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Preprocessing and feature extraction

AutoCCS

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.

Multiple analytical platformsUntargeted metabolomicsPython packageCommand lineOpen source
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Overview

AutoCCS calculates experimental collision cross sections from ion-mobility measurements using stepped-field, single-field and traveling-wave workflows. It applies mode-specific calibration functions to prepared feature and instrument metadata.

What can this tool do?

Spectral data reading and writing

Common uses

  • Calculate CCS values from stepped-field or single-field drift-tube IMS-MS measurements.
  • Calibrate traveling-wave or SLIM ion-mobility measurements using reference compounds.

Scientific fit

Primary function

Preprocessing and feature extraction

Other functions

Metabolite annotation and identification

Analysis types

Untargeted metabolomics

MS level

MS1

Acquisition

General or unspecified acquisition

Ion mobility

Ion mobility required

Data compatibility

Inputs

Feature or peak table, Sample metadata

Outputs

Feature or peak table

Input formats

Feature/target CSV, XML configuration and acquisition/calibrant metadata

Output formats

Experimental CCS result tables and calibration outputs

Scope and considerations

Designed for

  • Processing ion-mobility measurements into calibrated collision cross sections.

Not designed for

  • CCS prediction directly from a molecular structure or compound identification based on CCS alone.

Important requirements

  • Python environment, feature CSVs, an XML instrument configuration and acquisition metadata; single-field/TWIMS modes also require suitable calibrants and sample metadata.

Considerations

  • Calibration model, reference CCS values and acquisition conditions affect reported values. Check method applicability before comparing CCS across platforms.

Access and documentation

Primary accessDocumentation

BSD-2-Clause software with worked examples. Users must supply or generate instrument-compatible feature and calibration inputs.

License: BSD-2-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. AutoCCS: automated collision cross-section calculation software for ion mobility spectrometry–mass spectrometry. Bioinformatics (2021). doi:10.1093/bioinformatics/btab429

Related tools

asariSimilar function · Process high-resolution mass-spectrometry data into aligned feature tables.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.CCSfindSimilar function · CCSfind builds experimentally derived small-molecule databases from LC-drift-tube-ion-mobility-MS data.

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