This is a continuation of a long topic, addressed by post number rather than by page. Start at post 1.
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.
That is the version I would defend. It is not the version I started with.
Sensible. I would want the same detail before I acted on it either.
The honest answer on trifluoroacetate content is that it depends, and the useful part is the list of what it depends on. Four items, in rough order of how much they matter.
Most people get the first two right and then argue about the fourth.
Checked the trifluoroacetate content claim against the primary source this morning. It survives, with a narrower scope than the version quoted here. Posting the narrower scope.
On trifluoroacetate content I would separate what is worth knowing from what is worth acting on. The first list is long and the second is short, and conflating them is how threads get heated.
Coming back to post #64, because the follow-up matters more than the original answer.
Incomplete deprotection: mass higher by the protecting group mass. Usually markedly later eluting. A synthesis artifact from incomplete removal of protecting groups.
Counterpoint on trifluoroacetate content, offered without confidence: the same observation is consistent with a much duller explanation, and nobody has ruled the dull one out.
Post #67 describes the usual case. This is about the unusual one.
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.
Picking up post #70: that is the part I would want checked first.
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.
I have no interest in any supplier named above.
Careful with the language on trifluoroacetate content. "Not detected" and "not present" are different findings and the first is a statement about the method.
An impurity profile that changes between lots is more informative than the total. A stable profile suggests a controlled process; a shifting one suggests something is varying.
I had written a reply contradicting post #72 and deleted it. Here is what survived.
Two questions I would want answered before drawing anything from the trifluoroacetate content data above: how were the cases selected, and what happened to the ones that dropped out.
Grateful for the specificity. Vague answers to this question are what sent me looking.
Deletion sequences arise from incomplete coupling and are lower by one residue mass. Where they elute depends on the hydrophobicity of the residue that is missing, so they can appear on either side of the main peak.
Oxidation at methionine and tryptophan: adds 16 per oxygen. Usually elutes earlier. Oxidation is common in storage, especially if the solution is exposed to light or if antioxidants are not present.
Trifluoroacetate content was covered in the wiki last year and the page has a review date on it, which is a better starting point than my memory of a thread.
Answering the question post #77 raises rather than the one it answers.
Relative response factors mean impurities are not detected in proportion to how much of them is present. A one per cent peak is not one per cent by mass unless the response factors happen to match.
Everything in post #77 holds. The case it does not cover is the one I have.
The practical version of trifluoroacetate content is three sentences long. The rigorous version is three pages and reaches the same conclusion with the conditions attached.
Narrowing post #81, because the general version has more than one answer.
I would keep trifluoroacetate content and the decision it usually gets used for separate in this thread. They are related and they are not the same question, and merging them is why the last one went badly.
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 content looks different depending on whether you are reading the primary literature or the summaries of it, and the difference is not in our favour.
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.
Worth checking against a second source before it gets quoted onward.
The arithmetic in post #84 is right; the assumption feeding it is the part to check.
Peptide impurities that differ by a single residue are the hardest to resolve and the most likely to be biologically relevant, which is an unfortunate combination.
That is my reading. Someone else read the same page differently and was reasonable.
Post #86 put the caveat in the right place and I want to underline it.
An honest declaration on trifluoroacetate content: I have a prior here and it is strong enough that you should weight what I say downward. Stating it rather than hiding it.
This is the sort of exchange that makes the archive worth searching.
Trifluoroacetate content is worth one more sentence than it usually gets, and the sentence is the one about how the number was arrived at.