When looking at the settings in your Intact workflow or in the inspection view of your results, you will encounter the Minimum % of Local Base Peak setting under the Mass Area and Relative Intensity Options and the "Expected Type" column in the masses table. Below is a short description of what these settings do and how they relate with each other.
Minimum % of Local Base Peak:
The Minimum % of Local Base Peak controls if the Expected Type column in the inspection view shows "Ignored" or "Desired/Undesired":
In this example, the Minimum % of Local Base Peak is set to 10%. Since the mAb, G0F/G0F-Fuc fell below this 10% threshold, the Expected Type of this species displays "Ignored".
The Minimum % of Local Base Peak setting can be adjusted after project creation by going to Edit> Mass area and relative intensity options. Here, the setting can be adjusted to control the traffic light reporting on the summary tab in the reports.
Lastly, the Desired/Undesired Expected Type can also be controlled at project creation:
It can also be changed after project creation under Edit> Protein Table.