Agilent Configuration

Software Requirements

The Agilent Rapidfire-6560 workflow requires some additional software installation and configuration on top of the autonoms install.

The following software must be installed manually:

  • Agilent MassHunter Workstation Data Acquisition (version >= 11.0)

  • Pacific Northwest National Laboratory (PNNL) PreProcessor (version >= 3.0) (link)

  • Agilent RapidFire UI (version >= 6.1.1.2114)

  • MSConvert (version >= 3.0.22173) available via ProteoWizard

  • Skyline (version >= 22.2.0.351) (link)

Agilent MassHunter Configuration

AutonoMS currently relies on GUI element interaction with Agilent software. MassHunter allows for custom GUI layout configurations in data acquisition, so the layout must be configured to contain the necessary GUI elements for AutonoMS to use. Three elements must be present in the configured layout: The “Instrument Status”, “Method Editor”, and “Sample Run” panes. These elements are shown in the screenshot below boxed in red.

_images/mh-data-acquisition_layout.svg

Configuration file

A primary purpose of the configuration toml file is to point AutonoMS to the locations of the third-party executables. After installing the software described above, the configuration file must be updated accordingly. The Start_MassHunter_S.bat and MHFileSplitter.exe will be found in the software install files from the Agilent installations of the MassHunter and RapidFire software.

Note that the example configuration file uses a .lnk link for the Skyline executable. The Skyline.exe executable can be referenced directly in your configuration file.

The rapid_fire_data_dir corresponds to the top-level directory into which RapidFire/MassHunter is configured to deposit data.

The rf_ip entry corresponds to the RapidFire IP address on the local network and can be found under System Tools -> Network Settings in the RapidFire UI program.