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.
I keep a log for mass error in ppm specifically because my memory of it turned out to be systematically wrong in one direction. Six weeks of notes cost nothing and settled it.
Worth separating two things that post #30 runs together.
Two things can be true about mass error in ppm at once: the mechanism is plausible and the evidence for the size of the effect is thin. Most of the argument here is people defending the first against attacks on the second.
Post #32 answers the question as asked. The question underneath it is different.
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.
Not a conclusion. A place to stand while looking for one.
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.
If anyone has run this properly I would rather read that than my own guess.
Picking up post #32: that is the part I would want checked first.
I disagree with the framing of mass error in ppm above, and I think it is a substantive disagreement rather than a terminological one. Setting out why, so it can be checked.
The reasoning depends on an assumption that is doing a lot of work and is never stated. If the assumption holds, the conclusion follows. I do not think it holds generally.
On post #34 — agreed on the reasoning, with one qualification.
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.
One of those cases where knowing the mechanism does not help the decision.
Source for the mass error in ppm figure, since it was asked for. It is in the discussion rather than the abstract, which is why the version circulating is stronger than the paper is.
Reading the surrounding paragraph is worth the two minutes. The authors are more careful than their summarisers.
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.
I would rather be precise about what I do not know than vague about what I do.
Trifluoroacetate adducts are common in material purified with TFA and are one reason a mass spectrum from a peptide can look busier than expected.
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.
I have written this out at length because the short version keeps being misread.
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.
Written quickly, so the reasoning may be tighter than the wording.
Right — I had this wrong and I am glad to have read it before it mattered.
Adding the measurement that post #42 says would settle it.
The arithmetic for a doubly charged species is (M + 2 x 1.00728) / 2, and the analogous expression for higher charge states. Working it through once makes the reported values legible.
That has been true for the cases I have seen and I have not seen many.
I had written a reply contradicting post #44 and deleted it. Here is what survived.
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.
A modest claim, modestly supported.
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 treat that as a working assumption and revisit 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.
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.
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.
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.
Building on post #54 rather than restating it.
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.
The interesting part of this is the exception, and I do not understand the exception.
Post #56 put the caveat in the right place and I want to underline it.
The practical version of mass error in ppm is three sentences long. The rigorous version is three pages and reaches the same conclusion with the conditions attached.
Seconded. It reads as careful rather than confident, which is the right register.
Calibration matters: a high-resolution instrument out of calibration can report mass with ppm error large enough to be uninformative. Check when the instrument was last calibrated before trusting the reported accuracy.
It is worth stating the boring hypothesis before the interesting one.