What does co-elution of two species do to an LC-MS purity figure?

The lot number on the vial matches the certificate, which at least rules out the easy problem.

The figures are clear enough; the question is what they mean and what they do not.

I can supply the numbers if the specifics change the answer.

What would I need in addition before this supported a decision?

The relevant limitation is that mass spectrometric response is compound-dependent, so peak areas are not proportional to amount across different species.

Tandem mass spectrometry fragments a selected precursor and reads the b and y ion series, which is what localises a substitution to a specific residue rather than merely detecting it.

Because of that, purity by LC-MS peak area is not comparable to purity by UV area, and quoting one as though it were the other is a recurring source of confusion.

A mass spectrum without the acquisition parameters is a picture rather than a measurement.

Ask for the deconvoluted mass and at least two charge states.

Start with what you want confirmed. Intact mass confirms the molecular formula and nothing about the order of the residues; tandem fragmentation confirms sequence.

Worked example: a peptide of monoisotopic mass 4113.6 daltons appears at m/z 1372.2 for the triply charged species and 1029.4 for the quadruply charged. Two charge states agreeing on the deconvoluted mass is a much stronger identity claim than one.

Ion suppression from co-eluting matrix components can hide a species entirely. A clean-looking total ion chromatogram is weaker evidence than a clean UV trace at the same gradient.

Charge-state deconvolution from electrospray is standard practice and the arithmetic is the same for every peptide; agreement across charge states is the internal check.

Peak areas in mass spectrometry are not proportional to amount across different species and should not be read as if they were.

Mass-neutral substitutions need a digest. Ask for peptide mapping if identity is the question.