The particulars: MKM · ecnoglutide.
I have the document in front of me and I can read the numbers. What I cannot do is interpret them.
I am reasonably comfortable with statistics and completely uncomfortable with chromatography, or vice versa.
What is the correct interpretation, and what is the common misreading?
Answer first: the counter-ion is part of the mass you paid for and none of the peptide you wanted, and it can run to several per cent or more.
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.
In practice, 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.
Ion chromatography and fluorine NMR are the accepted quantitative methods for trifluoroacetate, and neither is a chromatographic purity method.
Water plus counter-ion is why gross mass and peptide mass differ.
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