Oxidation and deamidation mass shifts, tabulated — setting out what I have, and where I think it stops being reliable.
Reading back through what has been written here about Oxidation and deamidation mass shifts, three questions come up every time and only one has ever been answered properly.
Listing all three, with what I think the state of the answer is for each, so the thread can start further along than the last one did.
Adding the measurement that the opening post 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 looked this up rather than remembered it, which is the right order.
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.
If it helps: the failure mode here is usually boring rather than dramatic.
That is clearer than the version I had in my head. Thank you.
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 #3: that is the part I would want checked first.
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.
Coming back to post #3, because the follow-up matters more than the original answer.
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.
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.
Same conclusion as the reply above, reached differently, which is mildly reassuring.
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.
That holds for the case as described. Change the assumptions and it may not.
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.
I would be interested in a counterexample if anyone has one.
The arithmetic in post #8 is right; the assumption feeding it is the part to check.
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.
Staff rationale: Hidden by community flags. Contained an unredacted laboratory report with identifiers visible (R12). The analytical content has been quoted back into the topic without them.
Trifluoroacetate adducts are common in material purified with TFA and are one reason a mass spectrum from a peptide can look busier than expected.
I would put this at better than even and not much better.
The corresponding entry is in the public moderation log. Hidden posts are never deleted.
Noted, and thank you for writing it out rather than summarising it.
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.
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.
I have no interest in any supplier named above.
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 have deliberately not rounded that, because the rounding is where the argument starts.
I had written a reply contradicting post #15 and deleted it. Here is what survived.
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.
That is the version I would defend. It is not the version I started with.
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.
This is the sort of thing that ought to be settled and apparently is not.
I read post #19 twice before replying, because I had assumed the opposite.
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.
This is the sort of thing the wiki should carry and currently does not.
Worth separating two things that post #19 runs together.
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.
I would put the burden of proof on the interesting explanation, not the dull one.
Post #23 answers the question as asked. The question underneath it is different.
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.
Everything in post #23 holds. The case it does not cover is the one I have.
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.
Narrowing post #27, because the general version has more than one answer.
Trifluoroacetate adducts are common in material purified with TFA and are one reason a mass spectrum from a peptide can look busier than expected.
The confident version of this sentence would be wrong, so here is the hedged one.
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.
Where I would look next, rather than where I would stop.