About the Impurities & related substances category

Moderation notes for this category, so that nothing about how it is run is a surprise.

Topics get moved into and out of here regularly. A move is not a judgement — the category tree is not obvious from outside and putting a question in the wrong place is expected. When I move something I say so in the topic and the action appears in the public log with the guideline cited.

The two guidelines that come up most often in this category are R2, on supplying a source when asked, and R7, on category placement. Neither is used punitively.

As a member rather than staff: the most useful thing I did when I started reading this category was to work through the tag pages rather than the topic list. The topic list shows you what is recent. The tags show you what is settled.

Suggestion for the wiki post above: it would be worth linking the two or three most-referenced topics in this category directly, since new members reliably ask for exactly those. Happy to make the edit myself if nobody objects, with a revision note.

Residual solvents: traces of solvents used in purification. These are usually tested by gas chromatography, not by HPLC. A specification for residual solvents should be stated separately from the purity.

Coming back to post #4, because the follow-up matters more than the original answer.

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 disagree with the reply above, and I think the disagreement is substantive rather than terminological.

The distinction being drawn does not survive when you look at the published data for this specific question. I would be glad to be shown wrong on this, because the version I am arguing against is more convenient.

Disulfide formation: if a peptide contains cysteine, it can form disulfide bonds with itself or with other molecules. Under oxidising conditions multiple species appear. Reducing conditions (like DTT) convert them back.

This follows post #6 rather than contradicting it.

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.

I read post #8 twice before replying, because I had assumed the opposite.

Deamidation at asparagine and glutamine: adds 1 approximately. Frequently appears as a close-eluting pair. It is a chemical modification that occurs during storage.

Incomplete deprotection: mass higher by the protecting group mass. Usually markedly later eluting. A synthesis artifact from incomplete removal of protecting groups.