Set up a new MS method

Prerequisites

• Privileges: Project Management > Edit content of project , OpenLab CDS: Method Development > Edit identification parameters and OpenLab CDS: Data Analysis > Edit sample information . Privileges are configured in the Control Panel.

• If the project enforces method approval, the method status must be Generic. For details, see Method approval.

1. Load the data.

2. Link the data to a method that supports MS data (see MS method configurations).

3. Configure signal transformations:

   1. Align signals of multiple detectors (see Align chromatograms from multiple detectors)
   2. Configure blank subtraction (see Use blank subtraction)
   3. Configure signal smoothing (see Configure signal smoothing)

4. In the processing method, adjust the integration parameters. Use specific events for the MS signals.

   1. In the Integration Events > Standard node of the processing method, select the Use signal specific events check boxes for the EIC, SIM, TIC SCAN, or TIC SIM signals.
   2. Adjust the parameters for the relevant signals.

   For example, set Area reject to 200000 for TIC SCAN and to 10000 for EIC.

   The following functions may help you:

   • Integration Optimizer

   • Copy integration events to another signal

5. To extract ion chromatograms over a time window around each target peak rather than the entire run time: In the Extraction > Chromatogram node of the processing method, enter a value for the SIM/EIC extraction retention time window for target compounds .

   It is usually best to pick a time range that is wide enough to extend enough beyond the target peak to correctly assign the baseline points.

   If you provide both absolute and relative time ranges, a sum of both will be used (same principle as for the peak identification window). With zero values, EICs are extracted over the full time range.

6. Configure background subtraction for MS spectra.

   Choose appropriate settings in the Extraction > Spectrum node of the processing method. See Extract background-corrected MS spectra.

7. In the Compounds > Identification node of the processing method, in the Qualifier Setup tab, check the settings for qualifier ions (see Processing method: Compounds: Identification, Qualifier Setup tab).

8. To have the compound names displayed automatically, based on an MS library search: In the Spectral Analysis > MS Library Search node of the method, choose an MS library from the drop-down list. Click the + icon to add it to the method.

   NOTE

   If you want to use MS Library Search, you must install NIST MS Search and the required MS libraries first. NIST software can be acquired from Agilent.

   The status of the Automatically search TIC peaks check box is not relevant in this scenario.

9. Consider saving the method.

10. Reprocess the injection.

    All relevant peaks should now be integrated.

11. Consider adjusting the number of qualifies.

    If you do not want to use qualifiers, you can set the Number of qualifiers used for scan data to 0. You edit this value, in the Compounds > Identification node of the processing method, in the Qualifier Setup tab.

12. Add compounds, and check and complete the compound table

    1. Add MS compounds manually
    2. Add MS compound from a library hit
    3. Add/update MS compounds automatically
    4. Add MS compounds from other data

13. Name the compounds, and check and complete the compound table in the method.

14. In the Compounds > Calibration node of the method, provide the correct concentrations for your calibration levels.

    Consider saving the method.

15. In the Injection List window, provide the correct sample types and calibration levels.

16. Reprocess the data.

    During reprocessing, an EIC or SIM for each m/z value (of both target and qualifier ions) will automatically be extracted and listed in the injection tree.

    The response of qualifier ions is compared to the response of the target ion. If it is within a defined response window, the qualifier is listed as Passed in the Injection Results. See Evaluate MS qualifier results.