U.S. Department of Energy

Pacific Northwest National Laboratory

PNNL PreProcessor

Ion mobility mass spectrometry is an emerging method of molecular characterization. We provide here a software tool for applying various pre-processing algorithms to raw data generated by this technology: multidimensional smoothing, saturation repair, noise filtering and ion mobility demultiplexing.


In close collaboration with Agilent Technologies, we have developed this user-friendly tool which directly reads Agilent MassHunter (.d) data files and generates new data files with enhanced raw signal quality.

Software features:

  • Command-line and graphical user interfaces.
  • Single-click batch processing of multiple .d data files.
  • Multidimensional smoothing and repair of saturated peaks.
  • PNNL demultiplexing and artifact removal algorithm integrated.
  • A new algorithm to remove noise in form of ‘spikes’.
  • Ion mobility MS with/without any separation: LC-IM-MS, solid phase extraction (e.g. RapidFire) IM-MS and direct infusion IM-MS.
  • All-Ions data (data-independent acquisition).
  • Metadata export of ion mobility acquisition parameters.
  • Multidimensional smoothing for non-ion mobility TOF-MS data files (e.g. produced by 6544 and 6545 Agilent TOF instruments).
  • PNNL UIMF format supported.

New features:

  • New design of the user interface (workflow style).
  • Data compression (by frame and mobility) and filtering by retention time range.
  • Optional software installer.

Increase significantly the number of features consistently detected across your multiple runs while reducing the file size and time for downstream processing.

Smoothing example

Smoothing removes artifacts in jagged peaks, common in low abundance ions. Real signals are enhanced, and variations in abundance, elution and mobility/collisional-cross-section are reduced.

Disclaimer: the saturation repair software may produce incorrect results for ions with highly convoluted elution/mobility profiles caused by interferences. Please use the current version at your own risk and check the output log files in each data file to verify the repairs made.

If you use PNNL PreProcessor, please cite: Bilbao et al. coming soon…


Package icon Software8.73 MB
Package icon Software with installer4.19 MB
PDF icon User Guide4.14 MB


All publications that utilize this software should provide appropriate acknowledgement to PNNL and the OMICS.PNL.GOV website. However, if the software is extended or modified, then any subsequent publications should include a more extensive statement, as shown in the Readme file for the given application or on the website that more fully describes the application.



These programs are primarily designed to run on Windows machines. Please use them at your own risk. This material was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor the United States Department of Energy, nor Battelle, nor any of their employees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness or any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights.

Portions of this research were supported by the NIH National Center for Research Resources (Grant RR018522), the W.R. Wiley Environmental Molecular Science Laboratory (a national scientific user facility sponsored by the U.S. Department of Energy's Office of Biological and Environmental Research and located at PNNL), and the National Institute of Allergy and Infectious Diseases (NIH/DHHS through interagency agreement Y1-AI-4894-01). PNNL is operated by Battelle Memorial Institute for the U.S. Department of Energy under contract DE-AC05-76RL0 1830.

We would like your feedback about the usefulness of the tools and information provided by the Resource. Your suggestions on how to increase their value to you will be appreciated. Please e-mail any comments to proteomics@pnl.gov

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