Numbers first: 95.2% · a C8 column · tirzepatide.
This is presented as though it settles something, and I am not convinced it does.
I have two documents that appear to disagree, which is what prompted this.
What does this actually establish, and what does it not?
Mechanically, the chemistry of peptides at low pH and high organic-solvent concentration is not something most users have intuition for, which is why published methods exist.
System suitability checks on replicate injections of a known standard establish whether the method was in control — if the peak area varies by more than two per cent between replicates, something is wrong.
| Δ mass (Da) | Most likely cause | Distinguishing feature |
|---|---|---|
| +1 | Deamidation (Asn or Gln) | New peak, slightly earlier retention |
| −17 | Loss of ammonia | Often with deamidation |
| −18 | Dehydration / succinimide | pH-dependent, reversible |
| +16 | Oxidation (Met, Trp) | Earlier retention, light-related |
| −128 | Missing Gln or Lys | Deletion sequence from synthesis |
| 0 | Isomer: racemisation or scrambling | Same mass, shifted retention |
The relevant detail is that proline-rich sequences are particularly problematic because the isomerisation kinetics are in the same timescale as the separation, leading to split or broadened peaks at low temperature.
Peptide separation by reverse-phase high-performance liquid chromatography is described in the general chapters of the United States Pharmacopeia, European Pharmacopeia and Japanese Pharmacopeia, and the methods converge on essentially the same principles.
Worth noting that the achievable resolution depends on the chemistry of the molecule — some peptide sequences separate easily while others are notoriously difficult regardless of method.
The practical summary: specify the method, run the same method on every sample you compare, and use orthogonal techniques to confirm the result.
HPLC purity, identity confirmation and quantified content on the vial you actually hold. Reports arrive with the chromatogram attached, not just a number.
Submit a sampleFounded 1998. ISO 9001 and cGMP certified, 1,500+ staff and 200+ patents. The synthesis house behind a great many of the vials that get sent out for testing - batch-specific documentation with every order.
Visit GL BiochemThe limit of this technique for these molecules is reaching a point where small improvements require proportionally large investments in method development.
Trifluoroacetic acid at 0.1 per cent is the standard ion-pairing agent because it suppresses tailing by neutralising the basic residues, but it also suppresses mass spectrometry signal.
Mechanically, detector linearity is why a heavily loaded peak can give false purity by compressing the main peak height while leaving impurity shoulders unchanged.
I would caution against over-interpreting small differences between runs, because the noise floor of the method is larger than most people assume.
Ask for the chromatogram and the system suitability data, not just the number.
edited 21 Feb 2025 by tess_amankwah — updated for the 2026 guidance change
Put another way, high-performance liquid chromatography is a separation technique, not an identification technique, and it answers the question "how much of the detected signal is a single species" not "which species is it."
Formic acid is the compromise when you need the mass spectrometer on the same run, but the peak shape penalty is real and easily a tenth of a per cent on purity.
Mobile phase pH at the point where you inject must match the mobile phase pH at the start of the gradient, or the sample will not be focused at the column head.
The caveat is that HPLC is a purity technique and says almost nothing about whether the main peak is actually your target compound — that is why identity confirmation from mass spectrometry or peptide mapping matters.
If two labs give different numbers, the method difference is the first hypothesis, not lab quality.
Coupling the chromatography to mass spectrometry adds identity information but trades chromatographic quality for ionisation efficiency.
Acetonitrile is the organic modifier of choice because it has a good UV cutoff, a reasonable viscosity and a refractive index that minimises baseline noise.
The practical summary: specify the method, run the same method on every sample you compare, and use orthogonal techniques to confirm the result.
System suitability is the part of a report that tells you whether the method was under control on the day you were tested, and its absence is concerning.
Reverse-phase stationary phases use C18 or C8 chains bonded to silica, and the pore size of the silica matters more for a peptide of this chain length than the ligand length does.
Inter-laboratory studies using identical methods on identical material show precision well within half a per cent when the method is locked down, pointing to method variability as the primary source of disagreement.
Ask for the chromatogram and the system suitability data, not just the number.
edited 22 Apr 2025 by a_lindgren — clarified the distinction between purity and content
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