Mass spectrometry (MS)

Mass spectrometry ionises a sample and measures the mass-to-charge ratio of the ions produced. Because every peptide sequence has a specific molecular weight, a mass spectrum that shows the expected mass is strong evidence that the material is the intended compound. It is the identity test that pairs with the purity test from HPLC: HPLC says how much of the sample is one thing, mass spectrometry says what that thing is.

A certificate of analysis will usually quote an observed mass alongside the theoretical mass calculated from the sequence, and the two should agree within a small tolerance. For a peptide with a disulfide bridge, the observed mass is two units lower than the linear sequence because two hydrogens are lost when the bridge forms, so a correct spectrum also confirms the bridge is present. Peptides supplied as salts show the free peptide's mass, since the counter-ion separates during ionisation.

Mass spectrometry does not measure quantity or purity on its own, and a certificate that shows only a mass spectrum without HPLC, or only HPLC without a mass, is incomplete. The COA guide walks through both.