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temperatures and this is okay. In general use the lowest temperature which
provides acceptable chromatography. The manifold bakeout functions can be
used to do this overnight and reset the temperatures to operating conditions
automatically.
The trap temperature value selected should be high enough so that
chromatographic performance is not affected. We have found trap temperatures
can be 50-75°C below the ending temperature for the GC column temperature
ramp, without compromising chromatographic performance.
Certain compounds (e.g., straight chain hydrocarbons) will show more
fragmentation at hotter ion trap temperatures.
AGC Target TIC Value
In EI mode with AGC on, the target TIC value determines how many ions AGC
allows into the ion trap during the calculated ionization time. While increasing the
target TIC value will increase peak heights, increasing it too far will result in a
loss of mass resolution. This would be observed as mass misassignments and/or
incorrect isotope abundance ratios. For full-scan EI operation, a target TIC of
20,000 is a good starting point. Under special circumstances, e.g., MS/MS, a
much lower target TIC is required. As the m/z distribution of the stored ions
becomes smaller, fewer ions can be trapped without a loss of resolution.
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