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Fri, 21 Feb 2020 15:29:26 UTC — Version 2.18  

Instructions for Downloading and Running from MZmine PeakInvestigator® Edition and OpenMS PeakInvestigator® Edition


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Accessing PeakInvestigator™ using these tools requires registration with a login, password, and account number that can be obtained at

PeakInvestigator™ services are for research use only, and are not for use in diagnostic procedures.

MZmine PeakInvestigator® Edition

For information on using PeakInvestigator® software services through MZmine PeakInvestigator Edition, please consult PeakInvestigator Documentation.


  1. Install Java SE runtime (JRE) version 1.7 or later. For Windows, this is available from For Mac OS X, this is available from
  2. (Optional) Install Java3D (available from Java3D is required for the 3D visualizer module. On Mac OS X, Java3D is pre-installed by default.
  3. (Optional) Install R ( R is required for certain modules such as baseline correction or heat maps. The following packages must be installed in your R distribution: rJava, ptw, gplots, xcms and CAMERA.  To install them, run the following commands in R:
    install.packages(c("rJava", "ptw", "gplots"))

  4. Edit the startup script in a text editor and adjust the parameters in the script (e.g. HEAP_SIZE or JAVA_COMMAND), if necessary.  For integration with R you will need to correctly configure the following:

    R_HOME — This is the directory where R is installed, e.g. for Windows it will be something like C:\Program Files\R\R-3.0.3.

    R_LIBS_USER — This is the directory in which R installs third-party packages. It's usually a subdirectory of your personal directory, e.g. for Windows it will be something like %USERPROFILE%\Documents\R\win-library\3.0.

    PATH — Append the directory that contains R's libraries. It will be a subdirectory of %R_HOME%, e.g. for 64-bit Windows %R_HOME%\bin\x64 or for 32-bit Windows it will be something like %R_HOME%\bin\i386.

    JRI_LIB_PATH — This is the directory where rJava has installed its JRI libraries. It will be a subdirectory of %R_LIBS_USER%, e.g. for 64-bit Windows %R_LIBS_USER%\rJava\jri\x64 or for 32-bit Windows it will be something like %R_LIBS_USER%\rJava\jri\i386.

  5. (Optional) Install the MSFileReader library for reading Thermo RAW files directly (see the section RAW file import)


Download MZmine PeakInvestigator® Edition v2.23-PI

  1. Use the link above to download and unpack MZmine PeakInvestigator Edition into a folder of your choice.
  2. MZminePI is licensed under the GNU General Public License and the source code is also available for download.
  3. A editable startup script is provided for these systems.
    1. MS Windows (startMZmine_Windows.bat)
    2. Mac OS X (startMZmine_MacOSX.command)
    3. Linux (

OpenMS PeakInvestigator® Edition

This version of OpenMS, which is based on v2.1.0, incorporates the PeakInvestigator API for centroiding and deconvolving raw (profile) data into two new tools:

  • PeakInvestigatorSubmitJob for submitting raw, profile mass spec data to the PeakInvestigator servers for processing.
  • PeakInvestigatorFetchResults for retrieving results (mass lists) from the PeakInvestigator servers.

Download OpenMS-PI v2.1.0 from Github

For more information, and to sign-up for a Free Demo account, visit

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