The following approaches are commonly used for selecting peaks for reporting:
Approach 1: The total ion chromatogram or UV signal of the sample and the control are compared. The total ion chromatogram is commonly processed, e.g. into a base peak chromatogram before comparison
Approach 2: An algorithm is applied that automatically assigns peaks from individual/groups of ion traces in both samples and controls, which are then compared.
An approach where the samples are only screened versus a pre-set list of target compounds is generally not acceptable.