Run a sequence to optimize a parameter (LC/MS)

Before you run a sequence, you need to develop an acquisition method.

Then, you can develop a sequence. If you want to override the SIM ions in the method when running the sequence, see

You also need to enter the information in the Single Sample Analysis window before running the method; once the run has started, this information cannot be changed. The information in this window is not part of the method, and it is not saved when the method is saved. When you are running a sequence, you enter the information in the Sequence window before running a sequence.

You can use a sequence to optimize a method parameter. For example, you may want to find a good overall Gas Temperature for your compounds. First, you add a method override column to the sequence. You can override the Fragmentor voltage or one of the source parameters. Then, you add multiple rows to the Sequence table which run the same sample. For each row in the Sequence table, you vary the parameter that you want to optimize. For example, you can add five rows to the table and set the Gas Temperature to 250, 260, 270, 280, and 290. By comparing the data files, you can determine which Gas temperature is best for your compounds.

1. Develop a method. See Method Editor for SQ (LC/MS).
2. Click Sequence.

3. Open a sequence.
4. In the Sequence window, enter the Properties information.
   1. In the navigation pane at the left of the window, click General > Properties.
   2. Mark or clear the Audit Trail Activated check box.
   3. Enter the Description for the sequence.
5. Enter the Run Options information:
   1. In the navigation pane at the left of the window, click General > Run Options.
   2. Mark or clear the Use Barcode Reader Before Injection check box.
   3. Click either Inject anyway or Abort current injection.

6. Add a column to the Sequence table.
   1. In the navigation pane at the left of the window, click Injections > Table.
   2. In the upper left corner of the Sequence table, click . The Choose Columns dialog box opens.
   3. Click the Method Override Columns option.
   4. Select the column (or columns) that you want to display. You can only optimize one parameter at a time, but you can override multiple parameters in the method if you want to.

If you add a Method Override Column and enter values in the column, then even if the column is hidden, the Method Override will work. The only way to make the override not happen for that parameter is to clear the values in that column.

5. 5. Click OK.

7. Enter the Table information:
   1. In the navigation pane at the left of the window, click Injections > Table.
   2. Enter the information for an injection.
   3.  Repeat that row several times. Most of the values in these rows are the same. You only vary the sample name, the data file name, and the parameter that you want to optimize. You can only optimize one parameter at a time.
   4. For the parameter that you want to optimize, set the parameter in the first row to the lowest value that you want to check. The first sample file contains the data with the parameter at this value.
   5. In the second row, set the parameter to a slightly larger value. The second sample file contains the data with the parameter at this higher value.
   6. Continue to increase the value for that parameter in subsequent rows.

8. If needed, click Take. In this image, Take is already selected.

9. Click the Run button.
10. Review the data files to determine the optimum value to use for that parameter for your sample.

See Also

Run samples (LC/MS)

Method Editor for SQ (LC/MS)