Accepted answer
Nine per cent between two lots of the same product is a process-control statement: on a 10 mg label that is 0.9 mg of difference, which is more than three times the couple of per cent an assay against a good reference standard contributes. So it is a real difference between the lots rather than a disagreement between two measurements — which is the first thing to establish, and it is established by arithmetic rather than by argument. Then the candidate causes, in descending order of likelihood. Residual water: net peptide content excludes it, and a cake that was dried differently reads differently on the same peptide. Counter-ion: acetate and trifluoroacetate have different masses and different stoichiometries, and neither is peptide. Fill variation at the vialling step. And only after those three, an actual difference in the synthesis. Which means the diagnostic request is not "why is lot B low" but a Karl Fischer water figure and a counter-ion figure for both lots. Nine per cent is comfortably within what water plus counter-ion can account for on their own. A supplier who cannot produce those two numbers per lot is telling you what their process control is, whatever the certificate says.
Concretely, thermal history during shipping is different for every vial, so a lot that experienced thermal abuse may have internal variation even if it was originally homogeneous.
Acceptance Sampling by Attributes defines the number of samples you need from a lot to claim a specified quality level at a specified risk — it is in ANSI standard Z1.4.
Mass shifts and what they usually mean
| Δ mass (Da) | Most likely cause | Distinguishing feature |
|---|
| +1 | Deamidation (Asn or Gln) | New peak, slightly earlier retention |
| −17 | Loss of ammonia | Often with deamidation |
| −18 | Dehydration / succinimide | pH-dependent, reversible |
| +16 | Oxidation (Met, Trp) | Earlier retention, light-related |
| −128 | Missing Gln or Lys | Deletion sequence from synthesis |
| 0 | Isomer: racemisation or scrambling | Same mass, shifted retention |
The relevant detail is that the statistical foundation here is well-established, which is why sampling plans from decades ago are still valid.
Lyophilised peptide homogeneity studies show that vial-to-vial variation is usually small but occasionally large, depending on the distribution in the freeze-dryer.
The practical summary: a lot number without a sampling statement is a lot number without meaning.
This should be linked from the help pages. – j_wierzbicki 2 months ago add a comment