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Agilent ChemStation GC/MS

In this guideline, the integration process of an Agilent GC/MS controlled via ChemStation E.02.01 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 and
  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. NOTE: For Chemstation E.04.01 refer to the HPLC & LC/MS Agilent ChemStation instructions.

Specifications of the device's PC​

  • Operating system: Windows XP
  • Software Name: Agilent ChemStation E.02.01
  • 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 GC/MS computer and Chemotion ELN need access to a common network storage location that is set up as a virtual network drive on the GC/MS 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.

The macro will alert users after running an experiment if the connection to the network location has been lost. This is done by reading a file "connection.txt" permanently stored on the network location. The file connection.txt does not require any content.

Creating the macro:

Create a new file in ChemStation's main program folder: _\msdchem\1\macros appropriately named (example: ELN_Export.mac"). Make sure the file is of the _.mac file type. Open the file, for example using Notepad, and insert the following text, then save and close the file.

name ELN_Export Filesize "Z:\connection.txt" If size > -1 then Copy_DataPath$ + _DataFile$,"Z:\ELN" + _DataFile$,DONTASK Else Alert "No connection to the network path; Your data could not be backed up and exported to the ELN.",2 Endif remove ELN_Export

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.

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 "Method information" and accept. The "Method Information" window will open. Activate the "Post-Run Macros/Commands:" check box and select the previously created macro as target in "Instrument Control:" (example: C:\msdchem\1\macros\ELN_Export.mac)

Configurations in Chemotion ELN​

The Chemotion ELN’s data collector has to be configured to collect the GC/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.