Computational tools and algorithms for ion mobility spectrometry-mass spectrometry

Ross, Dylan H.; Bhotika, Harsh; Zheng, Xueyun; Smith, Richard D.; Burnum‐Johnson, Kristin E.; Bilbao, Aivett

doi:10.1002/pmic.202200436

Title: Computational tools and algorithms for ion mobility spectrometry-mass spectrometry

Journal Article · 03 March 2024 · Proteomics

DOI: https://doi.org/10.1002/pmic.202200436 · OSTI ID:2407038

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Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States). Environmental Molecular Sciences Laboratory (EMSL)

Ion mobility spectrometry-mass spectrometry (IMS-MS or IM-MS) is a powerful analytical technique that combines the gas-phase separation capabilities of IM with the identification and quantification capabilities of MS. IM-MS can differentiate molecules with indistinguishable masses but different structures (e.g., isomers, isobars, molecular classes, and contaminant ions). The importance of this analytical technique is reflected by a staged increase in the number of applications for molecular characterization across a variety of fields, from different MS-based omics (proteomics, metabolomics, lipidomics, etc.) to the structural characterization of glycans, organic matter, proteins, and macromolecular complexes. With the increasing application of IM-MS there is a pressing need for effective and accessible computational tools. This article presents an overview of the most recent free and open-source software tools specifically tailored for the analysis and interpretation of data derived from IM-MS instrumentation. This review enumerates these tools and outlines their main algorithmic approaches, while highlighting representative applications across different fields. Finally, a discussion of current limitations and expectable improvements is presented.

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Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States). Environmental Molecular Sciences Laboratory (EMSL)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institute of General Medical Sciences

Grant/Contract Number:: AC05-76RL01830

OSTI ID:: 2407038

Report Number(s):: PNNL-SA--192094

Journal Information:: Proteomics, Journal Name: Proteomics Journal Issue: 12-13 Vol. 24; ISSN 1615-9853

