as a shorter sequence, a modified residue or a degradation product. FDA’s term is active ingredient-related impurity.
The 2026 FDA impurity thresholds for peptides
On 28 July 2026 the FDA published 17 revised draft product-specific guidances for generic peptide products, updating its recommendations on impurity thresholds among other areas. The draft guidance on liraglutide (July 2026) is one of them, and sets out the thresholds and controls that may be applied to active ingredient-related impurities.
- Report above 0.1%. Every active ingredient-related impurity above 0.1% of the drug substance is reported.
- Identify above 0.5%. Every active ingredient-related impurity above 0.5% is identified.
- Common impurities have a ceiling. An impurity found in both the generic and the reference product should not exceed the level in the reference product or 1.0%, whichever is greater.
- New impurities should be reduced. Impurities not found in the reference product should be brought below 1.0% through manufacturing and control strategies.
- Totals are compared too. All impurities above 0.1% are summed and reported as a total, which should not exceed the total in the reference product.
The guidance also notes that an impurity above these levels does not by itself rule out an application, but that its potential risks are subject to scientific review and the applicant should justify it.
These are draft, nonbinding recommendations for generic drug applications that refer to specific approved products. They do not govern research materials. They are useful as a published yardstick for what a detailed impurity report looks like, not as a rule that applies to a research vial.
Where peptide impurities come from
A review by D’Hondt and colleagues (2014, Journal of Pharmaceutical and Biomedical Analysis) sorts the impurities most commonly seen in peptide medicines into groups. Most peptides are made by solid-phase peptide synthesis, and many impurities trace back to that process.
From synthesis
- Deletions and insertions. A missing amino acid comes from incomplete deprotection during synthesis. An extra one comes from excess reagent.
- Diastereomers. Deprotection steps can flip the configuration of a residue, giving a molecule with the same sequence and mass but a different shape.
- Adducts and side reactions. Protecting groups left on, or side chains reacting with synthesis reagents, add mass to the peptide.
- Oxidation and aggregates. Oxidised side chains and dimers or larger oligomers were also observed.
- Counter-ions. Trifluoroacetate from synthesis or purification can remain in the final material.
From degradation
The review also lists degradation routes typical of peptides, including beta-elimination, diketopiperazine, pyroglutamate and succinimide formation. Succinimide formation is one route by which an aspartate residue can convert to its beta-aspartyl form, the same kind of change that separated active from inactive material in the original DSIP study.
The authors add that these impurities can affect early functionality studies, possibly leading to erroneous conclusions. An impurity that is invisible in a purity percentage can still change what an experiment appears to show.
Reading impurity numbers on a certificate
A purity percentage is the main peak’s share of the total peak area in one chromatographic method. The impurity section is where the detail sits, and it is worth reading line by line.
- Individual peaks matter more than the total. A sample at 98% purity could carry twenty small impurities or one impurity at 2%, and those are very different materials.
- The reporting threshold sets what you see. If a certificate does not state the threshold it applied, there is no way to know how many smaller peaks were left out.
- Purity is not content. The USP review by McCarthy and colleagues (2023, Pharmaceutical Research) describes a mass balance approach to assigning a value to a peptide, which accounts for everything in the material, not only the main peak. Water, salts and counter-ions do not appear as impurity peaks at all.
- A clean peak can still hide something. A related impurity that co-elutes with the main peak inflates the purity figure. Detecting it takes a second method, as explained in orthogonal identification.
What impurity thresholds do not establish
- A threshold is not a safety statement. Meeting a reporting or identification threshold says how an impurity was handled analytically, not what it does.
- Numbers are method-specific. The same sample can give different impurity profiles on different columns or gradients.
- Sensitivity limits apply. Peaks near the limit of quantitation are less precise, so small differences close to 0.1% should be read with care.
- Research materials are not held to drug guidance. The FDA thresholds describe expectations for specific generic drug applications, not a standard any research supplier is required to meet.
