msbuddy 0.1.1

Bottom-up MS/MS interrogation-based molecular formula annotation for mass spectrometry data.

msbuddy

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msbuddy is in final training process and will be released soon.

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msbuddy is developed for molecular formula annotation in mass spectrometry-based small molecule analysis.

• msbuddy is able to provide formula annotations for:
  • metabolic features with or without MS1 isotopic pattern
  • metabolic features with or without MS/MS spectra
  • both positive and negative ionization modes
• msbuddy enables:
  • candidate space shrinkage via bottom-up MS/MS interrogation
  • accurate formula annotation via machine learning
  • false discovery rate estimation

Python API

The entire documentation is available at msbuddy Documentation.

Installation

msbuddy is available on PyPI, you can install it via pip:

pip install msbuddy

Quick Start

As a quick start, we here load a mgf file and annotate the molecular formula for each MS/MS spectrum:

from msbuddy import Buddy

# instantiate a Buddy object
buddy = Buddy()

# load data, here we use a mgf file as an example
buddy.load_mgf('input_file.mgf')

# annotate molecular formula
buddy.annotate_formula()

# retrieve the annotation result summary
result = buddy.get_summary()

To specify the parameter settings, you can use the BuddyParamSet object:

from msbuddy import Buddy, BuddyParamSet

# instantiate a BuddyParamSet object
param = BuddyParamSet(ppm = True, ms1_tol = 5, ms2_tol = 10,
                      halogen = False, timeout_secs = 300)
                      
# instantiate a Buddy object with the specified parameter settings
buddy = Buddy(param)

MS/MS spectra can also be loaded via their USIs:

buddy.load_usi('mzspec:GNPS:GNPS-LIBRARY:accession:CCMSLIB00003740036')

# you can also load a list of USIs at once
buddy.load_usi(['mzspec:GNPS:GNPS-LIBRARY:accession:CCMSLIB00003740036',
                'mzspec:GNPS:GNPS-LIBRARY:accession:CCMSLIB00003740037'])

Command-line API

msbuddy can also be used as a command-line tool:

msbuddy --mgf <mgf file> --output <output folder>

or for a csv file containing USI strings (one USI per line):

msbuddy --csv <csv file> --output <output folder>

Run the following command to see the full list of options:

msbuddy --help

Documentation

Link to msbuddy Documentation

Citation

S. Xing et al. BUDDY: molecular formula discovery via bottom-up MS/MS interrogation. Nature Methods 2023. DOI: 10.1038/s41592-023-01850-x

License

This work is licensed under the MIT license.

Contact

To contribute to msbuddy, please feel free to file an issue, or submit a pull request with improvements.

You are also welcome to directly contact the maintainer Shipei Xing ([e-mail]).