Named, unnamed and unspecified impurities as regulatory categories — the long version

This follows post #4 rather than contradicting it.

Dimer and higher-order multimers: two or more peptide molecules bonded together. They appear at double the mass and higher. They may or may not separate from the monomer on HPLC depending on the method.

I am not the right person to answer the follow-up to this.

Incomplete deprotection leaves a protecting group attached, raising the mass substantially and usually pushing retention much later. A late-eluting peak on a peptide chromatogram is worth asking about.

It is the kind of thing that is obvious once and never again.

Worth separating two things that post #18 runs together.

The honest reading of a purity figure: it is an upper bound on how much of what the method could see was the intended species, under one integration convention, on one sample.

Truncation products: fragments from incomplete synthesis or from degradation. They elute quite differently from the intact peptide because they are much smaller and have different hydrophobicity. They are usually well separated.

Storage-related degradation and synthesis-related impurity look different on a chromatogram. A growing oxidation peak over time is not a manufacturing finding.

Taking post #51 at face value and following it one step further.

Acetate content: counter-ion content. Trifluoroacetate or acetate from the salt form of the peptide. Affects mass calculations and should be stated on a complete certificate.

Post #63 put the caveat in the right place and I want to underline it.

Where an impurity is identified rather than merely counted, the certificate is telling you the manufacturer has characterised its own process. That is a meaningful difference in documentation quality.

I would put this at better than even and not much better.

Everything in post #77 holds. The case it does not cover is the one I have.

Reporting thresholds matter: below a stated threshold, peaks are usually not reported at all. A clean-looking table may reflect a high threshold rather than a clean synthesis.

Trifluoroacetate is a counter-ion rather than an impurity, and it appears in the mass balance rather than in the chromatogram. Conflating the two accounts for several confused threads here.