1
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Shepherd SO, Green AW, Resendiz ES, Newton KR, Kurulugama RT, Prell JS. Effects of Nano-Electrospray Ionization Emitter Position on Unintentional In-Source Activation of Peptide and Protein Ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:498-507. [PMID: 38374644 DOI: 10.1021/jasms.3c00371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Native ion mobility-mass spectrometry (IM-MS) typically introduces protein ions into the gas phase through nano-electrospray ionization (nESI). Many nESI setups have mobile stages for tuning the ion signal and extent of co-solute and salt adduction. However, tuning the position of the emitter capillary in nESI can have unintended downstream consequences for collision-induced unfolding or collision-induced dissociation (CIU/D) experiments. Here, we show that relatively small variations in the nESI emitter position can shift the midpoint (commonly called the "CID50" or "CIU50") potential of CID breakdown curves and CIU transitions by as much as 8 V on commercial instruments. A spatial "map" of the shift in CID50 for the loss of heme from holomyoglobin onto the emitter position on a Waters Synapt G2-Si mass spectrometer shows that emitter positions closer to the instrument inlet can result in significantly greater in-source activation, whereas different effects are found on an Agilent 6545XT instrument for the ions studied. A similar effect is observed for CID of the singly protonated leucine enkephalin peptide and Shiga toxin 1 subunit B homopentamer on the Waters Synapt G2-Si instrument. In-source activation effects on a Waters Synapt G2-Si are also investigated by examining the RMSD between CIU fingerprints acquired at different emitter positions and the shifts in CIU50 for structural transitions of bovine serum albumin and NIST monoclonal antibody.
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Affiliation(s)
- Samantha O Shepherd
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
| | - Austin W Green
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
| | - Elizabeth S Resendiz
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
| | - Kenneth R Newton
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
- Agilent Technologies, 5301 Stevens Creek Blvd, Santa Clara, California 95051, United States
| | - Ruwan T Kurulugama
- Agilent Technologies, 5301 Stevens Creek Blvd, Santa Clara, California 95051, 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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2
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Jia M, Song Y, Du C, Wysocki VH. Oxidized and Reduced Dimeric Protein Complexes Illustrate Contrasting CID and SID Charge Partitioning. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2166-2175. [PMID: 37590530 DOI: 10.1021/jasms.3c00142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
Charge partitioning during the dissociation of protein complexes in the gas phase is influenced by many factors, such as interfacial interactions, protein flexibility, protein conformation, and dissociation methods. In the present work, two cysteine-containing homodimer proteins, β-lactoglobulin and α-lactalbumin, with the disulfide bonds intact and reduced, were used to gain insight into the charge partitioning behaviors of collision-induced dissociation (CID) and surface-induced dissociation (SID) processes. For these proteins, we find that restructuring dominates with CID and dissociation with symmetric charge partitioning dominates with SID, regardless of whether intramolecular disulfide bonds are oxidized or reduced. CID of the charge-reduced dimeric protein complex leads to a precursor with a slightly smaller collision cross section (CCS), greater stability, and more symmetrically distributed charges than the significantly expanded form produced by CID of the higher charged dimer. Collision-induced unfolding plots demonstrate that the unfolding-restructuring of the protein complexes initiates the charge migration of higher charge-state precursors. Overall, gas collisions reveal the charge-dependent restructuring/unfolding properties of the protein precursor, while surface collisions lead predominantly to more charge-symmetric monomer separation. CID's multiple low-energy collisions sequentially reorganize intra- and intermolecular bonds, while SID's large-step energy jump cleaves intermolecular interfacial bonds in preference to reorganizing intramolecular bonds. The activated population of precursors that have taken on energy without dissociating (populated in CID over a wide range of collision energies, populated in SID for only a narrow distribution of collision energies near the onset of dissociation) is expected to be restructured, regardless of the activation method.
