Pausing or stopping a MassLynx sample list

Pausing a sample list

During data acquisition, you can pause a sample list to modify the system. For example, you can correct LC problems, add vials to a sample carousel, or refill a mobile phase reservoir. Note, however, that you must not pause and then resume a MassLynx sample queue if you are using an Inject head method (for example, LC-inj.cyx macro). If you must stop the sample list to add sample vials to the autosampler or to perform other tasks, then you must stop the sample list and then restart it to ensure that all the samples are injected correctly.

To pause data acquisition:

In the main MassLynx window, click .

Alternative: Click Run > Pause.

Result: The currently acquiring sample is completed, and the system waits for you to resume the acquisition. The information bar above the sample list updates to read "<sample list name, samples number>AcquiringQueue is Paused".

Rule: While the system is paused, the sample list cannot be modified. Any changes made are saved to the current sample list but do not add to a currently running sample queue.

To resume data acquisition:

In the main MassLynx window, click .

Alternative: Click Run > Pause.

Caution: Do not press   or click Run > Play. Doing so adds new samples to the queue.

Stopping a sample list

To stop data acquisition:

1. In the main MassLynx window, click .

Alternative: Click Run > Stop.

Result: The Masslynx dialog box appears stating that "The currently running batch will be deleted".

2. Click Cancel, to leave the system as it was, or click OK to delete a current batch from the queue.

Tip: If you click OK, the data acquisition stops immediately, but the LC method (if applicable) continues to run until it reaches its programmed end point, which includes any post-run methods.

To stop the LC method and MS method immediately:

Click the "hand" symbol.

Result: A MassLynx dialog box appears stating the following message: "Currently running the Run Method <filename> Do you wish to halt post run method also? Click <Yes> to halt everything and <No> to halt the run only".

If there are additional batches in the sample queue, and a batch is stopped, the queue pauses.

To resume the analysis:

1. Ensure the inlet method completes its cycle and is ready.
2. Click to resume running the remaining batches in the queue.

Note: If there are no further batches in the queue, after clicking the stop button, the MS system reverts to the ready state.