Posting this under the heading it deserves: Oxidation pathways for methionine and tryptophan Everything below is what sits behind that.
Working notes on oxidation pathways for methionine rather than a conclusion. I would rather post the reasoning while it can still be corrected than post the answer once I am committed to it.
Everything below is checkable. Where I have taken a figure from somewhere else I have said where; where I have estimated, I have said that too.
The opening post put the caveat in the right place and I want to underline it.
Two sentences on oxidation pathways for methionine and then I will stop, because the rest is speculation and the thread is better without mine.
What is documented is narrow. What is inferred from it is broad. The gap between them is where every argument here lives.
Narrowing the opening post, because the general version has more than one answer.
Off-target structures: if the sequence synthesis goes wrong, a completely different amino acid can be incorporated. The resulting off-target peptide is a structural isomer with the same mass but a different sequence. No chromatographic purity method detects this without a reference standard.
Adding this to the thread rather than to the wiki, because I am not confident enough for the wiki.
Oxidation pathways for methionine: I would want to see the raw numbers rather than the summary before agreeing. Summaries lose exactly the information that would settle this.
The arithmetic in post #4 is right; the assumption feeding it is the part to check.
Practical experience of oxidation pathways for methionine, offered as one case with the conditions stated, not as a general finding. Conditions first, because they are what make it interpretable.
Saving this. It is the version I will quote when the question comes round again.
The documentation on oxidation pathways for methionine is better than this thread and I say that as someone who has posted in the thread.
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.
I checked the source rather than the summary, and they differ.
The arithmetic in post #10 is right; the assumption feeding it is the part to check.
Careful with the language on oxidation pathways for methionine. "Not detected" and "not present" are different findings and the first is a statement about the method.
The practical version of oxidation pathways for methionine is three sentences long. The rigorous version is three pages and reaches the same conclusion with the conditions attached.
I would keep oxidation pathways for methionine 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.
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.
Having read the whole oxidation pathways for methionine thread before replying: the question in the first post has not actually been answered yet, and three of us have answered a nearby one instead.
Scavengers and cleavage-cocktail residues can persist and appear as small early-eluting peaks. They are process-related rather than sequence-related, which is a useful distinction when reading a profile.
Clear enough that I do not think I have a follow-up, which is unusual.
Picking up post #22: that is the part I would want checked first.
Distinguishing three things in the oxidation pathways for methionine discussion that keep getting used interchangeably: the observation, the proposed mechanism, and the recommendation that gets attached to both.
On post #25 — agreed on the reasoning, with one qualification.
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.
This is where my knowledge stops and I would rather mark the edge than blur it.
What I would tell a new member reading about oxidation pathways for methionine for the first time: the confident posts are not the reliable ones, and the reliable ones are longer.
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.
On oxidation pathways for methionine the community has more anecdote than the confidence in this thread implies, and I include my own contribution in that.