Configuration

All msbuddy parameters are stored in a single class called msbuddy.MsbuddyConfig.

Here is a quick example of how to create a msbuddy.MsbuddyConfig object and pass it to a msbuddy.Msbuddy object. Of note, parallel processing is available for msbuddy. To use it, set parallel=True and specify the number of CPUs to use with n_cpu. We would recommend considering parallel processing for large datasets (e.g. >1000 query metabolic features).

from msbuddy import Msbuddy, MsbuddyConfig

# create a config object
msb_config = MsbuddyConfig(
    ms_instr='orbitrap', # highly recommended to fill for the best annotation performance
                         # supported MS types: "qtof", "orbitrap" and "fticr"
    ppm=True, # use ppm for mass tolerance, otherwise use Da
    ms1_tol=5, # ms1 tolerance, see below for default values for each MS instrument
    ms2_tol=10, # ms2 tolerance, see below for default values for each MS instrument
    halogen=True, # enable halogen atoms in molecular formula annotation
    # parallel=True, # enable parallel processing, see note below
    # n_cpu=12, # number of CPUs to use
    timeout_secs=600, # timeout for each query in seconds
    batch_size=1000, # number of queries to process in each batch, a larger batch size will use more memory but will be faster
    c_range=(0, 100), # range of carbon numbers to consider
    h_range=(0, 150), # range of hydrogen numbers to consider
    ... # other parameters
    )

# create a Msbuddy object with the specified configuration
msb_engine = Msbuddy(msb_config)

It is highly recommended to set up ms_instr in the msbuddy.MsbuddyConfig to obtain the best annotation performance. The supported MS types are "qtof", "orbitrap" and "fticr".

The following mass tolerances will be used for each MS instrument:

qtof: ms1 tolerance = 10 ppm, ms2 tolerance = 20 ppm

orbitrap: ms1 tolerance = 5 ppm, ms2 tolerance = 10 ppm

fticr: ms1 tolerance = 2 ppm, ms2 tolerance = 5 ppm

If you do need to use a different mass tolerance, you can set the ppm, ms1_tol and ms2_tol parameters in the msbuddy.MsbuddyConfig to the desired values.

msb_config = MsbuddyConfig(ppm=True, ms1_tol=10, ms2_tol=10)

Note that the halogen parameter is set to False by default. If you are working with halogenated compounds, you will need to set this to True to enable halgoen atoms in molecular formula annotation.

Note

To enable parallel processing, set parallel=True and specify the number of CPUs to use with n_cpu. The code has to be run in if __name__ == '__main__': block.

For more information on the parameters, see msbuddy.MsbuddyConfig.