We recommend that you use a technique called "Single point calibration".
With the single point calibration technique, the only time that you use your full set of calibration points is when you are trying to determine where the linear range of your analytes are.
Once you have determined that all of your analytes are in the linear range, and you want to start quantifying unknown samples, you would include a single external standard on each of the plates that you run through the mass spectrometer.
There is a discussion of this in this paper:
https://pubs.acs.org/doi/full/10.1021/acs.analchem.8b04581
-- Nick