Varian Data

How can I load data from my Varian instrument?

PEAKS reads all PKL files produced from .trans files via the conversion tool embedded in the VarianMS software. The .trans type data (raw) is converted in Varian programs by clicking:

  • "File" > "Save As", then selecting the .pkl file format
  • or by clicking "File" > right clicking "Export", then selecting ".pkl".
    • If you are viewing a chromatogram with the Varian software, all the spectral data in the viewed chromatogram is converted to the .pkl format.
    If you are viewing a single spectrum and choose to convert the data, only the viewed spectra will be converted.
    For best results, it is important to note that raw data (un-preprocessed) often returns superior results when using the preprocessing options native to PEAKS.

    Then load it up!

  • Start PEAKS and select 'New Project' from the 'File' menu.
  • Give the new project a name and select the "Add data files..." button.
  • Browse to the location of the desired file and select it.
  • Multiple files can be loaded in as one sample by using the SHIFT or CTRL keys as multiple files are selected.
  • Press Open.
  • Complete the fields marked Instrument Vendor and Instrument Type.
  • Select whole sample or whole project, as most likely all files were produced by the same instrument.
  • Press OK to have the file loaded into PEAKS.
  • In the top left panel, marked Project View, a number of icons will appear.
  • First the Project node, then the Sample node and lastly the file node.
  • As the project loads, the file node will appear as a green outlined icon .
  • Wait until this icon turns solid green , this represents the file is completely loaded into PEAKS and is ready for processing.
  • For small files, users may not even notice the outlined icon, but larger files may take a short period of time to load.

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