Instructions to Import Xcalibur Processing Method file (*PMD) to create a new Master Method in TraceFinder

1. Open TraceFinder application.

2. Select the Method Development Work Area

3. Select “Create Method” from the method view section

4. In the “Create Master Method” pop-up box, select “Import Xcalibur Processing Method” and then “OK”.

5. In the “Import an Xcalibur method” pop up box, select the “…” button next to the “Xcalibur method to import ” box to browse for a method file.

6. In the “Select a processing method” pop-up box, navigate to the processing method, select the file by highlighting, then select “Open”

7. In the “Import an Xcalibur method” pop up box, select the “…” button next to the “Raw data file to associate” box to browse for a method file.

8. In the “Select a rawfile” pop-up box, navigate to a representative data file, select the file by highlighting, then select “Open”

9. In the “Import an Xcalibur method” pop up box, select the mass precession to be used for the import, a value of 2 is typically used for Unit Resolution data from a triple quad instrument, and a value of 4 or 5 is typically used for High Resolution Accurate Mass data. Then use the “OK” button to start the import.

10. In the “Edit compound dependent parameters” select the “Continue to Method” button. Optionally you may use the “add to CDS button” first, if you would like to add these compounds to the compound data store.

11. The method has now been imported to the Master Method View, and the General Tab should be active. The master method has been given the same name as the imported Xcalibur Processing Method, however if a method with this name already exists, the filename will be appended with a time date stamp. Verify the mass tolerance is set correctly, typically 500 MMU for unit resolution data and 10 PPM for High Resolution Accurate Mass Data.

Note: The Mass Tolerance and Mass Precision default values can be set in the Configuration work area (detection sub-section of the application configuration section) to avoid having to reset them routinely when creating new master methods!

12. In the General Tab of the Master method view use the pull down arrow in the Instrument Method box to select an instrument method to be used. This is an Xcaliber Instrument Method File (*.meth) located in the C:\Xcalibur\Methods folder. Instrument Methods can be moved or copied to this folder in Windows explorer as required.

13. Compound information can be reviewed/edited on the compound tab of the Master Method view. Information in the Acquisition List, Identification, Detection, Calibration Calibration Levels and QC levels sections were all typically imported exactly as they were in the Xcalibur processing method and should not typically require further modification. Information in the Real Time Viewer section will require set-up. Highlight the traces of data you would like to view in the displayable traces area and use the right arrow button to move them to the Traces to display area, up to 25 can be viewed real time while acquiring data.

14. Limits may be set up on the Limits tab of the Master Method view, however defaults have been established. Reports may be set in the reports view to be automatically generated, but could alternately be run manually in the report section of the Analysis work area.

15. The Master Method may be saved by using the icon, or you may pull down the file menu and select “Save as” to bring up the “Save Master Method” pop up box where you may rename the saved Master Method. The Master method is now ready for use.