80 Operation Manual
4 Operating in Chemical Ionization (CI) Mode 
CI Autotune 
CI Autotune
After the reagent gas flow is set, the lenses and electronics of 
the MS should be tuned (Table 7). 
Perfluoro-5,8-dimethyl-3,6,9-trioxidodecane (PFDTD) is used as 
the calibrant. Instead of flooding the entire vacuum chamber, 
the PFDTD is introduced directly into the ionization chamber 
through the GC/MS interface by means of the gas flow control 
module.
There are no tune performance criteria. If CI autotune 
completes, it passes.
 
CAUTION
Always verify MS performance in EI before switching to CI operation. 
Table 7 CI tune default settings 
Parameter Methane Isobutane Ammonia EI
Ion polarity Positive Negative Positive Negative Positive Negative N/A
Emission 150 A 50 A 150 A 50 A 150 A 50 A 35 A
Electron 
energy
150 eV 150 eV 150 eV 150 eV 150 eV 150 eV 70 eV
Filament 1
11111 1 or 2
Repeller 3 V 3 V 3 V 3 V 3 V 3 V 30 V
Ion focus 130 V 130 V 130 V 130 V 130 V 130 V 90 V
Entrance 
lens offset
20 V 20 V 20 V 20 V 20 V 20 V 25 V
Shutoff valve Open
Open Open Open Open Open Closed
Suggested 
flow
20% 40% 20% 40% 20% 40% N/A
Source temp 250 °C
150 °C 250 °C 150 °C 250 °C 150 °C 230 °C