The case in front of me: 96.8% · a C4 column · orforglipron.
The figures are clear enough; the question is what they mean and what they do not.
I can supply the numbers if the specifics change the answer.
How should I read this, and where are the traps?
Reverse-phase HPLC is the workhorse for peptide purity work, but it is almost universally run under conditions that are not optimal for a peptide of this chain length.
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.
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.
One qualification: the limit of detection on a reversed-phase HPLC is set by the noise on the baseline, which for these molecules is usually in the range of a tenth of one per cent or less, and anything smaller is not reproducibly detectable.
If two labs give different numbers, the method difference is the first hypothesis, not lab quality.
Aggregated, published test results and vendor ratings built from submitted batches. Methodology stated, dataset browsable, no listing fees.
Browse resultsConcretely, start by understanding what the detector is measuring and what that means about how the molecule needs to be prepared and handled before injection.
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.
In practice, temperature affects both the viscosity of the mobile phase and the dynamics of molecular interactions, and a method developed at 25 degrees and run at 40 degrees will not behave identically.
The limitation is that co-elution is invisible — if two species happen to have the same retention time, they will report as a single peak at their combined area.
The practical summary: specify the method, run the same method on every sample you compare, and use orthogonal techniques to confirm the result.
Stated carefully, 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."
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.
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.
The selectivity of a reverse-phase separation depends on the hydrophobicity of the side-chain profile, which is why two peptides can co-elute even if they differ by a residue.
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.
The most important parameter is the one that is almost never specified: the gradient slope during the region where your main peak elutes.
Wider-pore phases — 300 Angstrom rather than 100 Angstrom — have faster mass transfer and narrower peaks for peptides above three kilodaltons, which is almost every peptide you will see.
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.
If two labs give different numbers, the method difference is the first hypothesis, not lab quality.
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.
The 214 nanometre wavelength is chosen because it corresponds to the amide backbone absorption, making response roughly proportional to the number of peptide bonds.
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.
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.
The practical summary: specify the method, run the same method on every sample you compare, and use orthogonal techniques to confirm the result.
edited 7 Oct 2024 by Dr_Colm_Fitzhenry — fixed an arithmetic slip in the third paragraph
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