ArticleJournal of proteome research2022
A Preprocessing Tool for Enhanced Ion Mobility-Mass Spectrometry-Based Omics Workflows.
Article in Journal of proteome research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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Who cites it
50 citing papers in PubMed.
- A Legacy of Exposure: Lactational PFAS Transfer and Early-Life Accumulation in Northern Elephant Seals.Environment & health (Washington, D.C.) · 2026Article
- Solution Phase Protein Dynamics: Influences of ESI Buffers on Hydration.Analytical chemistry · 2026Article
- Rapid Chiral Analysis of Drugs with Multiple Stereocenters via High-Resolution Ion Mobility.Analytical chemistry · 2026Article
- Uncovering PFAS and halogenated chemicals using nontargeted analysis and the PFAS IMplementer for mass spectrometry (PIMMS).Science advances · 2026Article
- Insights into complementary exposomic targeted analysis and suspect screening approaches: a case study examining human serum for chemicals with LC-IMS-MS.Environmental science. Advances · 2026Article
- Evaluating Legacy and Emerging PFAS in Human Blood Collected from 2003 to 2021.Environmental science & technology · 2026Article
- Untargeted metabolomics and lipidomics to study autophagy induction in mouse embryonic fibroblasts.Analytical and bioanalytical chemistry · 2026Article
- Computational Tools for LC-IMS-MS Data Processing in Metabolomics.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Metabolomics Analysis of Trypanosomes Using Ion Mobility-Enhanced Mass Spectrometry.Methods in molecular biology (Clifton, N.J.) · 2026Article
- De novo sequencing of glycans by ion mobility-mass spectrometry using a self-expanding database.Nature communications · 2025Article
- Hydration (HJournal of the American Chemical Society · 2025Article
- Updated Guidance for Communicating PFAS Identification Confidence with Ion Mobility Spectrometry.Environmental science & technology · 2025Article
- Rapid Annotation Strategy forJournal of the American Society for Mass Spectrometry · 2025Article
- Structure revision of scytonemin imine and its relationship to scytonemin chromism and cyanobacterial adaptability.Scientific reports · 2025Article
- Novel PFAS in alligator blood discovered with non-targeted ion mobility spectrometry-mass spectrometry.The Science of the total environment · 2025Article
- Increasing Oligonucleotide Sequencing Information and Throughput with Ion Mobility Spectrometry-Mass Spectrometry.Journal of the American Society for Mass Spectrometry · 2025Article
- Evaluating Ion Mobility Data Acquisition, Calibration, and Processing for Small Molecules: A Cross-Platform Assessment of Drift Tube and Traveling Wave Methodologies.Journal of the American Society for Mass Spectrometry · 2025Article
- Novel PFAS in Alligator Blood Discovered with Non-Targeted Ion Mobility Spectrometry-Mass Spectrometry.bioRxiv : the preprint server for biology · 2025Article
- FluoroMatch IM: An Interactive Software for PFAS Analysis by Ion Mobility Spectrometry.Environmental science & technology · 2025Article
- Identification and Structural Elucidation of Acylsugars in Tomato Leaves Using Liquid Chromatography-Ion Mobility-Tandem Mass Spectrometry (LC-IM-MS/MS).Journal of the American Society for Mass Spectrometry · 2025Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
The ability to improve the data quality of ion mobility-mass spectrometry (IM-MS) measurements is of great importance for enabling modular and efficient computational workflows and gaining better qualitative and quantitative insights from complex biological and environmental samples. We developed the PNNL PreProcessor, a standalone and user-friendly software housing various algorithmic implementations to generate new MS-files with enhanced signal quality and in the same instrument format. Different experimental approaches are supported for IM-MS based on Drift-Tube (DT) and Structures for Lossless Ion Manipulations (SLIM), including liquid chromatography (LC) and infusion analyses. The algorithms extend the dynamic range of the detection system, while reducing file sizes for faster and memory-efficient downstream processing. Specifically, multidimensional smoothing improves peak shapes of poorly defined low-abundance signals, and saturation repair reconstructs the intensity profile of high-abundance peaks from various analyte types. Other functionalities are data compression and interpolation, IM demultiplexing, noise filtering by low intensity threshold and spike removal, and exporting of acquisition metadata. Several advantages of the tool are illustrated, including an increase of 19.4% in lipid annotations and a two-times faster processing of LC-DT IM-MS data-independent acquisition spectra from a complex lipid extract of a standard human plasma sample. The software is freely available at https://omics.pnl.gov/software/pnnl-preprocessor.
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