Lab Quality & Testing
LC-MS: Confirming Peptide Identity in One Run
Coupling chromatography to a mass spectrometer answers separation and identity questions simultaneously — and catches co-eluting impurities a UV trace hides.
August 21, 2026 · 5 min read · Novanta Research
How the coupling works
In LC-MS the effluent from the chromatography column flows directly into the ion source of a mass spectrometer. Every point on the chromatogram therefore has a mass spectrum attached to it.
That means you can ask not only how big a peak is but what is in it — including whether two different species are hiding under a single UV peak.
Charge states and deconvolution
Electrospray ionisation typically produces multiply charged ions, so a single peptide appears as a series of peaks at different mass-to-charge ratios. Software deconvolutes that series into one neutral mass, which is the number compared against the theoretical value.
A clean deconvoluted spectrum with a single dominant mass is strong evidence of a homogeneous product.
Common findings
Recurring impurities include deletion sequences missing a residue, oxidation adding sixteen daltons at methionine, and incomplete removal of protecting groups from synthesis. Each has a characteristic mass shift, which is why identity work is diagnostic rather than merely confirmatory.
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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.