Welcome to eMZed

Develop LCMS data analysis workflows the easy way

eMZed is an open source toolbox for rapid and interactive development of LCMS data analysis workflows in Python.

Example¶

import emzed

peak_map = emzed.io.load_peakmap("test.mzML")
peaks = emzed.run_feature_finder_metabo(
    peak_map,
    mtd_noise_threshold_int=10000,
)

emzed.gui.inspect(peaks)

For more examples, see the tutorials section and the more advanded example workflow repository.

The core packages of eMZed¶

emzed is the core library for headless environments such as servers and HPC systems. You can find its documentation including many examples at https://emzed.readthedocs.io.
emzed-gui provides interactive inspection tools for samples and peak lists. The documentation is hosted at https://emzed-gui.readthedocs.io.
emzed-spyder provides the IDE integration and development environment, with further documentation at https://emzed-spyder.readthedocs.io.

Publications¶

Original eMZed publications:

Schmitt Uwe, Hemmann Jethro, Zamboni Nicola, Vorholt Julia, Kiefer Patrick. eMZed 3: flexible and interactive development of scalable LC-MS/MS data analysis workflows in Python, Bioinformatics Advances, Volume 6, Issue 1, 2026, vbag138, https://doi.org/10.1093/bioadv/vbag138
Kiefer Patrick, Schmitt Uwe, Vorholt Julia. eMZed: an open source framework in Python for rapid and interactive development of LC/MS data analysis workflows, Bioinformatics, Volume 29, Issue 7, Pages 963–964 (2013), https://doi.org/10.1093/bioinformatics/btt080

For publications using eMZed see the publications section.