What are masks used for in Progenesis?
Masks can be applied to areas of runs you wish to exclude from the analysis due to the presence of noise or contaminants.
Excluding areas of noise through the use of masks can help to improve alignment where the noise is inconsistent across your data set in addition to ensuring contaminants aren’t picked as ions.
You can apply a mask by selecting Mask areas for peak picking… from the Actions dropdown menu at Import Data – at this screen, you can drag out areas on the ion intensity map to apply a mask. Once a mask has been applied you can adjust its m/z and RT range or remove it using the tools to the left of the screen.
If you want to exclude a specific section at the end or beginning of your runs from peak picking across the entire data set you might find the following article more useful: