Can two analytes have the same transitions in an MRM method in SCIEX OS software?

For research use only. Not for use in diagnostic procedures.

Answer

Occasionally two different analytes in the same MRM method in SCIEX OS software may have identical Q1 and Q3 masses for their respective MRM transitions. As long as these transitions are correct and that they truly represent the compounds of interest, it is not problematic to have two identical transitions for two different compounds.
However, certain conditions must be met:

1. The two compounds must be separated by an LC gradient and have different retention times (RTs). , separate Otherwise, quantitation of the individual compounds will not be possible using these transitions, and only the total of the two transitions can be reported. 
2. Each of the two peaks must be assigned to the correct compound.

The best way to identify each analyte is to inject each one separately and determine their respective RTs. If no standards are available and only a mixture can be obtained, then analysts must rely on reports in the literature and chemical structures to assign the correct peak to the correct analyte. Addtionally, identification of a secondary transition that is unique to one analyte could be used to assign the correct RT to that compound.