Computational tools and algorithms for ion mobility spectrometry‐mass spectrometry

Abstract

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.

PeakQC: A Software Tool for Omics-Agnostic Automated Quality Control of Mass Spectrometry Data

“…Future improvements could also include additional metrics for MS2 matching (since currently it is limited to visualization) and for LC, like full-width-at-half-maximum and peak asymmetry. Moreover, alternative error detection methods will be implemented by leveraging modern AI techniques, which offers an exciting opportunity to reimagine algorithms which operate seamlessly from the MS raw data …”

“…To address these challenges, we developed PeakQC, a novel software tool designed for omics-agnostic automated QC of MS data. It performs automated extraction of QC metrics and supports various instrumentations and acquisition schemes, from infusion experiments, to liquid chromatography (LC), and ion mobility spectrometry (IMS) front-end separations, and with/without fragmentation spectra from data-dependent acquisition (DDA) or data-independent acquisition (DIA) modes . We illustrate how PeakQC applies omics-agnostic algorithmic strategies and leverages machine learning techniques to provide a robust framework for rapid, accurate, and unbiased assessment of MS data quality.…”

Elucidation of Dithiol-yne Comb Polymer Architectures by Tandem Mass Spectrometry and Ion Mobility Techniques

“…Theoretical Ω values were calculated using the MOBCAL program and He as collision gas [ 42 ]. For each comb copolymer, the corresponding x, y, and z coordinates of each atom, including the sodium counter ion, were copied into the software, and the calculations were run for 50 conformations.…”

Exploring Ion Mobility Mass Spectrometry Data File Conversions to Leverage Existing Tools and Enable New Workflows

“…12 When used in conjunction with AMRT, CCS provides an additional metric that increases confidence for annotating ion species. 13 MS-based identification strategies also typically rely on ion fragmentation. Fragmentation strategies are generally split into data-dependent acquisition (DDA) and data-independent acquisition (DIA) methodologies.…”

“…IM ATs can be converted to collision cross section (CCS) values which are correlated with the structure of the molecule and therefore show better agreement across instrument platforms and with different instrument methods . When used in conjunction with AMRT, CCS provides an additional metric that increases confidence for annotating ion species …”