Hi everyone,
We experienced a strange pattern in some spectra coming from HRMS/MS analysis. In particular, in the MS1 spectrum a base peak at m/z=M and a smaller peak at m/z=M+5Da appear, but in the MS/MS spectrum, the M signal disappears, while the M+5Da remains. Can anyone explain such a behaviour? We hypothezised a kind of isotopic pattern, but we cannot explain the fragmentation of just the lighter one.
Dear Barbara,
the difference of 5 Da in MS1 spectra may be due to the pseudomolecular ion [M+Na]+, compared to [M+NH4]+.
Sodium adducts are known to be more stable in MS/MS, so the [M+NH4]+
is fragmented, but [M+Na]+ is (at least partially) retained. Since your data is HRMS, you can test this hypothesis by calculating the sum formula.
Note that "pseudo-molecular ion", even "quasi-molecular ion", do not agree with the modern MS nomenclature.
"The terms quasi-molecular ion and pseudo-molecular ion are deprecated and should not be used in place of cationized (anionized) molecule."
Definitions of terms relating to mass spectrometry (IUPAC Recommendations 2013); Pure Appl. Chem., Vol. 85, No. 7, pp. 1515–1609, 2013.
Hello Barbara Benedetti,
there could also be another reason why the suspected isotope peak is not fragmented.
Which isolation width in u do you use to fragment the spectrum?
If the isolation is too small, the M+5 peak will not be fragmented.
The usual isolation widths are 2 -4 u around the 13C M+1 peak, this range is too small to capture the M+5 peak. Why don't you check how the isolation width is set? I use the HRMS from Agilent (Q-ToF) and Thermo (Orbitrap). Agilent offers the isolation widths 1.2, 4 and 9 u; with Thermo I can freely select the isolation width and thus optimise it.
Otherwise I agree with Andre Stratmann, different adducts can also fragment differently due to their different stabilities.
Best regards
Joachim Horst
Dear Joachim,
Thank you very much for your answer .
I did not specify that, but we actually did not select any isolation window, since we are working in Data Independent Acquisition. Therefore we fragment every ion that is formed in the ion source.
We'll still keep in mind your advice if working in Data Dependent Acquisition.
Barbara Benedetti
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