What is mass spectrometry used for?

A purity figure for the wrong compound is worse than no figure, because it looks like reassurance. Mass spectrometry is the check that prevents that: the measured mass is compared against the mass calculated from the intended sequence.

It also confirms specific structural features, because each shifts the expected mass in a predictable way. A C-terminal amide, as on sermorelin. An N-terminal acetyl group, as on thymosin alpha-1 and SNAP-8. An acyl modification, as the trans-3-hexenoyl group on tesamorelin. A ring closure in a cyclic peptide such as melanotan II or PT-141.

For that reason identity and purity are reported together on every certificate. Neither is sufficient alone.

What a mass result can and cannot distinguish

Mass is highly discriminating but not absolutely so, and the limits are worth knowing. Two peptides with the same amino acid composition in a different order have identical masses, so mass alone cannot separate a correct sequence from a scrambled one. Leucine and isoleucine are structural isomers with the same mass. Sequence-level confirmation requires fragmentation — MS/MS — rather than a single mass measurement.

In practice this is a small gap, because a synthesis that assembled the right residues in the wrong order is a far less likely failure than one that dropped a residue or left a protecting group in place. Both of those change the mass, and both are what the measurement is looking for.

The observed value on a certificate may also differ slightly from the calculated one depending on whether the figure is monoisotopic or average mass, and on the charge state observed. A result within a few tenths of a mass unit of the calculated value is a confirmation, not a discrepancy.