QTof, Qual exclude MS/MS experiments with low abundance

Question

Hi, 
 
 I am using Qual 12 for LC-QTof. If I use Find-by-Formula I receiced hits with multiple MS/MS-experiments. In this case 11 scans. 
 
 Where can I set the parameters that I only have the 4 largest experiments (green) and exclude the red one. That's important for the average MS/MS spectrum. 
 
 Thanks!

howard_sanford · Answer

Hello beerbaum , 
 From what I can find, only the MS spectrum can be limited to the top x percent of the peak. This setting is on the Find by Formula->Peak Spectrum (MS) tab and is only available if you have enabled Show Advanced Settings in the Configuration menu 
 
 I'm not finding a way to limit the MS/MS spectrum averaging directly, but you can set thresholds on the Fragment Peak Filter tab that can clean up the averaged MS/MS spectrum. 
 Here is an example from the demo data showing the MS/MS spectrum of a peak with no thresholds set. 
 And here is the same spectrum using the default threshold settings. 
 
 For this data it is not a very dramatic difference, but it should be possible to adjust these values to help clean up your spectrum depending on your data.