1. A method for automatically optimizing an FTMS variable, comprising: for a plurality of FTMS samples each having a substantially similar number of molecules, repeatedly and automatically: obtaining a plurality of data sets, each data set from the plurality of data sets obtained by: applying a trapping plate voltage to at least one trapping plate of an FTMS cell; and measuring a composite amplitude of an FTMS spectral output signal; for the plurality of data sets, determining a variance for the composite amplitude; and changing an FTMS variable; until the variance is substantially minimized.