Reference library

Confirming identity by mass spectrometry

Research use only — not for human or animal consumption

Mass spectrometry confirms a compound's identity by measuring its molecular mass. The instrument ionises the sample and measures the mass-to-charge ratio of the ions produced. If the observed mass matches the expected mass for the target compound, that supports its identity — answering a different question from purity, which HPLC measures.

Identity vs purity — two different questions

Purity asks how much of the sample is the target. Identity asks whether the target is what it claims to be. A sample can be highly pure and still be the wrong molecule; conversely, the right molecule can be present at modest purity. Reliable characterisation needs both, which is why a good certificate of analysis pairs HPLC purity with mass-spec identity.

How mass spectrometry works, briefly

Ionisation — the molecules are given a charge (for peptides, soft methods such as electrospray ionisation are common because they keep the molecule intact).
Mass analysis — the instrument separates ions by their mass-to-charge ratio (m/z).
Detection — it records the abundance of each ion, producing a spectrum.

The result is compared with the expected mass calculated from the compound's molecular formula. A match within the instrument's accuracy supports the assigned identity. For larger molecules the spectrum may show several charge states; these resolve to a consistent molecular mass.

What a match does and doesn't prove

A correct molecular mass is strong evidence for identity, but mass alone cannot always distinguish molecules of the same mass (isomers, for example). That is why mass-spec identity is read together with the HPLC profile and, where relevant, sequence-level information. The combination is far more informative than any single test.

Reading identity on a COA

On a certificate of analysis, look for:

the expected (theoretical) mass;
the observed mass; and
a statement that the two are consistent within tolerance.

If a certificate reports purity but says nothing about identity, you only have half the picture.

How Amino Society confirms identity

Every batch we release is independently analysed for both identity and purity. Mass spectrometry confirms the molecular mass against the expected value, and HPLC confirms the purity; both results are recorded on the batch COA tied to your lot code. We list a compound as in stock only once that documentation is complete.