The confident answers on residual solvents and scavengers and the well-sourced answers are not the same answers, which is the most useful thing I have learned reading this category.
On the subject in the title: Residual solvents and scavengers: what is looked for Working notes rather than a conclusion.
I would like to know what people here actually do about residual solvents and scavengers, as distinct from what is usually recommended. Those have diverged in every other subject I have looked at closely.
Mine is below, with the reasoning, including the parts I am not confident about.
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.
The reasoning is more useful than the number, which is why I have shown it.
Adding the boring version of residual solvents and scavengers, because the interesting version keeps getting posted and the boring one is usually right.
Check the ordinary explanations, in order, and stop when one of them accounts for what you are seeing. Most of the time the second one does.
This follows post #6 rather than contradicting it.
Comparing impurity profiles across suppliers is much more informative than comparing purity figures, and almost nobody has the documents to do it.
I would be glad to be shown a cleaner way of putting this.
Worth separating two things that post #4 runs together.
Worth separating residual solvents and scavengers as a question about the compound from residual solvents and scavengers as a question about the documentation. They get answered by different people and only one of them is answerable here.
That is a fair summary of where the discussion has got to.
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.
Truncation products are substantially lower in mass and usually well separated chromatographically, which makes them the easiest class to see and the least likely to be missed.
This is the first time the answer has come with its own limits attached. Appreciated.
Adding the measurement that post #11 says would settle it.
What I can speak to on residual solvents and scavengers is narrow, so I will keep it narrow rather than generalising from it. Beyond that boundary I do not know.
Summarising the residual solvents and scavengers thread so far, since it is long and the answer is buried: the first reply has the method, the fourth has the correction to it, and the rest is people agreeing at length.
Deamidation at asparagine or glutamine adds approximately one dalton and frequently produces a close-eluting pair. It is the impurity most likely to be integrated into the main peak by accident.
This is the sort of thing the wiki should carry and currently does not.
Answering the question post #15 raises rather than the one it answers.
I would call the community position on residual solvents and scavengers likely rather than established, and I would be comfortable defending that hedge.
The arithmetic in post #15 is right; the assumption feeding it is the part to check.
Residual solvents and scavengers is a question about a distribution, not about a value, and treating it as a value is what produces the confident wrong answers.
I read post #15 twice before replying, because I had assumed the opposite.
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.
Adding it because I spent an afternoon working it out and nobody should have to twice.
Post #19 answers the question as asked. The question underneath it is different.
A note on how residual solvents and scavengers gets discussed rather than on residual solvents and scavengers itself: the confident posts get the replies and the careful ones get ignored, and the careful ones have been right more often.
On residual solvents and scavengers: the maintained page in the documentation commons covers the general case with citations and a review date, which is more reliable than any reply here including this one.
Aggregates may be a multiple of the monomer mass and may not elute at all under a standard method. What does not come off the column does not appear in the area percentage.
Adding a source would improve this post and I do not have one to hand.
Reading rather than contributing, but this is the most useful thread I have found on it.
The question underneath residual solvents and scavengers is usually "how would I tell?" rather than "what is true?", and that one has a method attached to it.
Write down what you would expect to see under each hypothesis before you collect anything. If they predict the same observation, collecting it will not help.
| Topic | Participants | Replies | Views | Activity |
|---|---|---|---|---|
|
Impurity thresholds: where the common numbers come from
Impurity thresholds: where the common numbers come from — setting out what I have, and where I think it stops being reliable. I have spent a fortnight trying to pin impurity thresholds down and I want to set…
|
+11 | 15 | 825 | 2d |
|
A rising related-substance total over six months: degradation or method drift?
Asking directly, because I could not find a straight answer: A rising related-substance total over six months: degradation or method drift? Rising related-substance — I have the observation and I do not trust…
|
+37 | 42 | 37k | 23mo |
|
Second pass at: Where impurities in solid-phase peptide synthesis come from
Posting this under the heading it deserves: Second pass at: Where impurities in solid-phase peptide synthesis come from Everything below is what sits behind that. Working notes on impurities in solid-phase…
|
+47 | 51 | 3.3k | 5mo |
|
Coming back to: Oxidation pathways for methionine and tryptophan
Oxidation pathways for methionine and tryptophan Writing it up because I had to work it out twice and would rather nobody else did. Reading back through what has been written here about Oxidation pathways for…
|
+1 | 5 | 36k | 15mo |
|
Trifluoroacetate content and its consequences
Trifluoroacetate content and its consequences — setting out what I have, and where I think it stops being reliable. What changes if the standard account of trifluoroacetate content is wrong? I ask because I…
|
+123 | 134 | 31k | 5mo |
| Topic | Participants | Replies | Views | Activity |
|---|---|---|---|---|
|
Blinding yourself: practical methods and their limits
On the subject in the title: Blinding yourself: practical methods and their limits Working notes rather than a conclusion. A methods question rather than a substantive one, about blinding yourself. Everyone…
|
+40 | 44 | 33k | 5d |
|
Second pass at: Isotonicity and what happens when you get it wrong
Second pass at: Isotonicity and what happens when you get it wrong — setting out what I have, and where I think it stops being reliable. Something about Isotonicity does not reconcile and I would like a…
|
+1 | 5 | 2.6k | 11mo |
|
Why most self-reports here are not experiments, and that is fine
Why most self-reports here are not experiments, and that is fine — that is the question, and I have not found it answered plainly anywhere I have looked. A question about what a single-person experiment can…
|
2 | 46k | 11mo | |
|
Washout with a one-week half-life: the arithmetic
Washout with a one-week half-life: the arithmetic — setting out what I have, and where I think it stops being reliable. Washout: setting out the arithmetic in full, because I have had to do it twice and I…
|
+90 | 96 | 44k | 20mo |
|
Revisiting: Why I ask for the gradient before I discuss the number
Posting this under the heading it deserves: Revisiting: Why I ask for the gradient before I discuss the number Everything below is what sits behind that. I would like to understand what this number means…
|
+15 | 19 | 43k | 10mo |