Lab Quality & Testing
HPLC vs Mass Spectrometry: Two Questions, Two Instruments
One tells you how much of the sample is the intended peptide. The other tells you whether that peptide is the right molecule. You need both.
August 23, 2026 · 6 min read · Novanta Research
What HPLC measures
Reverse-phase high performance liquid chromatography separates components of a sample by how strongly they interact with a hydrophobic stationary phase as a solvent gradient runs through the column. Each component leaves the column at a characteristic retention time and produces a peak.
Purity is calculated as the area of the main peak divided by the total peak area, expressed as a percentage. Crucially, this is a relative measure of everything the detector can see — it says nothing about the identity of the main peak.
What mass spectrometry measures
Mass spectrometry ionises the sample and measures mass-to-charge ratios. For a peptide, the observed mass should match the mass calculated from the sequence within a tight tolerance.
High-resolution instruments can resolve compositions that differ by fractions of a dalton, which is how truncation products, oxidations and incorrect residues are caught.
Why one without the other fails
A pure sample of the wrong molecule passes HPLC. A correct mass reading on a badly contaminated sample passes MS. Only the combination establishes that the vial contains the intended sequence at the stated purity.
That is why every Novanta lot carries both, from an independent laboratory, with the raw traces attached.
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For laboratory and research use only. Not for human or veterinary consumption. Novanta Research is not a compounding pharmacy and nothing in this article is medical advice or a claim that any compound diagnoses, treats, cures or prevents any condition.