Why HPLC and mass spectrometry answer different questions

HPLC separates detected components

A chromatographic purity result is derived from a defined separation and detection method. It can show whether one signal dominates the detected profile and whether secondary peaks are present under those conditions. The result depends on the method, detector, wavelength or response, integration rules, and sample preparation.

That makes the chromatogram and method context important. A percentage without the underlying method and trace does not show how peaks were separated or integrated.

Mass spectrometry contributes identity evidence

Mass spectrometry compares observed mass-to-charge signals with the molecular form expected for the stated compound. It contributes identity evidence, but it does not by itself provide the same impurity profile or area-percent purity result as a chromatographic method.

The most useful certificate keeps the conclusions distinct: identity evidence is reported with its observed and expected signals, while purity is reported with its own method, chromatogram, integration, and acceptance criterion.

Review the methods as an evidence pair

For procurement, the practical question is not which method is better. It is whether the analytical package uses suitable, documented procedures to answer the required identity and purity questions for the offered lot. Method suitability and validation characteristics should be considered in relation to the procedure's intended purpose.