Before running an experiment, bring the input protein samples and the kit used to design the method file to the instrument.

To prepare the samples and load the samples in the kits, see Prepare the samples.


Ensure the instrument door is closed before running a method.

Run a method file created using the Experiment Designer desktop software application on the AccelerOme instrument as follows.


  1. On the home screen, tap Login.
  2. In the Login dialog, enter your username and password and tap Login.
  3. The home screen appears.
  4. To use an existing experiment method file, tap Start with Method.
  5. Tap Import Method.
  6. Alternatively, you can run the default method files (created using Quick Start) appearing on the screen or export them to the Experiment Designer for editing.
  7. Import the method file from a USB or a network drive.
  8. If the instrument is connected to the network, import the method file from the Experiment Designer. If it is not connected, import by copying the method file to a USB drive.
  9. Review and verify the method before you run it. Tap Run Method.
  10. (Optional) Scan the QR barcode on the kit to confirm the method settings match the kit. Tap Skip to skip this step.
  11. For detailed instrument loading steps, tap Guide Me.
  12. Alternatively, tap Start to run the method immediately and skip the guided setup (steps 8 and 9).
  13. Follow the guided steps for loading your input plate and kit components on the instrument deck.
  14. Confirm the locations of the kit components and samples.
  15. Close the instrument door, and tap Start (Or Done for Quickstart).
  16. The deck validation process precedes the experiment run. If the deck validation fails, an error message pops up. The failure details are available in the event log.
  17. Follow the run progress.
  18. (Optional) Tap View Details to view the experiment details. Tap Done to return to the home screen.
  19. Tap Abort to cancel the experiment run (see Run an experiment using a method file).
  20. NOTE

    If you tap Abort after reactions have begun, the partially processed samples cannot be recovered.

  21. (Optional) Tap View Results to view the experiment details.
  • Tap the Overview tab to view the run results overview.
  • Tap the Input Table tab to view the input peptide amounts and locations.
  • Tap the Input Plate tab to view the sample setup on the input plate.
  • Tap the Output Table tab to view output peptide amounts and locations.
  • Tap the Output Plate tab to view the sample setup on the output plate.
  • Do one of the following:
  • Tap Unload Instrument.
  • Remove all instrument content and tap Done.
  • Resolve, acknowledge and clear any alarms or alerts, if they appear, after the run.
  • Refrigerate or freeze samples promptly after use, to prevent degradation.
  • Abort an experiment or test run

    Abort a run on the instrument if you need to cancel it.


    1. Tap Abort.
    2. Select if you want to Continue Run, Stop Run Immediately, or Stop Run After Current Step.
    3. If you select Stop Run After Current Step, click Stop Run next. When a run is aborted after the current step, the abort action can be undone using the Cancel Abort button, within a few seconds.
    4. Clear all alarms after aborting a run, if they appear, by resolving and acknowledging them.
    5. Tap Unload Instrument.
    6. Remove all the instrument content and tap Done.
    7. (Optional) Tapping View Results allows you to view the results of the aborted run. The results can also be exported to a USB or a network drive.


    Do not use the PAL terminal during a run. Wait at least 30 seconds before starting an experiment run or accessing the service tools from the instrument interface before using the PAL terminal. In case of an error related to PAL terminal use during a run, shut down and restart the AccelerOme instrument.

    When the instrument is not in use for at least an hour, it enters an idle state. This includes when the actual instrument hardware is in use, when the instrument interface is in use, or when a process is running on the instrument either physically or on the instrument interface.

    Accessing the instrument interface when the instrument is in an idle state for at least an hour requires logging in again.