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Agilent ChemStation HPLC & LC/MS

In this guideline, the integration process of an Agilent HPLC or LC/MS controlled via ChemStation B.04.01 in Windows XP into the Chemotion ELN is explained. The procedure is split into two aspects that can be set up independently or in parallel:

  1. Remote connection to the device
  2. transfer of experiment data to the ELN.

General preparation aspects can be found here.

Considering all these aspects, this procedure has been conducted on the following system configurations. However it is likely to work on systems with different software versions as well.

Specifications of the device's PC​

  • Operating system: Windows XP
  • Software Name: Agilent ChemStation B.04.01
  • Connected to LAN (Intranet only): Yes
  • Data files generated: ChemStation *.D Folder with multiple files
  • Static IP address has been configured


  • Remote Device Control
  • Data transfer to Chemotion ELN inbox


Remote Device Control​


General guideline regarding the configurations of remote device control can be found here.

Data transfer​

Data will automatically be transferred to the Chemotion ELN once ChemStation has finished recording data of the current run. The user is required to input a valid file output name according to the naming convention for the Chemotion ELN to sort the file into the correct user's inbox.


Please take care that you communicate name conventions to all users of the Chemotion ELN.

Necessary configuration in ChemStation​

Data transfer is coordinated by a macro configured to be executed as a post-method macro.

The HPLC or LC/MS computer and Chemotion ELN need access to a common network storage location that is set up as a virtual network drive on the device's computer. The network storage can be set up on a third-party storage (a NAS server, shared storage of another PC etc.). In this case, the LSDF storage service from KIT has been used.

Creating the macro:

Create a new file in ChemStation's main program folder: _\Chem32\CORE\ appropriately named (example: ELN_Export.mac"), make sure the file is of the _.mac file type. If a Folder MACROS does not exist it can be created or the file can be saved to another location. Open the file, for example using Notepad, and insert the following text, then save and close the file.

Name ELN_Export

COPY _DataPath$+ _DataFile$, "Z:\ELN"+ _DataFile$, DONTASK COPY _DataPath$+ _DataFile$, "Z:\data"+ _DataFile$, DONTASK


In the macro substitute: Z:\ELN\ with the drive letter of the virtual network drive and folder path where the data is to be copied to. As shown in this example the file can be saved to one or multiple locations. One for pickup by Chemotion ELN's folder watcher and another as a permanent backup.

Configuring the method to run the macro:

In ChemStation load the method that should transfer data. NOTE: This configuration needs to be done in every method that will be run on the chromatograph. From the "Method" menu of ChemStation's main window choose "Edit Entire Method...". In the pop-up window choose "Run Time Checklist" and accept with OK. The "Run Time Checklist: Instrument X" window will open. Activate the "Post-Run Command / Macro:" check box and enter the command to run the macro (example: "Macro "ELN_Export.mac", go")

Configurations in Chemotion ELN​

The Chemotion ELN’s data collector has to be configured to collect the HPLC or LC/MS data from the network location.

As for the file collector mechanism, there are two options.

  • Collecting attachment files from emails
  • Collecting file or folder from local drives or over SCP

For this procedure the folder collection from local drives or over SCP needs to be chosen and configured to collect the data from the network drive where the ChemStation macro has uploaded it to.