This is a continuation of a long topic, addressed by post number rather than by page. Start at post 1 · go to the accepted answer.
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.
Anyone who has looked at this more carefully, please correct the record.
Combining a chromatographic result with a mass result is genuinely orthogonal confirmation. Either alone leaves a specific class of problem invisible, and the two classes do not overlap much.
That has held every time I have looked, which is not the same as always.
Useful. I had the fact and not the reason, which turns out to be the important half.
Post #61 describes the usual case. This is about the unusual one.
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.
That holds under the stated conditions and I have stated them.
Sample preparation for mass spectrometry can itself introduce modifications, particularly oxidation. A finding at trace level may be telling you about the preparation rather than the material.
Same conclusion as the reply above, reached differently, which is mildly reassuring.
I would be cautious about generalising from the distinguishing a deletion sequence example above. It is a good example. It is one example.
A mass match establishes that the measured mass is consistent with the proposed composition. It does not establish purity, sequence order, or the absence of an isomer, and all three are frequently claimed from it.
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.
Adding the measurement that post #68 says would settle it.
Trifluoroacetate adducts are common in material purified with TFA and are one reason a mass spectrum from a peptide can look busier than expected.
That is where I would start, not where I would stop.
Post #70 describes the usual case. This is about the unusual one.
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.
Happy to be the one who is wrong here if it settles the question.
Thank you for the correction. I would rather find out here than later.
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.
On post #79 — agreed on the reasoning, with one qualification.
Summarising the distinguishing a deletion sequence 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.
Picking up post #79: that is the part I would want checked first.
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.
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.
Happy to expand any of that if it is the useful part.
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.
Worth checking against a second source before it gets quoted onward.
Reading back through, this was answered upthread and I missed it. My fault.
This follows post #83 rather than contradicting it.
An acylated peptide has a mass that reflects the modification, so comparing against the mass of the unmodified backbone gives a mismatch that is not an error.
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.
That is all the detail I have. Someone else will have more.
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.
This is the sort of thing that ought to be settled and apparently is not.
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 have left out the parts I could not verify.