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.

We will be soon releasing a python package pybuddy (hopefully in May 2023).

If you want to use BUDDY in large scale or in a more customizable manner, please stay tuned.

You are welcome to contact Shipei Xing ([email protected]) and Tao Huan ([email protected]) should you have any questions or suggestions.

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.

Any feedback or bug report is welcome. (https://github.com/Philipbear/BUDDY_Metabolomics/issues)

Shipei Xing, Sam Shen, Banghua Xu and Tao Huan. Molecular formula discovery via bottom-up MS/MS interrogation. bioRxiv, 2022.