Publisher:: WileyCopyright Statement

Country of Publication:: United States

Language:: English

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The Role of Ion Rotation in Ion Mobility: Ultrahigh-Precision Prediction of Ion Mobility Dependence on Ion Mass Distribution and Translational to Rotational Energy Transfer Harrilal, Christopher P.; Garimella, Sandilya V. B.; Chun, Jaehun The Journal of Physical Chemistry A, Vol. 127, Issue 25 https://doi.org/10.1021/acs.jpca.3c01264	journal	June 2023
Collision Cross Section Prediction Based on Machine Learning Li, Xiaohang; Wang, Hongda; Jiang, Meiting Molecules, Vol. 28, Issue 10 https://doi.org/10.3390/molecules28104050	journal	May 2023
imzML — A common data format for the flexible exchange and processing of mass spectrometry imaging data Schramm, Thorsten; Hester, Zoë; Klinkert, Ivo Journal of Proteomics, Vol. 75, Issue 16 https://doi.org/10.1016/j.jprot.2012.07.026	journal	August 2012
Tandem-trapped ion mobility spectrometry/mass spectrometry (tTIMS/MS): a promising analytical method for investigating heterogenous samples Liu, Fanny C.; Ridgeway, Mark E.; Park, Melvin A. The Analyst, Vol. 147, Issue 11 https://doi.org/10.1039/D2AN00335J	journal	January 2022
Coupling High-Field Asymmetric Waveform Ion Mobility Spectrometry with Capillary Zone Electrophoresis-Tandem Mass Spectrometry for Top-Down Proteomics Xu, Tian; Wang, Qianjie; Wang, Qianyi Analytical Chemistry, Vol. 95, Issue 25 https://doi.org/10.1021/acs.analchem.3c00551	journal	May 2023
High-end ion mobility mass spectrometry: A current review of analytical capacity in omics applications and structural investigations Delafield, Daniel G.; Lu, Gaoyuan; Kaminsky, Cameron J. TrAC Trends in Analytical Chemistry, Vol. 157 https://doi.org/10.1016/j.trac.2022.116761	journal	December 2022
High-Sensitivity Ion Mobility Spectrometry/Mass Spectrometry Using Electrodynamic Ion Funnel Interfaces Tang, Keqi; Shvartsburg, Alexandre A.; Lee, Hak-No Analytical Chemistry, Vol. 77, Issue 10, p. 3330-3339 https://doi.org/10.1021/ac048315a	journal	May 2005
Structural amyloid plaque polymorphism is associated with distinct lipid accumulations revealed by trapped ion mobility mass spectrometry imaging Michno, Wojciech; Wehrli, Patrick M.; Koutarapu, Srinivas Journal of Neurochemistry, Vol. 160, Issue 4 https://doi.org/10.1111/jnc.15557	journal	December 2021
Carbon cluster cations with up to 84 atoms: structures, formation mechanism, and reactivity von Helden, Gert; Hsu, Ming Teh; Gotts, Nigel The Journal of Physical Chemistry, Vol. 97, Issue 31 https://doi.org/10.1021/j100133a011	journal	August 1993
The power of ion mobility-mass spectrometry for structural characterization and the study of conformational dynamics Lanucara, Francesco; Holman, Stephen W.; Gray, Christopher J. Nature Chemistry, Vol. 6, Issue 4 https://doi.org/10.1038/nchem.1889	journal	March 2014
A fully automated FAIMS-DIA mass spectrometry-based proteomic pipeline Reilly, Luke; Lara, Erika; Ramos, Daniel Cell Reports Methods, Vol. 3, Issue 10 https://doi.org/10.1016/j.crmeth.2023.100593	journal	October 2023
Ion Mobility-Mass Spectrometry Imaging Workflow Mesa Sanchez, Daniela; Creger, Steve; Singla, Veerupaksh Journal of the American Society for Mass Spectrometry, Vol. 31, Issue 12 https://doi.org/10.1021/jasms.0c00142	journal	August 2020
Dynamic Time-Warping Correction for Shifts in Ultrahigh Resolving Power Ion Mobility Spectrometry and Structures for Lossless Ion Manipulations Hollerbach, Adam L.; Conant, Christopher R.; Nagy, Gabe Journal of the American Society for Mass Spectrometry, Vol. 32, Issue 4 https://doi.org/10.1021/jasms.1c00005	journal	March 2021
Software Requirements for the Analysis and Interpretation of Native Ion Mobility Mass Spectrometry Data Allison, Timothy M.; Barran, Perdita; Benesch, Justin L. P. Analytical Chemistry, Vol. 92, Issue 16 https://doi.org/10.1021/acs.analchem.9b05792	journal	July 2020
Breaking Down Structural Diversity for Comprehensive Prediction of Ion-Neutral Collision Cross Sections Ross, Dylan H.; Cho, Jang Ho; Xu, Libin Analytical Chemistry, Vol. 92, Issue 6 https://doi.org/10.1021/acs.analchem.9b05772	journal	February 2020
AlphaTims: Indexing Trapped Ion Mobility Spectrometry–TOF Data for Fast and Easy Accession and Visualization Willems, Sander; Voytik, Eugenia; Skowronek, Patricia Molecular & Cellular Proteomics, Vol. 20 https://doi.org/10.1016/j.mcpro.2021.100149	journal	January 2021
Evaluating Software Tools for Lipid Identification from Ion Mobility Spectrometry–Mass Spectrometry Lipidomics Data Ross, Dylan H.; Guo, Jian; Bilbao, Aivett Molecules, Vol. 28, Issue 8 https://doi.org/10.3390/molecules28083483	journal	April 2023
Native LESA TWIMS-MSI: Spatial, Conformational, and Mass Analysis of Proteins and Protein Complexes Hale, Oliver J.; Sisley, Emma K.; Griffiths, Rian L. Journal of the American Society for Mass Spectrometry, Vol. 31, Issue 4 https://doi.org/10.1021/jasms.9b00122	journal	February 2020
gc-ims-tools – A new Python package for chemometric analysis of GC–IMS data Christmann, Joscha; Rohn, Sascha; Weller, Philipp Food Chemistry, Vol. 394 https://doi.org/10.1016/j.foodchem.2022.133476	journal	November 2022
Drift time-specific collision energies enable deep-coverage data-independent acquisition proteomics Distler, Ute; Kuharev, Jörg; Navarro, Pedro Nature Methods, Vol. 11, Issue 2 https://doi.org/10.1038/nmeth.2767	journal	December 2013
Predicting Ion Mobility Collision Cross-Sections Using a Deep Neural Network: DeepCCS Plante, Pier-Luc; Francovic-Fontaine, Élina; May, Jody C. Analytical Chemistry, Vol. 91, Issue 8 https://doi.org/10.1021/acs.analchem.8b05821	journal	February 2019
Investigating Performance of the SLIM-Based High Resolution Ion Mobility Platform for Separation of Isomeric Phosphatidylcholine Species Kedia, Komal; Harris, Rachel; Ekroos, Kim Journal of the American Society for Mass Spectrometry, Vol. 34, Issue 10 https://doi.org/10.1021/jasms.3c00157	journal	September 2023
New frontiers for mass spectrometry based upon structures for lossless ion manipulations Ibrahim, Yehia M.; Hamid, Ahmed M.; Deng, Liulin The Analyst, Vol. 142, Issue 7 https://doi.org/10.1039/c7an00031f	journal	January 2017
A novel projection approximation algorithm for the fast and accurate computation of molecular collision cross sections (I). Method Bleiholder, Christian; Wyttenbach, Thomas; Bowers, Michael T. International Journal of Mass Spectrometry, Vol. 308, Issue 1 https://doi.org/10.1016/j.ijms.2011.06.014	journal	November 2011

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97 MATHEMATICS AND COMPUTING
59 BASIC BIOLOGICAL SCIENCES
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proteomics
software

Title: Computational tools and algorithms for ion mobility spectrometry-mass spectrometry

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