Answering the narrow version, because the broad one does not have a single answer. Inter-laboratory variation comes from real methodological differences, not sloppiness: which reference standard was used and how it was itself calibrated, the gradient and column, the detection wavelength, and where the integration baseline was drawn. A percentage point or two between competent labs is expected. What is not expected is a large gap, and the usual explanation there is that one report is not of the batch in your hand.

Happy to go further on any of that.

Dr.RaviCardio said:

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

That is correct as far as it goes, and here is where it stops going. One addition: an unstated method makes a report close to uninterpretable. "99% pure" without the technique, the standard and the conditions is a claim, not a measurement.

DoseLogDan said:

I have a certificate reporting 99.2% purity and 6.1mg content on a vial sold as 5mg, and I cannot work out whether those two numbers are consistent or…

This matches mine closely enough to be worth saying so. They are not contradictory, they measure different things, and this is the single most common misreading of a certificate. Purity is a relative area measurement: the main peak as a percentage of total peak area in the chromatogram. Content is an absolute mass measurement against a reference standard. A vial can be 99% pure and contain 6.1mg — pure material, overfilled — or 99% pure and contain 3mg, which is pure material and a short fill. Purity tells you what fraction of what is there is the right molecule; content tells you how much of it there is. You need both, and a certificate with only purity is telling you half the story.

Adding the clinical framing, because it changes how the question reads.

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: 15.3 minutes (consistent with semaglutide reference standard)
Peak purity: 98.4%
Related substances: 0.7% (single impurity at 9.2 minutes — likely a synthesis intermediate)
Mass spec: m/z 4113.6 (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.