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Preprocessing and feature extraction

PNNL PreProcessor

Preprocess multidimensional ion-mobility mass-spectrometry data with demultiplexing, smoothing, noise filtering, saturation repair, and format-conversion utilities.

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Overview

PNNL PreProcessor is a desktop preprocessing utility developed for ion-mobility mass spectrometry. It supports Agilent MassHunter and UIMF data from drift-tube and SLIM IM-MS platforms and provides operations including data compression/interpolation, ion-mobility demultiplexing, multidimensional smoothing, intensity-threshold and spike filtering, saturation repair, metadata export, and selected conversions that make IM information usable in downstream LC-MS-oriented workflows.

What can this tool do?

Spectral deconvolution

Common uses

  • Improve signal quality before downstream LC-IM-MS data processing.
  • Demultiplex and smooth ion-mobility data and remove low-intensity or spike noise.
  • Convert selected IM-MS data representations for use with downstream workflows.

Scientific fit

Primary function

Preprocessing and feature extraction

Other functions

Data conversion and import, Quality control and filtering

MS level

MS1, MS/MS

Acquisition

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

Ion mobility

Ion mobility required

Data compatibility

Inputs

Raw instrument data

Outputs

Raw instrument data

Input formats

Vendor raw format, Other, Agilent MassHunter .d, UIMF

Output formats

Vendor raw format, Other, Enhanced vendor-format MS files

Scope and considerations

Designed for

  • Preprocessing Agilent drift-tube and SLIM ion-mobility MS data before downstream omics analysis.

Not designed for

  • General-purpose metabolite annotation or statistical analysis.

Important requirements

  • Compatible Agilent MassHunter .d or UIMF input data and a supported desktop environment.

Considerations

  • Saturation repair can produce incorrect results for highly convoluted elution or mobility profiles; output logs should be inspected.

Access and documentation

Primary accessSource repository

The project distributes the binary free of charge, but the source code is closed because of vendor-format restrictions and use is subject to third-party library terms.

Evidence and review

Added from the 2026 computational-metabolomics review population and Springer computational-metabolomics methods coverage; scope and limitations checked against official PNNL documentation on 10 September 2026.

Core publications

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

  1. Bilbao A, et al. A Preprocessing Tool for Enhanced Ion Mobility-Mass Spectrometry-Based Omics Workflows. J Proteome Res (2021). doi:10.1021/acs.jproteome.1c00425
  2. Stow SM, et al. Exploring Ion Mobility Mass Spectrometry Data File Conversions to Leverage Existing Tools and Enable New Workflows. J Am Soc Mass Spectrom (2024). doi:10.1021/jasms.4c00220

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. 2026-09-10 · First committed entry

    Add PNNL PreProcessor tool entry

    View change · Entry at this revision

Full GitHub history