MassCube Documentation

Hello! Welcome to the MassCube documentation!

Date: 2026-01-26 Version: 1.2.15

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 v1.2.15

• Scan-to-scan correlation values are now reported for annotated adducts and in-source fragments.
• Isotope state is clearly specified in the feature table (e.g. M+2 instead of “isotope”)
• Isotope recognition accuracy has been improved for high-resolution MS data: C and S isotopes can be better distinguished
• Feature grouping speed is now improved by 10-fold
• Bug fix: mzXML file may not correctly specify the isolation window for DDA, which can trigger an error for precursor ion fraction calculation
• Bug fix: in very rare cases, feature segmentation may fail
• Feature alignment speed is improved.
• Scan index (the index of the MS/MS scan in the raw reference file) is now provided for the MS/MS spectrum in the feature table that is used for annotation.

Previous patch notes can be found here.