How to set up MassLynx to run a pos/neg switching experiment on a quadrupole system - WKB230199

OBJECTIVE or GOAL

Acquire data in both positive and negative ion modes in the same MS method.

ENVIRONMENT

• All Waters quadrupole instruments  
• MassLynx (all versions)

PROCEDURE

1. Open the Tune file and select the positive ion mode (EI+, APCI+, and so on).
2. Set the appropriate voltages, temperatures, and gas flow rates for the assay being run.
3. Save the Tune file.
4. Switch to negative ion mode (EI-, APCI-, and so on).
5. Set the appropriate voltages for the assay. Leave the temperatures and gas flow rates the same as in positive ion mode. (Note: The temperatures and gas flow rates must be the same in positive and negative modes because they cannot switch fast enough as the system alternates between positive and negative modes.)
6. Save the Tune file with the same name. (Note: One Tune file saves both sets of parameters in a single file.)
7. Open the MS method editor.
8. Add the appropriate MS functions for the compounds in the assay being run. Setting the ion mode, SIR, or MRM values (or m/z range for full scan), you need separate functions for positive ion mode and negative ion mode.
9. Save the MS method.
10. In the sample list, browse the MS method created to the MS file column and the Tune file created to the MS Tune file column.

ADDITIONAL INFORMATION

When the data are acquired, positive and negative data will be saved to separate function files within the .raw file.