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Export of Raw Data from openlab 2.8 to a format compatible with MZmine

Simon-Larsen

Hi, I am working with openlab 2.8, it is controlling a 1260 HPLC connected with a  MSDiQ.  I am trying to transfer/export the raw data to a format that can be read by MZmine. Until now I have tried to use  the post processing method AIA to get a netCDF file and CSV in the tools section of the method editor. It looks like I only get the TIC and not the complete raw data. IS there anyway I can get all ion traces and not only the TIC.  Best Regards Simon Larsen

  • 0

    Hello,

    You can export the MS data for Chemstation if that software will import Chemstation data. As a single AIA or CSV file you cannot export all the raw data. The export utility only exports the TIC, SIM, and EIC channels. 

    Marty Adams

    This procedure explains how to export both ChemStation raw data files (.ch format) and MS spectra (.ms format) into the same .D folders.

      1. In the Tools > Post Processing Plugins node of the processing method, add the following plugins:

        • ChemStation export

        • AIA export

      2. Ensure that ChemStation export runs first, and AIA export runs afterwards. If required, click  or  to adjust the sort order.

      1. For the ChemStation export plugin, provide an export path where you want the .D folders to be created.

    For example, C:\CDSProjects\MSD data\Results\Export. The .D folders will be automatically created using the given data file names.

      1. For the AIA export plugin, use the same export path, but append the <DX>.D.

    For example, C:\CDSProjects\MSD data\Results\Export\<DX>.D.

    <DX> is the token for the data file name. A folder with the name <DX>.D has been created by the ChemStation export plugin. The .ms files will then be created inside the correct .D folders.

  • 0 in reply to martin.adams

    Hello Martin Adams,

    Thank you for your suggestion. Unfortunately this did not solve my problem, as the other softwares does not support Chemstation files. Both the mzMine software and the MSconvert software can not handle chemstation data. The MSconvert can handle Masshunter data. Is it possible to convert openlab data into Masshunter format?

    I have approximately 650 compounds being analysed on 8 columns with 5 different eluents, at 3 pH values, 2 gradient times and 2 temperatures. So I am generating a lot of chromatograms, where I need to extract the retention times in an easy way. Do you have any suggestions on how to do this in Openlab? 

  • 0 in reply to Simon-Larsen

    Hello  ,

    Starting with MassHunter Quant 11 it is possible to convert OL CDS data files to MassHunter format. Only the latest versions of DA software will be able to open the resulting data files. You would need to verify that MSConvert can open these files.

  • 0 in reply to Simon-Larsen

    Hello,

    I am not sure what you mean by extract the retention times. You can have the software auto extract EICs but only if you have the compounds in your calibration table. MassHunter can convert CDS data but that is done in the MassHunter software not by any export function in CDS. 

    Marty Adams

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