Mass spectrometry (MS) is one of the oldest and most trusted analytical methods for chemical identification. Advances in biology, such as metabolic analysis and proteomics, have fueled a growing number of refinements in this method. Unfortunately, isomers, for example, o- and p-xylene, are seldom identifiable by MS because they produce identical spectra. Time-consuming and less sensitive multidimensional methods are subsequently required for structural determination. The sensitivity of MS coupled with shaped femtosecond laser pulses that control molecular fragmentation and ionization results in a new, fast, and reproducible method for molecular identification which is used here to distinguish positional and geometric isomer compounds and quantify their relative concentration in mixtures.