Analyzing multiple ADC's in the same project can be easily accomplished using the ADC workflow and corresponding DAR calculations in the report (for a primer, see this article.) Multiple ADC's follow the same process as any other ADC workflow remembering to maintain Drug(#) is first in the Delta mod name, where the # corresponds to number of warheads. Because the Drug(#) nomenclature isn't necessarily linked to the mass of the payload, we can give "Drug" the mass of 0 and add the warhead as an additional modification in the delta masses list, making sure the warhead and drug counts match.
Below we demonstrate adding WarheadX and WarheadY to the same project and maintain accurate counts.
In the above set up, we can assign payloads for both Warhead X (100Da) and Y (111 Da), and the report would calculate the correct DAR. Note that it is important to make sure Drug(0) is still present within the table.
In case the masses of the warheads are very similar, one can use the Samples ID column to restrict the mass assignment to only the samples they are expected in to avoid misassignments.