1. A method of performing a mass spectrometry analysis, the method comprising: labeling each of a plurality of samples with a corresponding chemical tag selected from a plurality of chemical tags; forming a first plurality of ions from molecules in the samples; selecting a subset of the first plurality of ions; forming a second plurality of ions by fragmenting ions in the subset; and measuring a plurality of reporter ions indicative of a relative quantity of each of the plurality of chemical tags present in each of the plurality of samples, wherein selecting the subset is based, at least in part, on an estimated probability that the subset will generate the plurality of reporter ions.