How we separate what a document says from what it is taken to mean is set out in how we write.
Impurity thresholds on a certificate of analysis
A certificate that takes impurity thresholds seriously makes them visible. These are the points to look for.
- Reporting threshold stated, so you know which peaks were counted
- Individual impurity peaks listed with their percentages, not only a total
- Total impurities stated alongside the purity figure
- Larger impurities identified, for example as a deletion, oxidation or truncated sequence
- Chromatogram attached, with the integration of each peak visible
- Identity of the main peak confirmed by mass spectrometry
- Counter-ion, water or peptide content stated, since these never appear as impurity peaks
- Lot number on the certificate identical to the lot on the vial label
Shorter sequences are a common related impurity for any peptide that breaks down in fragments, a point covered for one compound in our TB-500 profile.
- Impurity thresholds decide which impurities are reported, identified and limited
- FDA’s 2026 draft peptide guidance reports above 0.1% and identifies above 0.5%
- Those numbers apply to generic drug applications, not to research materials
- Peptide impurities come from synthesis and from degradation
- A purity percentage hides how the remainder breaks down
Frequently asked questions
It is a level, expressed as a percentage of the main substance, at which an impurity triggers an action. Above the reporting threshold it must be listed individually. Above the identification threshold its structure must be established. Further limits set the maximum acceptable level for a single impurity or for the total.
In its July 2026 draft product-specific guidances for generic peptide products, FDA recommends reporting active ingredient-related impurities above 0.1% and identifying those above 0.5%. Impurities shared with the reference product should not exceed the reference level or 1.0%, whichever is greater, and new impurities should be reduced below 1.0%. These are draft, nonbinding recommendations for specific generic drug applications.
No. They are written for generic drug applications that refer to specific approved products. Research materials are not held to them. They are still a useful published benchmark for how detailed an impurity report can be.
Mainly from synthesis and from degradation. A 2014 review lists deletions, insertions, diastereomers, protection adducts, oxidation, aggregates and leftover counter-ions such as trifluoroacetate from synthesis, and beta-elimination, diketopiperazine, pyroglutamate and succinimide formation from degradation.
The figure alone cannot answer that. It depends on what the remaining 1% is, whether any single impurity is large, which reporting threshold was used, and whether the main peak was confirmed as the right molecule. A certificate that lists individual peaks and confirms identity by mass spectrometry says far more than the percentage does.
Read a COA like an analyst
Members get annotated certificates of analysis that show each impurity peak, its threshold and what it does and does not tell you.
- ✓Full VIP video and document library
- ✓Annotated COAs, research summaries and guides
- ✓New content added regularly
- ✓Approval-based members area
- US Food and Drug Administration, 2026. Draft guidance on liraglutide (product-specific guidance, NDA 022341). Recommended March 2020, revised July 2026. View source
- US Food and Drug Administration, 2026. FDA publishes revised draft product-specific guidances for certain generic peptide products. Drug alerts and statements, 28 July 2026. View source
- D’Hondt M, Bracke N, Taevernier L, Gevaert B, Verbeke F, Wynendaele E, De Spiegeleer B, 2014. Related impurities in peptide medicines. Journal of Pharmaceutical and Biomedical Analysis, 101, 2 to 30. DOI
- McCarthy D, Han Y, Carrick K, Schmidt D, Workman W, Matejtschuk P, Duru C, Atouf F, 2023. Reference standards to support quality of synthetic peptide therapeutics. Pharmaceutical Research, 40, 1317 to 1328. DOI
- 23 Sep 2026: First published.
This article is general educational information about analytical chemistry and published guidance. It is not medical, legal or regulatory advice, and nothing in it describes or recommends the use of any compound in people or animals. Compounds discussed are for Research Use Only: not for human or veterinary use, not for diagnostic use, and not for use as a food, dietary supplement or cosmetic.
