MassCube Documentation

Hello! Welcome to the MassCube documentation!

Date: 2025-07-24 Version: 1.2.9

What is MassCube?

MassCube is a Python computing library for mass spectrometry data processing in metabolomics.

Features

• Open-source: Free for non-commercial use.

• Workflows: Run the entire data processing pipeline with a single command.

• Accurate: Efficient large-scale data processing with human-expert level accuracy.

• Modules: 16 modules to cover the whole workflow.

Getting Started

Release Notes for v1.2.9

• Only one database is needed for the untargeted metabolomics workflow. Make sure you download the latest version of MS/MS database.

• Improve the speed of gap filling by 30-40%.

• Bug fixes and performance improvements.