I am attempting to add an exclusion list to an analysis I am running with a Q Exactive HF Orbitrap. I ran a series of samples with a Full MS-ddMS2 method that included polarity switching and generated an exclusion list from ions that are above my ddMS2 triggering threshold that are present throughout my run (i.e., ubiquitous elevated baseline) or that were present as defined peaks at specific retention times. As a result, some ions in the exclusion list do not have start and end times, so they are excluded for the entire run, and some ions have a retention time window. The total list, which includes both positive and negative mode ions, has >3,000 individual rows. Then, I reran my samples with this exclusion list added to my method. When reviewing the results, I see that the instrument is still triggering MS2 scans for ions that are on the exclusion list; however, some ions are being successfully excluded.
I verified that the "exclusion list" parameter on my method settings is turned on for both polarities. I have also noticed that for some compounds there is a co-eluting ion that is triggering the MS2, and the excluded ion is within the isolation window (already set pretty narrowly at 0.7 m/z) of the triggering ion; I can live with the fact that in these situations there is likely little I can do. However, there are many other cases where an excluded ion is eluting well within my retention time window and there are no co-eluting ions but an MS2 is still triggered. Mass differences between the observed ion and the mass in the list are well within 5 ppm.
Any help or suggestions would be greatly appreciated!
Interesting question @mnewmeyer! Are you calculating the 5 ppm within excluded mass directly from the scan header that triggered the relevant ms2 scan? For the exclusion list itself did you set both the m/z and charge to exclude or just the m/z itself (or maybe you used formula plus adduct)?
To calculate the mass difference I looked at the mass in the MS1 spectrum in the scan immediately prior to the MS2 scan and compared it to the mass in the exclusion list. I did not indicate a charge state in the exclusion list itself, I only added an m/z value. Also, I did not indicate this in the original post but I also set the mass tolerance for the exclusion list to the instrument default (the value of which I cannot find anywhere).
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