PNNL PreProcessor

Ion mobility-mass spectrometry (IM-MS) provides an increasingly popular platform for analyzing complex samples due to its separation power and ability to differentiate structural isomers, which are difficult to resolve using conventional LC-MS systems. Here we provide a software tool with various algorithms and utilities to improve workflows using this technology: data compression and interpolation, ion mobility demultiplexing, multidimensional smoothing, noise filtering by low intensity threshold and spike removal, saturation repair and metadata export.


In close collaboration between Pacific Northwest National Laboratory and Agilent Technologies, we have developed this user-friendly tool for Agilent MassHunter (.d) and UIMF mass spectrometry data files (MS-files) from drift tube (DT) and structure for lossless ion manipulations (SLIM) IM-MS platforms, to generate new MS-files in the same instrument data format with enhanced signal quality.


Software features:

New features:


Smoothing removes artifacts in jagged peaks, which are 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 the PreProcessor, please cite: Bilbao et al. A Preprocessing Tool for Enhanced Ion Mobility-Mass Spectrometry-Based Omics Workflows. Journal of Proteome Research 2021



Hardware Requirements

The hardware configuration used for development and testing, which provides reasonable performance:

An example hardware configuration that has significant processing time improvements for demultiplexing:

Software Requirements


All publications that utilize this software should provide appropriate acknowledgement to PNNL and the PNNL-Preprocessor publication. 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