What counter-ion should I expect on a BCH cagrilintide lot?

The specifics, since they change the answer: BCH · cagrilintide.

I have read the primary source rather than the summary, which has left me with more questions.

I understand the headline. I do not understand the footnotes, and the footnotes look important.

How should I read this, and where are the traps?

Acetate is generally preferred to trifluoroacetate for biological work, which is why the exchange is done at all.

Net peptide content — the fraction of gross mass that is the peptide itself — is the figure that folds water and counter-ion together and is what you should ask for if you ask for anything.

Stated carefully, the number of basic residues drives counter-ion load, because each protonated basic site pairs with one counter-ion. A sequence with several lysines and arginines carries proportionally more.

The caveat is that a purity figure is completely blind to counter-ion content, and the two are routinely conflated.

Count the basic residues and you can estimate the counter-ion load.

Start with which counter-ion the process produced, because trifluoroacetate from reverse-phase purification and acetate from a salt exchange behave differently and are quantified differently.

Peptides purified by reverse-phase chromatography with a trifluoroacetic acid mobile phase are isolated as trifluoroacetate salts. The trifluoroacetate content depends on the number of basic residues and can run from a few per cent to well over ten by mass on a heavily basic sequence.

Put another way, a supplier who reports both water and counter-ion has given you everything needed to reconcile the vial, and on this site that is a very short list.

Trifluoroacetate effects in cell culture are documented and are the technical basis for salt exchange to acetate.

Trifluoroacetate unless a deliberate exchange was done. Ask which.

Put another way, a net-peptide-content figure already accounts for it, which is why net content is the number worth asking for.

Worked reconciliation: a 10 mg vial at four per cent water and eight per cent trifluoroacetate contains 10.0 × 0.88 = 8.8 mg of peptide, a twelve per cent shortfall against label with a perfectly clean purity figure.

Counter-ion content scales with the number of basic residues, following directly from charge balance.

Ask for net peptide content. It folds water and counter-ion into one usable number.

The short version: peptides are supplied as salts, the salt is real mass, and neither purity nor a chromatogram will tell you how much of it there is.

Quantification differs by ion: trifluoroacetate by ion chromatography or by fluorine nuclear magnetic resonance, acetate by ion chromatography or by capillary electrophoresis. Neither shows up on a UV chromatogram.

Peptides from reverse-phase purification with trifluoroacetic acid mobile phases are isolated as trifluoroacetate salts, which is standard synthesis practice.

Water plus counter-ion is why gross mass and peptide mass differ.