MassCube Documentation

Hello! Welcome to the MassCube documentation!

Date: 2026-03-19 Version: 1.2.19

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.

Patch notes for v1.2.19

• Improved the alignment accuracy by optimizing the alignment strategy. RT and m/z errors were considered together for better alignment results.
• The finally reported m/z value for aligned feature is now the median m/z value across all samples instead of the m/z value in the reference sample.
• Upper limits for mz_tol_ms1 and mz_tol_ms2 were set to 5.0 Da (0.02 Da before) for low-resolution MS data.
• Code updates for database loading.
• Default centroid_mz_tol (i.e. MS1 ions with m/z difference lower than this value will be combined before processing, designed for bad data deconvolution from Orbitrap MS) is changed from 5 mDa to 2 mDa.
• Other minor changes of code notes.
• New safe float function for better raw data loading.
• Better indicators for error handling in the workflow.

Previous patch notes can be found here.