MassCube Documentation

Hello! Welcome to the MassCube documentation!

Date: 2025-11-12 Version: 1.2.12

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: Complete 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

Must reads

• Starting from MassCube ver. 1.2.8, only one database is needed for the untargeted metabolomics workflow. Make sure you download the latest version of MS/MS database.

Release Notes for v1.2.12

• Split the feature segmentation method into a standalone module.

• Re-optimized parameters for gf-prominence method (sigma = 0.6, prom_ratio = 0.02).

• Fixed overly long peak shape output in the aligned feature table.

• Updated formula_to_isotope_distribution function.

• Minor text and code edits.