Create an experiment workflow - Create an experiment workflow - Orbitrap Tribrid Apex Small Molecule Method Editor Help - Orbitrap Apex Small Molecule MS - Orbitrap Tribrid Apex Small Molecule Method Editor Help - Create an experiment workflow - Experiment workflow and instrument method - Scan parameters - topic

Procedure

1. On the Global Parameters page, specify the following parameters, as applicable:
1. Specify the global MS settings in the Settings area.
2. Specify the parameters for the Ion Source, Syringe, Divert Valve, and Output Contact Closure.
2. On the Scan Parameters page, do the following:
1. Specify the experiment’s start time and end time in the "Time Range (min)" box.

2. NOTE

   The Method Duration box displays the latest time of any of the experiments in the saved method. When experiment timelines overlap, the MS cycles between them.

2. Select Standard View , and then double-click or drag a scan icon to the "Place Scan Here" node.
3. The object appears with a purple border to indicate that it is the active node.
3. In the right-side properties pane, specify the master scan parameters.
4. Hover the pointer over a parameter to view its tooltip description.
3. Filter the result of the master scan as follows:
1. (Optional) Create a data-dependent experiment by double-clicking the appropriate filter icon to insert it below the selected master scan node.
2. For more information on the filter types, see Filter types.
2. In the right-side properties pane, specify the filter parameters, as applicable.
3. (Optional) Add additional filters to the workflow and specify their parameters, as applicable.
4. (Optional) Create a data-dependent scan (ddMSⁿ or ddSIM) by doing the following:
1. Select the scan or filter that is located above the "Place Scan Here" node.
2. Double-click an MSⁿ or SIM icon, or drag it to the "Place Scan Here" node.
3. In the right-side properties pane, specify the data-dependent scan properties, as applicable.
4. In the workflow area, select the Cycle Time box and specify the maximum cycle time (in seconds) for the experiment.

5. NOTE

   The MS does not execute scans that cannot be completed in the specified time. The minimum time is equal to the resolution-dependent full-scan time plus 100 ms. This value typically works for an MS/MS scan. If you specify a time that is less than the minimum value, the box turns red. Divide the peak width by the number of points across the peak that you want to acquire. For example, to acquire 10 points across the peak for a 30 second peak, set the cycle time to 3 seconds.

   The exception is that any "remaining" MSⁿ acquisitions (e.g., an MS³ acquisition that would be triggered from a preceding MS² acquisition is allowed to stretch beyond the cycle time).

5. To proceed further for a particular data-dependent scan, do the following:
1. Move an appropriate filter icon to the last ddMSⁿ or ddSIM scan node.

2. TIP

   To duplicate a filter with its set properties, press CTRL and drag the appropriate filter to the empty outcome node.

3. NOTE

   The Apex Detection filters work only with an MS Full master scan.

2. Review the filter parameters in the properties pane.
3. Double-click an MSⁿ or SIM Scan icon to move it to the appropriate "Place Scan Here" node, and then set the parameters in the properties pane.
4. In the workflow area, select the Number of Scans box , and specify the number of dependent scans to perform.

5. NOTE

   If there are multiple outcomes at this level, “scans” refers to the total number of scans, not the number of peaks to evaluate.

6. To proceed further in the experiment, repeat step 5.