We have now released msbuddy as a Python package and a command-line tool.

msbuddy: https://github.com/Philipbear/msbuddy

msbuddy documentation: https://msbuddy.readthedocs.io/en/latest

Note: msbuddy and BUDDY and two different tools that share the same core algorithm. They generate different annotation results. msbuddy is newly developed for flexible molecular formula analysis with refined algorithmic design and model training. We'd recommend using msbuddy for your latest analysis.

BUDDY is an open-source cheminformatic software platform developed for MS-based metabolomics research, capitalizing on bottom-up MS/MS interrogation and experiment-specific global peak annotation.

Bottom-up MS/MS interrogation aims to determine molecular formulae for all metabolic features with significance estimation. Experiment-specific global peak annotation is achieved to select the optimal molecular network considering both individual peak annotations and peak interrelationships.

Check out our Youtube tutorial video here.

BUDDY can be freely downloaded on this GitHub release page.

We provide a graphical user interface shown as below.

• MS/MS library search
• Bottom-up MS/MS interrogation
• Experiment-specific global peak annotation

• Single query import (pop-up window)
• Batch import (metabolic feature table, mzML file, mgf file)

• Single export (a single query feature)
• Batch export in a hierarchical manner (file – metabolic feature – candidate formula – explained MS/MS)

Detailed instructions on BUDDY can be found in BUDDY user manual.

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