97.6 per cent is a statement about area, and the other 2.4 per cent is everything the detector saw and did not assign to your peak. Read it as 97.6 of every 100 units of peak area at whatever wavelength was used, not as 97.6 per cent of the mass in the vial. With the date of analysis attached you can at least see how the figure was produced, which is the difference between a measurement and a claim. What it still does not tell you is content: how many milligrams are actually there.
The part that matters: the single most important distinction is between what purity measures — the fraction of detected material that is your target — and what you actually want to know — how much of the material in the vial is your target.
Sample solvent strength affects peak shape — if you inject in strong solvent on a gradient starting in weak solvent, the solvent peak can distort your main peak or create a false shoulder.
What each test answers
| Test | Answers | Does NOT answer |
|---|
| RP-HPLC, area % | What fraction of detected material is the target | How much target is present |
| Quantified content | Milligrams of peptide per vial | What the impurities are |
| ESI-MS identity | Whether the molecular weight matches | Purity, or isomeric substitution |
| Peptide mapping | Sequence, localised to a fragment | Quantity |
| Karl Fischer | Water content of the solid | Solvent content |
| LAL endotoxin | Pyrogen load in EU/mg | Sterility |
| Sterility test | Growth in defined media over 14 days | Endotoxin, or bioburden count |
Buffer versus acid in the mobile phase changes the ionisation state of basic and acidic residues, shifting retention and selectivity — same vial, potentially different separation.
The Arrhenius relationship for peptide degradation is the basis of accelerated stability testing and also governs how quickly methods drift with temperature.
Worth noting that method standardisation is poor in the research-grade space compared to pharmaceutical work, so identical-looking methods can produce different results.
If you are ranking vendors, specify a method and have all samples tested at the same place.