Sirius Fingerprint#

Processes: .mgf

Returns: CSI:FingerID (.tsv)

This step serves as a python interface to the Cli mode of Sirius. The general functionality of the step is simple; The step takes a list of .mgf files and creates CSI:FingerID for all compounds.

Requirements#

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

Download Sirius

Arguments#

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

  • sirius_path: Python Path containing the absolute path to the Sirius executable

  • instrument: Indicate what instrument was used. Possible values are orbitrap, qtof and fticr

  • set_max_mz: Boolean, indicating weather maxmz should be used. When set to true Only consider compounds with a precursor m/z lower or equal max_mz. All other compounds in the input will be skipped.

  • (Optional) max_mz: If set_max_mz is True, this value is considered (and required!). Otherwise, the value is skipped. When set only consider compounds with a precursor m/z lower or equal max_mz. All other compounds in the input will be skipped. Default value is Infinity

Data processing#

Note

All step descriptions are directly copied from the SIRIUS CLI --help command

This step imports all provided .mgf files. It then does the following steps:

  1. Compound Tool: Identify molecular formulas for each compound individually using fragmentation trees and isotope patterns.

  2. Compound Tool: Predict molecular fingerprints from MS/MS and fragmentation trees for each compound individually using CSI: FingerID fingerprint prediction.

  3. Compound Tool: Search in molecular structure db for each compound individually using CSI: FingerID structure database search.

  4. Write summary files from a given project space into the given project space or a custom location.

Default paths#

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

  • Windows: -

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

  • Linux: /home/{username}/sirius/bin/sirius

Usage#

from expectmine.steps.steps.sirius_fingerprint import SiriusFingerprint

pipeline.add_step(
    SiriusFingerprint,
    {
        "sirius_path": Path(
            "/Applications/sirius.app/Contents/MacOS/sirius", absolute=True
        ),
        "set_max_mz": False,
        "instrument": "orbitrap",
    },
)

from expectmine.steps.steps.sirius_fingerprint import SiriusFingerprint
from expectmine.io.io.dict_io import DictIo

pipeline.add_step(
    SiriusFingerprint,
    DictIo({
        "sirius_path": Path(
            "/Applications/sirius.app/Contents/MacOS/sirius", absolute=True
        ),
        "set_max_mz": False,
        "instrument": "orbitrap",
    }),
)

from expectmine.steps.steps.sirius_fingerprint import SiriusFingerprint
from expectmine.io.io.cli_io import CliIo

pipeline.add_step(
    SiriusFingerprint,
    CliIo()
)

Further Info#