Autotune reports PFTBA ion ratios. If the MSD does not pass this part of tune, do not acquire data. Check the following:
Check the resolution of adjacent peaks. Very wide peaks sometimes cause higher-than-normal isotope ratios or missing isotopes. Very narrow peaks sometimes give lower-than-normal isotope ratios.
If you are acquiring data in scan mode and experience problems with missing isotopes or incorrect isotope ratios, try reducing the scan speed.
If you are acquiring data in SIM mode and experience problems with missing isotopes or incorrect isotope ratios, try increasing the dwell time.
High electron multiplier voltage can cause or contribute to this problem. Lower the voltage about 200 V. If results improve, continue to adjust the voltage until you find the optimum setting. If the electron multiplier voltage is high enough to cause isotope problems, it will probably also cause peaks with flat tops.
A high repeller voltage can cause precursors or make them larger. Decrease the repeller voltage and see if the precursors decrease.