Documentation

MassCube Documentation

Hello! Welcome to the MassCube documentation!

Date: 2026-08-17 Version: 1.2.21

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

Installation Quick Start

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 v1.2.20 and v1.2.21

Added structured file metadata and consistent extension-free filenames.
Replaced scan id with the clearer raw_file_id, with compatibility for older mzpkl files.
Improved MS/MS library loading and annotation error handling. Empty experimental MS/MS spectra can now be correctly handled. We thank Kruttika for reporting the issue.
Refined feature finalization, peak boundaries, and visualization.

Previous patch notes can be found here.