Distinguishing a deletion sequence by mass alone posts 91–120

Confirming post #104 from a second method, which matters more than confirming it from a second person.

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.

That is the version I use. It may not be the version that is correct.

I had written a reply contradicting post #102 and deleted it. Here is what survived.

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.

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.

Distinguishing a deletion sequence is worth one more sentence than it usually gets, and the sentence is the one about how the number was arrived at.

Where the distinguishing a deletion sequence reasoning breaks down for me is the step from the group result to the individual case. That step is almost never argued for.

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.

That is the practical version. The rigorous version is longer and says the same thing.

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.

Post #109 is right about the mechanism and I think understates the practical bit.

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.

Worth separating two things that post #109 runs together.

The claim about distinguishing a deletion sequence upthread is stronger than its source supports. I have read the source. The source says "associated with" and the post says "causes".

This is the sort of exchange that makes the archive worth searching.

I had written a reply contradicting post #113 and deleted it. Here is what survived.

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.

It cost nothing to check and would have cost something not to.

Confirming post #113 from a second method, which matters more than confirming it from a second person.

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.

It reads as pedantry until the day it does not.

Something worth flagging about distinguishing a deletion sequence: the strongest-sounding claims in this thread are the ones with no source attached, which is the usual pattern and not a coincidence.

I have three months of notes on distinguishing a deletion sequence and the honest summary is that the trend is real and the week-to-week numbers are noise. I nearly drew the opposite conclusion from the first fortnight.

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.

I would want to see it done twice before believing it once.

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.

This has been discussed before and I could not find the thread, so, again.