-
|
I tested the EI mode for Xanax (C17H13ClN4) which has a molar mass of 308.77 g·mol−1. The resulting MS (obtained with PlotMS) does show a molecular peak at an m/z ratio of 308.08. However, there exist peaks for m/z ratio up to 313.09 with some having significant intensity (for ex: [(309.09, 18.7), (310.08, 32.4), (311.08, 6.04)] where [(m/z_ratio, intensity)]). The only explanation that comes to mind is that this is due to the isotopic abundance of the molecular atoms. However, the high intensity casts doubt on it and I wonder whether I should consider this effect as a simulation artefact and filter these peaks out. |
Beta Was this translation helpful? Give feedback.
Replies: 3 comments 5 replies
-
|
The M+ peak is always the one you put in as a structure, there can be no artificial larger peak due to the QCxMS calculation. So it definitely stems from the isotope pattern. You can switch off plotting the isotope pattern by using the |
Beta Was this translation helpful? Give feedback.
-
|
By sampling time, do you mean the parameter |
Beta Was this translation helpful? Give feedback.
-
|
Exactly. However, while running a simulation longer enables a better distribution of the internal/excess energy, it does not guarantee that the provided energy is large enough for fragmentation. If you want to increase the electron beam impact energy, use |
Beta Was this translation helpful? Give feedback.
-
|
Thank you for the advice ! Now I'd like to have better guesses for |
Beta Was this translation helpful? Give feedback.
-
|
@psireal9 can you post the final spectrum? What is the cosine similarity score when compared to the experimental spectrum here: https://webbook.nist.gov/cgi/cbook.cgi?ID=C28981977&Mask=200
|
Beta Was this translation helpful? Give feedback.
-
|
here is what i got for the following setting: 15.023475 1.412298591549295601 |
Beta Was this translation helpful? Give feedback.
-
|
As you see, the isotope pattern vanishes. The intensity of the M+ peak can be reduced as I described before. Otherwise, this looks good, but as you see, you only get an averaged value without isotope pattern (because I didn't implement this feature in great detail) |
Beta Was this translation helpful? Give feedback.
-
|
Also isotopic pattern are here
|
Beta Was this translation helpful? Give feedback.
The M+ peak is always the one you put in as a structure, there can be no artificial larger peak due to the QCxMS calculation. So it definitely stems from the isotope pattern. You can switch off plotting the isotope pattern by using the
-poption to check if this is really the case. The high intensity comes from the large intensity of surviving molecular ions, check if the fragment ions might be too low in intensity too. If so, either increase the impact energy or the sampling time.