Thermo Scientific ISQ, User Manual

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4
Creating a Method
Creating a Method for the ISQ Mass Spectrometer
38 ISQ User Guide Thermo Scientific
3. Set the Ion Source Temperature . You can enter a value between 0 and 350 °C. The
optimal temperature depends on the analyte. Higher temperatures will keep the ion
source cleaner, but will lead to increased fragmentation, which may reduce sensitivity. For
most compounds, a source temperature of 275 °C (default) is adequate.
4. Select the Acquisition Threshold checkbox and enter a value for the minimum peak
height for the data file, if needed. If your peak has an intensity that is below this
threshold, it will not be stored. This setting may help reduce noise, but it may also alter
the reported isotope ratios because the smaller isotope signals will be preferentially
reduced.
5. Select EI from the Ionization Mode pull-down menu.
6. In the Run Completion group, select the action you want to occur at the end of a run:
Note
For best results, tune the instrument at the same temperature you will run the
analyses in your method.
Note Only use CI if you have installed a CI ion volume in the ISQ instrument and you
have connected CI reagent gas to your system. If you have CI, select a CI Gas Type from
the pull-down menu and set the CI Gas Flow. (There will be a two-minute delay when
you change ports for the CI Gas Type.) Typical values for Methane CI for NCI are
1.0–1.5 mL/min. For Methane CI for PCI, the gas flows are typically 1.5–2.0 mL/min.