This is a continuation of a long topic, addressed by post number rather than by page. Start at post 1.
Post #90 answers the question as asked. The question underneath it is different.
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.
I have deliberately not rounded that, because the rounding is where the argument starts.
I read post #90 twice before replying, because I had assumed the opposite.
Freeze-drying itself does not generate impurities in any significant way. Handling before and after it does, which is why transit conditions belong in the discussion.
The disagreement above is smaller than it looks once the terms are fixed.
Small methodological point on trifluoroacetate content: repeating a measurement is cheap and resolves most of what is being argued about here at no cost to anyone.
Narrowing post #92, because the general version has more than one answer.
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.
The rule of thumb is fine; the edge cases are where it earns its keep.
Trying to state the trifluoroacetate content position in a way that someone who disagrees would recognise as fair, because I do not think the version in this thread passes that test.
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.
The strongest argument against my own position on trifluoroacetate content, stated as well as I can state it, since nobody else has yet.
Deletion sequences (incomplete coupling during synthesis): lower in mass by one residue. Chromatographically they usually elute earlier or later depending on the residue's hydrophobicity. They are the most common impurity in solid-phase synthesis.
If that reads as pedantic, it is, and it has saved me twice.
I think the trifluoroacetate content question is answerable and has not been answered, which is a more optimistic position than most of this thread.
Where I part company with post #104, and it is a narrow parting.
Deamidation at asparagine and glutamine: adds 1 approximately. Frequently appears as a close-eluting pair. It is a chemical modification that occurs during storage.
Where the trifluoroacetate content reasoning breaks down for me is the step from the group result to the individual case. That step is almost never argued for.
A note on scope: what I am saying about trifluoroacetate content applies to the case in the first post and I would not extend it further without checking.
This follows post #106 rather than contradicting it.
The related-substances total is only as informative as the method that generated it. Two per cent by a method that resolves everything is a different statement from two per cent by a method that resolves little.
Second-hand on trifluoroacetate content, so weight it accordingly — someone whose method I trust told me this and I have not verified it myself.
Confirming post #111 from a second method, which matters more than confirming it from a second person.
A supplier that can tell you what its principal impurity is has answered a harder question than one that can tell you its purity, and the answer is more useful.
Not a strong opinion, just a consistent one.
I have three months of notes on trifluoroacetate content and the honest summary is that the trend is real and the week-to-week numbers are noise. I nearly drew the opposite conclusion from the first fortnight.
The bit of trifluoroacetate content that nobody enjoys is that the answer changes depending on what you are trying to decide with it. Say what the decision is and the thread will converge.
Coming back to post #111, because the follow-up matters more than the original answer.
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.
I have written this out at length because the short version keeps being misread.
That last point is the ceiling on what any purity figure can claim. A method that cannot see a species cannot exclude it, and no certificate says which species its method cannot see.
Adding thanks rather than a view. I do not have a view worth the space.
Post #115 put the caveat in the right place and I want to underline it.
The claim about trifluoroacetate content upthread is stronger than its source supports. I have read the source. The source says "associated with" and the post says "causes".
Adding what did not work for me on trifluoroacetate content, since the failures never get written up and they are half the useful information.