Why mass spectrometry cannot tell you about an epimer

Why mass spectrometry cannot tell you about an epimer I have a specific reason for asking rather than idle curiosity, and the context is below.

I have spent a fortnight trying to pin mass spectrometry down and I want to set out where I have got to, because I suspect the honest answer is duller than the thread this will produce.

What I have: a consistent observation across a small number of cases, collected the same way each time. What I do not have: any controlled comparison, or any reason to think my cases are representative.

The specific question is whether the pattern survives once the obvious confounder is removed. I cannot remove it with what I have.

Adducts — sodium and potassium especially — shift the observed mass in predictable increments. A report showing an unexplained plus twenty-two is usually showing you a sodium adduct.

Two people can read the same figure differently here and both be reasonable.

Answering the question the opening post raises rather than the one it answers.

Mass error in parts per million is (observed minus theoretical) divided by theoretical, times a million. On a high-resolution instrument a low single-digit figure is unremarkable and expected.

What mass accuracy establishes: the measured mass is consistent with a specific composition. What it does not establish: purity, sequence order, stereochemistry, or the absence of an isobaric species. Every one of those requires something else.

Quantitation by MS: most quantitation is done by LC-UV detection at 214 nm, not by MS, because extinction coefficients are better known. MS can quantify if an internal standard is used but that requires preparation.

It took me longer than it should have to see that.

Everything in post #6 holds. The case it does not cover is the one I have.

Purity and identity are different questions: LC-MS establishes that the species at a retention time has the expected mass. It does not establish how much of the sample is that species (that is what LC-UV purity answers).

One of those cases where knowing the mechanism does not help the decision.

Adding a note of thanks rather than an opinion. I did not know most of that.

Coming back to post #6, because the follow-up matters more than the original answer.

Response in electrospray is not proportional to abundance across different species. Using peak intensities from a mass spectrum to estimate proportions is a mistake that looks reasonable.

Monoisotopic and average mass are different numbers and both appear on documents. At this molecular weight the difference is a few daltons, which is more than the tolerance being claimed.

Picking up post #10: that is the part I would want checked first.

The thing about mass spectrometry that took me longest to accept is that a plausible mechanism is not evidence of an effect. It is a reason to look, not a result.

Tandem mass spectrometry with fragmentation gives sequence information that intact mass cannot. It is the analysis that would actually confirm identity, and it is rarely supplied.

I would rather post the uncertainty than round it away.

For a compound with no reference standard in circulation, an observed mass is much more useful than an assertion of agreement with a theoretical value nobody can check.

I had written a reply contradicting post #12 and deleted it. Here is what survived.

The honest summary of what a mass result buys you: it narrows the field of what the material could be, considerably. It never closes it, and no certificate should be read as though it had.