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McCabe JW, Jones BJ, Walker TE, Schrader RL, Huntley AP, Lyu J, Hoffman NM, Anderson GA, Reilly PTA, Laganowsky A, Wysocki VH, Russell DH. Implementing Digital-Waveform Technology for Extended m/ z Range Operation on a Native Dual-Quadrupole FT-IM-Orbitrap Mass Spectrometer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2812-2820. [PMID: 34797072 PMCID: PMC9026758 DOI: 10.1021/jasms.1c00245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Here, we describe a digital-waveform dual-quadrupole mass spectrometer that enhances the performance of our drift tube FT-IMS high-resolution Orbitrap mass spectrometer (MS). The dual-quadrupole analyzer enhances the instrument capabilities for studies of large protein and protein complexes. The first quadrupole (q) provides a means for performing low-energy collisional activation of ions to reduce or eliminate noncovalent adducts, viz., salts, buffers, detergents, and/or endogenous ligands. The second quadrupole (Q) is used to mass-select ions of interest for further interrogation by ion mobility spectrometry and/or collision-induced dissociation (CID). Q is operated using digital-waveform technology (DWT) to improve the mass selection compared to that achieved using traditional sinusoidal waveforms at floated DC potentials (>500 V DC). DWT allows for increased precision of the waveform for a fraction of the cost of conventional RF drivers and with readily programmable operation and precision (Hoffman, N. M. . A comparison-based digital-waveform generator for high-resolution duty cycle. Review of Scientific Instruments 2018, 89, 084101).
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Affiliation(s)
- Jacob W McCabe
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Benjamin J Jones
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Thomas E Walker
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Robert L Schrader
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Adam P Huntley
- Department of Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Jixing Lyu
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Nathan M Hoffman
- Department of Chemistry, Washington State University, Pullman, Washington 99164, United States
| | | | - Peter T A Reilly
- Department of Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
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Abstract
Native mass spectrometry (MS) is aimed at preserving and determining the native structure, composition, and stoichiometry of biomolecules and their complexes from solution after they are transferred into the gas phase. Major improvements in native MS instrumentation and experimental methods over the past few decades have led to a concomitant increase in the complexity and heterogeneity of samples that can be analyzed, including protein-ligand complexes, protein complexes with multiple coexisting stoichiometries, and membrane protein-lipid assemblies. Heterogeneous features of these biomolecular samples can be important for understanding structure and function. However, sample heterogeneity can make assignment of ion mass, charge, composition, and structure very challenging due to the overlap of tens or even hundreds of peaks in the mass spectrum. In this review, we cover data analysis, experimental, and instrumental advances and strategies aimed at solving this problem, with an in-depth discussion of theoretical and practical aspects of the use of available deconvolution algorithms and tools. We also reflect upon current challenges and provide a view of the future of this exciting field.
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Affiliation(s)
- Amber D Rolland
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
| | - James S Prell
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States.,Materials Science Institute, University of Oregon, Eugene, Oregon 97403-1252, United States
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McCabe JW, Shirzadeh M, Walker TE, Lin CW, Jones BJ, Wysocki VH, Barondeau DP, Clemmer DE, Laganowsky A, Russell DH. Variable-Temperature Electrospray Ionization for Temperature-Dependent Folding/Refolding Reactions of Proteins and Ligand Binding. Anal Chem 2021; 93:6924-6931. [PMID: 33904705 DOI: 10.1021/acs.analchem.1c00870] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Stabilities and structure(s) of proteins are directly coupled to their local environment or Gibbs free energy landscape as defined by solvent, temperature, pressure, and concentration. Solution pH, ionic strength, cofactors, chemical chaperones, and osmolytes perturb the chemical potential and induce further changes in structure, stability, and function. At present, no single analytical technique can monitor these effects in a single measurement. Mass spectrometry and ion mobility-mass spectrometry play increasingly essential roles in studies of proteins, protein complexes, and even membrane protein complexes; however, with few exceptions, the effects of the solution temperature on the stability and structure(s) of analytes have not been thoroughly investigated. Here, we describe a new variable-temperature electrospray ionization (vT-ESI) source that utilizes a thermoelectric chip to cool and heat the solution contained within the static ESI emitter. This design allows for solution temperatures to be varied from ∼5 to 98 °C with short equilibration times (<2 min) between precisely controlled temperature changes. The performance of the apparatus for vT-ESI-mass spectrometry and vT-ESI-ion mobility-mass spectrometry studies of cold- and heat-folding reactions is demonstrated using ubiquitin and frataxin. Instrument performance for studies on temperature-dependent ligand binding is shown using the chaperonin GroEL.
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Affiliation(s)
- Jacob W McCabe
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Mehdi Shirzadeh
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Thomas E Walker
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Cheng-Wei Lin
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Benjamin J Jones
- Department of Chemistry, Ohio State University, Columbus, Ohio 43210, United States
| | - Vicki H Wysocki
- Department of Chemistry, Ohio State University, Columbus, Ohio 43210, United States
| | - David P Barondeau
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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