Thermo extractor CLI

The instrument settings are extracted from Thermo raw files by several (Windows-only) command-line applications: ThermoMetaData.exe extracts some metadata pertaining to the experiment, ThermoStatusLog.exe extracts the status log data, and ThermoTuneMethod.exe extracts the tune method data. All executables are included in the iMonDB Core jar package, and will be unpacked automatically when operating on Thermo raw files.

Because these extractors depend on the Thermo raw file functionality included in ProteoWizard, they are only available on a Microsoft Windows platform.

Running

The executables can be run from the command line and accept a single file name as argument; e.g.:

ThermoStatusLog.exe example-file.raw

The metadata extractor outputs the experiment's date and the instrument's accession number in the PSI-MS controlled vocabulary. The status log and tune method extractors output specific instrument parameters. All instrument parameters are printed on a separate line, with the name and value separated by a tab.

Dependencies

The extractor command-line applications depend on the following libraries that need to be installed before they can be run:

• Microsoft Visual C++ 2012 Redistributable (x86) (download from Microsoft)

Building

The Thermo extractor applications are based on ProteoWizard and can be built from source in the same fashion.

To build the Thermo extractor applications, first download the ProteoWizard source bjam build including vendor reader support, and extract the downloaded archive. The extracted sources will be available in the folder pwiz-src-version_number/. Next, the Thermo extractor sources need to be added. Create a new folder in the pwiz root folder called imondb/ and add all C++ source files and the JAM build file from here to this folder. This should result in the following directory structure:

pwiz-src-version_number
    imondb
        Jamfile.jam
        ThermoMetaData.cpp
        ThermoStatusLog.cpp
        ThermoTuneMethod.cpp
    libraries
    pwiz
    pwiz_aux
    pwiz_tools
    scripts
    clean.bat
    Jamroot.jam
    quickbuild.bat

Now the executables can be built by executing the following command from inside the pwiz root folder:

quickbuild.bat imondb --i-agree-to-the-vendor-licenses