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Analytics · Mass spectrometry · continued

MS/MS sequence confirmation: what it costs and when it is worth it — what changed since posts 31–40

This is a continuation of a long topic, addressed by post number rather than by page. Start at post 1.

NT
nl_translatorTL2Translator · NL26 May 2026#31
n.duarte, post #3: Isotope pattern is a check that costs nothing to look at. A species at this molecular weight has a characteristic envelope, and something with the wrong envelope is not what it says it is. Not the whole picture, but the part of it I can speak to. Go to post

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.

1 like in reply to #3 2mo
BD
b.dumitruTL229 May 2026 · edited#32
c.silva, post #27: 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. Go to post

Positional isomers and epimers are mass-identical. Any argument that a mass result rules them out is wrong, and it is the commonest overclaim in this subcategory.

That much is documented. The rest is how I have interpreted it.

0 likes in reply to #27 2mo
KR
k.redgraveTL2Member1 Jun 2026#33

That is consistent with mine, for whatever one more account is worth.

16 likes 2mo
ZS
z.szaboTL23 Jun 2026#34

Post #31 is the version of this I will quote in future. One addition.

Resolution and mass accuracy are different specifications. An instrument can resolve two species and still assign their masses imprecisely, and the reverse is also possible.

The conclusion is tentative; the arithmetic underneath it is not.

6 likes 2mo
CP
citation_peakTL3Regular6 Jun 2026#35

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.

Nothing above should be read as advice about what anyone else should do.

3 likes 2mo
SI
s.ivaturiTL29 Jun 2026#36
z.szabo, post #34: Post #31 is the version of this I will quote in future. One addition. Resolution and mass accuracy are different specifications. An instrument can resolve two species and still assign their masses imprecisely, and the reverse is also possible. The conclusion is tentative; the arithmetic underneath it is not. Go to post

Picking up post #35: that is the part I would want checked first.

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.

That is all I can say without guessing.

0 likes in reply to #34 2mo
C
CFairweatherTL1Member12 Jun 2026#37

I had written a reply contradicting post #35 and deleted it. Here is what survived.

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.

22 likes 2mo
AC
a.cabreraTL215 Jun 2026#38

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.

10 likes 1mo
FP
forest_plotTL3Evidence synthesis18 Jun 2026 · edited#39
c.serrano, post #12: Resolution: "high resolution" commonly means I would put the burden of proof on the interesting explanation, not the dull one. Go to post

Worth separating two things that post #35 runs together.

Calibration state at the time of the run determines whether the ppm figure means anything. A report that states when the instrument was last calibrated is unusual and is worth more than one that does not.

That is what the documentation says. What happens in practice is usually close.

5 likes in reply to #12 1mo
NV
n.villalobosTL220 Jun 2026#40

Thank you for the correction. I would rather find out here than later.

1 like 1mo
This topic was closed 30 days after the last reply. Closing is automatic for quiet topics so that a settled answer does not collect new questions underneath it. If you have a follow-up, open a new topic and link back to this one — that keeps both readable and gives your question its own title.

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