Mass spectrometry for multiplexed quantitation using multiple frequency notches

At least one non-transitory computer readable medium encoded with instructions that, when executed, perform a method, the method comprising:

• determining the mass-to-charge ratio of a first plurality of ions, wherein each of the plurality of ions is labeled with a chemical tag that produces reporter ions when fragmented;
• determining a conversion efficiency for each of the first plurality of ions, wherein the conversion efficiency represents the probability that an associated ion will produce a reporter ion when fragmented;
• and
• generating information to control a mass spectrometer to select a subset of the first plurality of ions based on at least one selection criterion, wherein the at least one selection criterion is based at least on the conversion efficiency for each of the first plurality of ions.