Purity tells you how much of a sample is one component. Identity tells you which component that is. They are answered by different instruments, and a certificate reporting only one of them has told you half of what you need.
How the measurement works. A mass spectrometer ionises the sample, accelerates the resulting ions through an electric or magnetic field, and measures their mass-to-charge ratio. For a peptide of known sequence, the theoretical mass is arithmetic — the sum of its residues, less the water lost at each bond formed. So the test is a direct comparison: the observed mass either falls within the method’s tolerance of the calculated mass, or it does not.
Why a spectrum shows several peaks. Electrospray ionisation, the usual technique for peptides, typically produces a series of multiply-charged ions rather than a single one. The neutral mass is reconstructed from that charge-state envelope. A spectrum showing several related peaks is normal and is not evidence of impurity.
LC-MS: separating and identifying in one run. Coupling liquid chromatography to a mass spectrometer answers a question neither instrument answers alone. Chromatography alone reports that an impurity peak is 0.8% of the total area; it cannot say what the impurity is. To an ultraviolet detector, a truncated sequence, a deletion product, an oxidised residue and an entirely unrelated contaminant are all simply “a peak”. By mass they are distinguishable — and the distinction matters, because those four findings have very different implications for the material.
What a mass match cannot establish. Mass is not sequence. Two peptides built from the same residues in a different order have the same mass. Some substitutions are effectively invisible to a mass measurement — an isomeric swap changes the arrangement without changing the total. So “identity confirmed by MS” is a statement that the observed mass matched the expected mass, which is strong evidence and not the same thing as having read the sequence.
What would establish sequence. Tandem mass spectrometry fragments the peptide and measures the fragments, so the sequence can be reconstructed from the mass differences between them. Edman degradation reads residues from the N-terminus chemically. Either is a materially stronger identity claim than an intact-mass match, and either should be described as what it is rather than folded into the same phrase.
Quantitation is a separate limitation. Different molecules ionise with different efficiency, so signal intensity is not a reliable proxy for how much of something is present unless the method has been calibrated against a matched reference standard. Mass spectrometry is excellent at answering “what is this” and needs careful method design to answer “how much of it is there”.
Why identity failure ends a lot. An out-of-specification purity result can have an assignable laboratory cause and be legitimately re-run. A mass that does not match the expected mass is not a measurement problem to investigate — it means the material is not what it was labelled as. There is no second test that fixes that.