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Preprocessing and feature extraction

DEIMoS

An open-source Python and command-line toolkit for high-dimensional mass-spectrometry processing, including feature detection and alignment, CCS calibration, isotope detection, and MS/MS spectral deconvolution.

Multiple analytical platformsUntargeted metabolomicsPython packageCommand lineOpen source
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Overview

DEIMoS provides an API and command-line components for multidimensional MS processing, including feature detection, alignment, isotope detection, CCS calibration and MS/MS deconvolution. Users compose these components into workflows appropriate to their acquisition dimensions.

What can this tool do?

Peak or feature detectionRetention-time alignmentSpectral deconvolutionMS/MS processing

Common uses

  • Process multidimensional MS datasets using multiple measured dimensions simultaneously.
  • Detect and align features while retaining ion-mobility or other separation dimensions.
  • Perform CCS calibration and MS/MS spectral deconvolution.

Scientific fit

Primary function

Preprocessing and feature extraction

Other functions

Spectral processing and comparison, Metabolite annotation and identification

Analysis types

Untargeted metabolomics

MS level

MS1, MS/MS

Acquisition

Full-scan MS, Data-dependent acquisition (DDA), Data-independent acquisition (DIA), General or unspecified acquisition

Ion mobility

Ion mobility supported

Data compatibility

Inputs

Mass spectra, Feature or peak table

Outputs

Feature or peak table, Mass spectra

Input formats

mzML, HDF5

Output formats

CSV or TSV, HDF5

Scope and considerations

Designed for

  • High-dimensional mass-spectrometry data processing where dimensions such as retention time and ion mobility improve separation.

Not designed for

  • Predicting CCS from molecular structures or automatically identifying compounds solely from detected features.

Important requirements

  • A Python environment with DEIMoS dependencies and data represented in the dimensions expected by the selected processing functions; calibration data are needed for CCS calibration.

Considerations

  • DEIMoS is code-oriented and requires users to design or adapt a processing workflow around its API/CLI.

Access and documentation

Primary accessSource repository

BSD-3-Clause source distribution; consult the installation and API documentation when composing a workflow.

License: BSD-3-Clause

Evidence and review

Enveda intake rechecked against official README/documentation, repository access terms and primary publication metadata on 2026-10-27. Editorial source review only; no software execution or independent benchmarking. See docs/enveda-expansion-review-2026-10-27.md.

Core publications

Resource papers, direct updates and tool-specific methods. Selection policy.

  1. DEIMoS: An Open-Source Tool for Processing High-Dimensional Mass Spectrometry Data. Analytical Chemistry (2022). doi:10.1021/acs.analchem.1c05017

Related tools

asariSimilar function · Process high-resolution mass-spectrometry data into aligned feature tables.AutoCCSSimilar function · An open-source Python tool for calculating and calibrating experimental collision cross sections from ion-mobility mass-spectrometry data across drift-tube and traveling-wave workflows.BreathXplorerSimilar function · breathXplorer processes high-resolution breath mass-spectrometry data with feature extraction, alignment and breath-recognition functions.CAMERASimilar function · Group and annotate related LC-MS signals after XCMS peak detection.

Entry history

Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.

  1. 2026-10-27 · First committed entry

    Add 27 source-reviewed tools from Enveda intake

    View change · Entry at this revision

Full GitHub history