MZmine3#

Processes: .mzML

Returns: .mgf

This step serves as a python interface to the batch process of the MZmine3 CLI. The general functionality of the step is simple; The step takes a batchfile (XML) adds the input of the previous step of the pipeline, applies the batchfile to it and exports the data as .mgf for Sirius to use.

Requirements#

To be able to use MZmine3 you need to have MZmine3 installed and know where the executable is stored. If you are unsure where to find it, take a look at the documentation of MZmine3.

Download MZmine3

Note

If you dont include input or output steps in your batchfile, default steps are atomatically added to your batchfile.

To find out how you can create a batchfile, check out the following link: Batch mode

Arguments#

To step requires the following arguments (if combined with DictIO):

  • mzmine3_path: Python Path containing the absolute path to the MZmine3 executable

  • batchfile: Python Path containing the path to the batchfile which should be used.

  • (Optional) spectral_library_files: Python list of Path If spectral library files where included in the batchfile, provide paths to the files used.

Data#

This step is processing regular .mzML files. It requires a batchfile to then process the given data using the recipe given by the batch file. After processing, the step outputs a .mgf file produced by the regular Export for  SIRIUS function from MZmine3. As all input files are imported simultaneously by MZmine3, the output will be a single .mgf file, regardless on how many input files where provided.

Default paths#

The default mzmine3_path is depending on the operating system you use:

  • Windows: -

  • Mac: /Applications/MZmine.app/Contents/MacOS/MZmine

  • Linux: /opt/mzmine-linux-installer/bin/MZmine

Usage#

from expectmine.steps.steps.mzmine3.mzmine3 import MZmine3

pipeline.add_step(
    MZmine3,
    {
        "mzmine3_path": Path(
            "/Applications/MZmine.app/Contents/MacOS/MZmine", absolute=True
        ),
        "batchfile": Path("testdata/2.xml"),
    },
)

from expectmine.steps.steps.mzmine3.mzmine3 import MZmine3
from expectmine.io.io.dict_io import DictIo

pipeline.add_step(
    MZmine3,
    DictIo({
        "mzmine3_path": Path(
            "/Applications/MZmine.app/Contents/MacOS/MZmine", absolute=True
        ),
        "batchfile": Path("testdata/2.xml"),
    }),
)

from expectmine.steps.steps.mzmine3.mzmine3 import MZmine3
from expectmine.io.io.cli_io import CliIo

pipeline.add_step(
    MZmine3,
    CliIo()
)

Known Issues#

  • When using peak finder (multithreaded) the export to sirius module can break. It is therefore recommended using the regular peak finder.

  • Using any other output step other than Export for SIRIUS can break the sirius export.

Further Info#