Counter-ion content and its effect on measured mass posts 91–109

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.

Not the whole picture, but the part of it I can speak to.

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.

Take the reasoning and check the arithmetic; I do not always get it right.

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.

If the premise is wrong, everything after it is decoration.

Post #91 is right about the mechanism and I think understates the practical bit.

Counter-ion 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.

Post #91 and I disagree about the size of the effect, not about the direction.

Counter-ion content sits at the boundary between what this community can usefully discuss and what it cannot, and I think it falls on the discussable side, narrowly.

Mass accuracy is expressed in parts per million. It is the difference between observed and theoretical mass divided by theoretical mass, multiplied by a million. A high-resolution instrument in good calibration achieves low single-digit ppm on a peptide of this size.

That is the shape of it. The detail is where I would expect to be corrected.

Noted, and thank you for writing it out rather than summarising it.

Common adducts: sodium adds ≈22, potassium adds ≈38 compared to hydrogen. A [M+Na]+ peak is common and its mass is predictable from the base mass.

I would rather post the uncertainty than round it away.

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).

Adding the measurement that post #99 says would settle it.

Tandem mass spectrometry: MS/MS fragments the molecular ion and uses fragment masses to confirm identity and detect modifications. A simple identity confirmation by LC-MS does not address post-translational modifications or impurities with the same or very close mass.

I had written a reply contradicting post #99 and deleted it. Here is what survived.

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.

Resolution: "high resolution" commonly means <5 ppm across the mass range. Unit-resolution instruments achieve ±1 Da at best and cannot distinguish two species differing by less than 1 Da in total mass.

The interesting part of this is the exception, and I do not understand the exception.

Deamidation adds approximately one dalton and produces a species that frequently elutes very close to the parent. It is the hardest common impurity to see chromatographically and the easiest to see by mass.

If that reads as pedantic, it is, and it has saved me twice.

Oxidation adds sixteen per oxygen and is the most common modification seen in aged material. Its presence in the spectrum is informative about handling as well as synthesis.

A modest claim, modestly supported.