Combining tandem mass spectrometry with ion mobility separation to determine the architecture of polydisperse proteins

Shepherd, Dale A.; Marty, Michael T.; Giles, Kevin; Baldwin, Andrew J.; Benesch, Justin L. P.

doi:10.1016/j.ijms.2014.09.007

Cited by 16 publications

(15 citation statements)

References 55 publications

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“…Charges in IM-MS spectra are usually assigned using the m/z dimension, but this is challenging in complex and overlapping spectra, where more sophisticated experimental approaches are required. 37…”

Section: Resultsmentioning

confidence: 99%

Bayesian Deconvolution of Mass and Ion Mobility Spectra: From Binary Interactions to Polydisperse Ensembles

et al. 2015

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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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Section: Resultsmentioning

confidence: 99%

Bayesian Deconvolution of Mass and Ion Mobility Spectra: From Binary Interactions to Polydisperse Ensembles

et al. 2015

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“…The difficulty arises in having to decide on the number of conformational families present in the data, and the selection of appropriate width for each Gaussian. Higher resolution IM instrumentation and use of tandem IM-MS approaches might enable the separation and resolution of overlapping populations, at least for certain types of samples. − …”

Section: Computational Considerations In Converting Native Im-ms Data...mentioning

confidence: 99%

Computational Strategies and Challenges for Using Native Ion Mobility Mass Spectrometry in Biophysics and Structural Biology

et al. 2020

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Native mass spectrometry (MS) allows the interrogation of structural aspects of macromolecules in the gas phase, under the premise of having initially maintained their solution-phase non-covalent interactions intact. In the more than 25 years since the first reports, the utility of native MS has become well established in the structural biology community. The experimental and technological advances during this time have been rapid, resulting in dramatic increases in sensitivity, mass range, resolution, and complexity of possible experiments. As experimental methods are improved, there have been accompanying developments in computational approaches for analysing and exploiting the profusion of MS data in a structural and biophysical context. Here, based on discussions within the EU COST Action BM1403 on Native MS and Related Methods for Structural Biology with broad participation from Europe and North America, we consider the computational strategies currently being employed by the community, aspects of best practice, and the challenges that remain to be addressed.

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“…Ion mobility spectrometry (IMS) is a well-established analytical method that separates ions and charged particles based on differences in their mobilities through a “buffer” gas. , IMS applications at present include the detection of chemical warfare agents, − illicit drugs, − and explosives − and more recently have been combined with mass spectrometry (i.e., ion mobility (IM)-MS) for the detection, separation, and characterization of biomolecules, e.g., in metabolomics, − glycomics, − and proteomics applications. − A constraint of contemporary IMS technology is its limited ability to resolve species with similar mobilities (<2%) in a mixture, particularly in conjunction with achieving high sensitivity. , In drift tube IMS, the resolving power ( R ) is often defined by where t D corresponds to an ion’s drift time, Δ t is the peak width at half-maximum (fwhm), q is the ion charge, T is the temperature, k b is Boltzmann’s constant, L is the length of the drift tube, and E is the electric field. Eq indicates resolving power can be increased by increasing E and L , or decreasing T , but the square root dependence makes achieving significantly higher resolution increasingly difficult.…”

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Ultra-High Resolution Ion Mobility Separations Utilizing Traveling Waves in a 13 m Serpentine Path Length Structures for Lossless Ion Manipulations Module

et al. 2016

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We report the development and initial evaluation of a 13 m path length Structures for Lossless Manipulations (SLIM) module for achieving high resolution separations using traveling waves (TW) with ion mobility (IM) spectrometry. The TW SLIM module was fabricated using two mirror-image printed circuit boards with appropriately configured RF, DC, and TW electrodes and positioned with a 2.75 mm intersurface gap. Ions were effectively confined in field-generated conduits between the surfaces by RF-generated pseudopotential fields and moved losslessly through a serpentine path including 44 “U” turns using TWs. The ion mobility resolution was characterized at different pressures, gaps between the SLIM surfaces, and TW and RF parameters. After initial optimization, the SLIM IM-MS module provided about 5-fold higher resolution separations than present commercially available drift tube or traveling wave IM-MS platforms. Peak capacity and peak generation rates achieved were 246 and 370 s-1, respectively, at a TW speed of 148 m/s. The high resolution achieved in the TW SLIM IM-MS enabled, e.g., isomeric sugars (lacto-N-fucopentaose I and lacto-N-fucopentaose II) to be baseline resolved, and peptides from an albumin tryptic digest were much better resolved than with existing commercial IM-MS platforms. The present work also provides a foundation for the development of much higher resolution SLIM devices based upon both considerably longer path lengths and multipass designs.

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Combining tandem mass spectrometry with ion mobility separation to determine the architecture of polydisperse proteins

Cited by 16 publications

References 55 publications

Bayesian Deconvolution of Mass and Ion Mobility Spectra: From Binary Interactions to Polydisperse Ensembles

Bayesian Deconvolution of Mass and Ion Mobility Spectra: From Binary Interactions to Polydisperse Ensembles

Computational Strategies and Challenges for Using Native Ion Mobility Mass Spectrometry in Biophysics and Structural Biology

Ultra-High Resolution Ion Mobility Separations Utilizing Traveling Waves in a 13 m Serpentine Path Length Structures for Lossless Ion Manipulations Module

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