Mass spectrometry and identity confirmation

Identity is the answer to the question "is this material the compound named on the label?" It is a yes-or-no result, not a percentage. A laboratory confirms identity by measuring a property of the material that is characteristic of the named compound and checking it against the expected value. For peptides and small molecules the property most commonly used is molecular mass, and the instrument that measures it is a mass spectrometer.

A mass spectrometer ionises the sample, then sorts the ions by their mass-to-charge ratio and records how many arrive at each value. The output is a mass spectrum: a set of peaks, each at a specific mass-to-charge ratio. For a pure compound, the dominant peaks correspond to the intact molecule carrying one or more charges.

Every compound has a calculable molecular mass, determined by its formula. If the observed mass matches the calculated mass for the named compound within the instrument's tolerance, identity is confirmed. If it does not, the material is not what the label says, whatever the purity figure looks like.

An HPLC chromatogram with one clean peak tells you the sample is homogeneous. It does not tell you what the peak is. A wrong compound, a truncated sequence or a mislabelled vial can each give a beautiful chromatogram. That is why what HPLC purity actually measures is a different question from what the material is, and why a certificate should report both. A lot that does not meet specification on either is never listed here.

On the certificate, look for the method named against the identity result — mass spectrometry — and the statement that the observed mass is consistent with the expected mass. Some certificates print the expected and observed values; some print a pass statement. Either way, the thing to check is that the result refers to the compound named at the top of the certificate and to the lot number printed on your vial. A certificate is only ever about one lot; see lot numbers and lot discipline.

Both results on our certificates come from a third-party laboratory with no commercial interest in the outcome. That matters more for identity than for almost anything else: a supplier confirming its own labels is a circular check. An independent laboratory confirming that the material in a lot has the mass of the compound on the label is the check that breaks the circle. We explain why we set it up this way in why independent third-party testing matters.

Identity could in principle be confirmed by other properties — retention time, an absorbance spectrum, elemental composition — and laboratories sometimes use several. Molecular mass is the standard first line for peptides and small molecules because it is calculable exactly from the formula, measurable precisely, and hard to fake by accident: a wrong molecule with the right mass is a coincidence that happens rarely, and a truncated or modified version of the right molecule has a different mass by a predictable amount. That makes the mass spectrum a discriminating test rather than a permissive one. It is the reason the identity line on a certificate names mass spectrometry as the method, and why the quality page puts identity by mass spectrometry beside purity by HPLC as the two results that every lot must pass before it is listed. A certificate for a lot you hold is sent the same business day on request to support.

A confirmed identity says the lot was the named compound at the time of testing. It says nothing about how the material behaves in any application, and nothing we publish describes one. It also says nothing about the material after it has left the laboratory — that is a matter of storage and handling, which are the researcher's responsibility and are covered on the certificate under storage conditions. All material is supplied for in-vitro laboratory research only, as set out on the research use only page.