eMZed 3: flexible and interactive development of scalable LC-MS/MS data analysis workflows in Python

TL;DR

eMZed 3 is a Python framework that offers flexible, scalable, and interactive tools for LC-MS/MS data analysis, supporting diverse workflows and environments.

Contribution

It introduces a modular, Python 3-based framework with enhanced features like chromatogram support and interactive visualization, building on its predecessor.

Findings

Supports both targeted and untargeted metabolomics.

Enables integration into headless Python environments and notebooks.

Provides scalable, reproducible LC-MS data analysis workflows.

Abstract

Liquid chromatography-mass spectrometry (LC-MS/MS) data analysis requires adaptable software solutions to meet diverse analytical needs. We present eMZed 3, a modern Python framework for flexible and interactive analysis of LC-MS/MS data. eMZed 3 enables users to develop scalable workflows tailored to their specific requirements while leveraging Python's extensive ecosystem of libraries. Building on its predecessor, eMZed 3 is now Python 3-based and includes substantial enhancements, including support for chromatogram-based LC-MS data, a new SQLite-based backend supporting optional out-of-memory processing, and rich interactive visualization tools. Compared to the previous version, eMZed 3 is now split into three packages: emzed (core functionalities), emzed-gui (interactive data visualization), and emzed-spyder (an integrated development environment). This modular architecture allows straightforward integration of the emzed core library into headless Python environments, including computational notebooks (such as Jupyter) or high-performance computing clusters. eMZed 3 incorporates well-established libraries such as OpenMS, and is highly suited for both targeted and untargeted metabolomics. Overall, eMZed 3 supports the efficient development of scalable and reproducible LC-MS data analysis and is accessible to both novice and advanced programmers. Availability and Implementation: eMZed 3 and its documentation are freely available at https://emzed.ethz.ch, the source code is hosted at https://gitlab.com/groups/emzed3. An online-executable example workflow is available on Binder at: https://mybinder.org/v2/gl/emzed3%2Femzed-example-workflow/HEAD?labpath=example.ipynb.