Bottom-up MS/MS interrogation-based molecular formula annotation for mass spectrometry data.
Project description
msbuddy
.
msbuddy is in final training process and will be released soon.
.
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 (philipxsp@hotmail.com).
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