Getting rid of those peaks!

I'm collecting some MS fragmentation spectra for my students, and as expected, our MS is very sensitive and labels (peak picks) more than I want.  I can't seem to fiddle with the post acquisition parameters to figure out how to "raise the labeling threshold", so now I've moved on to the acquisition parameters.  I'm currently adjusting the "threshold (counts)" in my MS parameters.  If I'm in the right neighborhood, can someone explain what this value is, and how best to set it to remove very low-level signals that are either noise or unimportant to my undergraduate students?  Thank you!

  • The description of threshold from the MassHunter help is "Abundance values below this entered threshold value are not recognized as ions."  What is means is that the MS only keeps the data for responses above this value.  The default threshold value in the MS acquisition parameters is 150.  A higher threshold value would eliminate the smaller peaks.  It may also cause the baseline to go to zero if the background is below the threshold value.  As for an appropriate value, it would probably take some experimentation to determine.

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