Bayesian Deconvolution of Mass and Ion Mobility Spectra: From Binary Interactions to Polydisperse Ensembles
Open accessAbstract
Interpretation of mass spectra is challenging because they report a ratio of two physical quantities, mass and charge, which may each have multiple components that overlap in m/z. Previous approaches to disentangling the two have focused on peak assignment or fitting. However, the former struggle with complex spectra, and the latter are generally computationally intensive and may require substantial manual intervention. We propose a new data analysis approach that employs a Bayesian framework to separate the mass and charge dimensions. On the basis of this approach, we developed UniDec (Universal Deconvolution), software that provides a rapid, robust, and flexible deconvolution of mass spectra and ion mobility-mass spectra with minimal user intervention. Incorporation of the charge-state distribution in the Bayesian prior probabilities provides separation of the m/z spectrum into its physical mass and charge components. We have evaluated our approach using systems of increasing complexity, enabling us to deduce lipid binding to membrane proteins, to probe the dynamics of subunit exchange reactions, and to characterize polydispersity in both protein assemblies and lipoprotein Nanodiscs. The general utility of our approach will greatly facilitate analysis of ion mobility and mass spectra.
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UniDec was developed to handle highly heterogeneous spectra, which has been critical for interpreting native protein mass spectra.
“UniDec was developed to handle highly heterogeneous spectra, which has been critical for the interpretation of native protein mass spectra [127].”
From Top-down proteomics: challenges, innovations, and applications in basic and clinical research (2020) · cites this paper as [127]
Charge state deconvolution with UniDec software detected larger proteoforms having molecular weights as high as 57 kDa.
“Using charge state deconvolution with UniDec software, 41 we were able to detect larger proteoforms with molecular weight up to 57 kDa (Figure S6).”
From Sensitive Top-Down Proteomics Analysis of a Low Number of Mammalian Cells Using a Nanodroplet Sample Processing Platform (2020) · cites this paper as [41]
Spectral interpretation of native MS has largely relied on manual analysis, although deconvolution software such as UniDec and iFAMS has been developed in recent years.
“Spectral interpretation of native MS has largely relied on manual analysis, although deconvolution software such as UniDec and iFAMS has been developed in recent years.60,114”
From Higher-order structural characterisation of native proteins and complexes by top-down mass spectrometry (2020) · cites this paper as [114]
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- Authors
- Marty, M. T., Baldwin, A. J., Marklund, E. G., Hochberg, G. K. A., Benesch, J. L. P., & Robinson, C. V.
- Affiliations
- University of Oxford (GB)
- Corresponding author
- Robinson, Carol V.
- ORCID
- Venue
- Analytical Chemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 2015-04-01
- Volume
- 87
- Issue
- 8
- Pages
- 4370-4376
- ISSN
- 0003-2700 (ISSN-L)
- 1520-6882
- PMC
- PMC4594776
- OpenAlex
- W2334348545
- Cited by
- 1,000
- References
- 47
- Citations by year
- 2026: 123 · 2025: 147 · 2024: 140 · 2023: 117 · 2022: 113 · 2021: 111 · 2020: 97 · 2019: 65 · 2018: 35 · 2017: 29 · 2016: 14 · 2015: 9
- FWCI
- 12.91
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Analytical Chemistry (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Biotechnology and Biological Sciences Research Council
- European Research Council (268851)
- Engineering and Physical Sciences Research Council
- Medical Research Council (G1000819)
- Carl Tryggers Stiftelse för Vetenskaplig Forskning
- Royal Society
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
- Keywords
- Bayesian deconvolution, ion mobility mass spectrometry, charge state distribution, polydispersity, protein-lipid binding, membrane proteins, protein assembly, binary interaction
- MeSH terms
- Algorithms, Bayes Theorem, Proteins, Spectrometry, Mass, Electrospray Ionization
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