nick_SD_fit said:

Inter-laboratory variation comes from real methodological differences, not sloppiness: which reference standard was used and how it was itself…

Mass spectrometry confirmation for certificates of analysis: beyond HPLC purity, mass spec tells you the molecule's exact molecular weight. This confirms identity — not just purity.

Why this matters: HPLC can show you a "pure" compound, but if it's pure of the WRONG compound, purity is meaningless. Mass spec at m/z 4113.58 Da confirms it's actually semaglutide. My Janoshik report includes both HPLC and mass spec.

If your testing provider only offers HPLC, consider upgrading to include mass spec for at least your first batch from a new vendor.

A narrower follow-up, since the general answer is now clear:

Whether a purity figure and a content figure can disagree without one of them being wrong?

DanielChem_CHI said:

Mass spectrometry confirmation for certificates of analysis: beyond HPLC purity, mass spec tells you the molecule's exact molecular weight.

My HPLC chromatogram analysis for certificates of analysis — I sent my batch to Janoshik and here's what the results showed:

Main peak retention time: 16.3 minutes (consistent with semaglutide reference standard)
Peak purity: 99.5%
Related substances: 0.8% (single impurity at 10.3 minutes — likely a synthesis intermediate)
Mass spec: m/z 4113.5 (matches expected molecular weight)

This is a clean result. The mass spec confirmation is particularly important — it proves the molecule is actually semaglutide and not a substitution.

OP back with an update, since a thread like this is useless without one.

Purity and content being different measurements was the piece I was missing. The vial was overfilled and pure, which is a very different problem from the one I thought I had.

Dr.LipidDallas said:

My HPLC chromatogram analysis for certificates of analysis — I sent my batch to Janoshik and here's what the results showed: Main peak retention time:…

Agreed, and mass spec answers a question purity does not: identity. High purity tells you one thing dominates the chromatogram, not that it is the molecule you ordered. A mass within about a dalton of expected is the identity check.