Waters/Micromass (MassLynx) Data

How do I load data from my Waters Instrument?

PEAKS can import RAW data from Waters/MicroMass QTOF instruments, provided that the MassLynx 4.1 software is installed on the same computer.
In the event that you would like to install PEAKS on a different computer than your computer with MassLynx we have a converter that can be used to transfer the data. Please contact This e-mail address is being protected from spambots. You need JavaScript enabled to view it to obtain this converter. For MassLynx 4.0 users, a utility called wolf.exe (originally created as part of the Sashimi Project) can be used to convert the raw files to mzXML format in command line. Further, to run PEAKS with older versions of MassLynx an older version of MassWolf is required.

Then load it up!

  • Start PEAKS and load up the data by selecting '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.

    • But what if I want to load in txt files exported from MassLynx?

    Some researchers use the Waters average scans option to merge scans together and then to load the data into PEAKS. In order to load txt files from Waters into PEAKS, they still need to be in PKL format. There is a really easy option from here to do this:

  • Open the txt file in notepad or word pad.
  • Remove the top line of the file and replace it with:
      • m/z [tab] intensity [tab] charge
  • Save the file and remove the .txt and add .pkl.
  • The file can now be loaded into PEAKS.

    • Experiencing Difficulty with Waters RAW Files?
    In very rare cases, researchers with PEAKS installed on the same computer as MassLynx have still experienced difficulty; not to worry, there is a small tool that uses MassWolf to convert the files to mzXML. Contact support and we will provide you with the download link.

    • To run the program, open 'massWolfConverter.jar'.
    • Select the Browse button to choose the raw files to be converted.
    • Use the 'select output folder' browse button to select where to place the converted files.
    • Select the massWolf executable browse button to use a different version of massWolf if you use an older version of MassLynx.
    • The converted mzXML files can be loaded into PEAKS on a computer that does not have MassLynx on it.