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Affiliation(s)
- Mengxuan Jia
- The Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Yang Song
- The Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Chen Du
- The Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Vicki H Wysocki
- The Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
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3
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Du C, Cleary SP, Kostelic MM, Jones BJ, Kafader JO, Wysocki VH. Combining Surface-Induced Dissociation and Charge Detection Mass Spectrometry to Reveal the Native Topology of Heterogeneous Protein Complexes. Anal Chem 2023; 95:13889-13896. [PMID: 37672632 PMCID: PMC10874503 DOI: 10.1021/acs.analchem.3c02185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Charge detection mass spectrometry (CDMS) enables the direct mass measurement of heterogeneous samples on the megadalton scale, as the charge state for a single ion is determined simultaneously with the mass-to-charge ratio (m/z). Surface-induced dissociation (SID) is an effective activation method to dissociate non-intertwined, non-covalent protein complexes without extensive gas-phase restructuring, producing various subcomplexes reflective of the native protein topology. Here, we demonstrate that using CDMS after SID on an Orbitrap platform offers subunit connectivity, topology, proteoform information, and relative interfacial strengths of the intact macromolecular assemblies. SID dissects the capsids (∼3.7 MDa) of adeno-associated viruses (AAVs) into trimer-containing fragments (3mer, 6mer, 9mer, 15mer, etc.) that can be detected by the individual ion mass spectrometry (I2MS) approach on Orbitrap instruments. SID coupled to CDMS provides unique structural insights into heterogeneous assemblies that are not readily obtained by traditional MS measurements.
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Affiliation(s)
- Chen Du
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sean P Cleary
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Marius M Kostelic
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Benjamin J Jones
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jared O Kafader
- Departments of Chemistry, Molecular Biosciences, The Chemistry of Life Processes Institute, The Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
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4
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Liu Z, Chen X, Yang S, Tian R, Wang F. Integrated mass spectrometry strategy for functional protein complex discovery and structural characterization. Curr Opin Chem Biol 2023; 74:102305. [PMID: 37071953 DOI: 10.1016/j.cbpa.2023.102305] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 03/10/2023] [Accepted: 03/15/2023] [Indexed: 04/20/2023]
Abstract
The discovery of functional protein complex and the interrogation of the complex structure-function relationship (SFR) play crucial roles in the understanding and intervention of biological processes. Affinity purification-mass spectrometry (AP-MS) has been proved as a powerful tool in the discovery of protein complexes. However, validation of these novel protein complexes as well as elucidation of their molecular interaction mechanisms are still challenging. Recently, native top-down MS (nTDMS) is rapidly developed for the structural analysis of protein complexes. In this review, we discuss the integration of AP-MS and nTDMS in the discovery and structural characterization of functional protein complexes. Further, we think the emerging artificial intelligence (AI)-based protein structure prediction is highly complementary to nTDMS and can promote each other. We expect the hybridization of integrated structural MS with AI prediction to be a powerful workflow in the discovery and SFR investigation of functional protein complexes.
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Affiliation(s)
- Zheyi Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiong Chen
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Shirui Yang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruijun Tian
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China.
| | - Fangjun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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5
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Sipe SN, Lancaster EB, Butalewicz JP, Whitman CP, Brodbelt JS. Symmetry of 4-Oxalocrotonate Tautomerase Trimers Influences Unfolding and Fragmentation in the Gas Phase. J Am Chem Soc 2022; 144:12299-12309. [PMID: 35767842 DOI: 10.1021/jacs.2c03564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The recent discovery of asymmetric arrangements of trimers in the tautomerase superfamily (TSF) adds structural diversity to this already mechanistically diverse superfamily. Classification of asymmetric trimers has previously been determined using X-ray crystallography. Here, native mass spectrometry (MS) and ultraviolet photodissociation (UVPD) are employed as an integrated strategy for more rapid and sensitive differentiation of symmetric and asymmetric trimers. Specifically, the unfolding of symmetric and asymmetric trimers initiated by collisional heating was probed using UVPD, which revealed unique gas-phase unfolding pathways. Variations in UVPD patterns from native-like, compact trimeric structures to unfolded, extended conformations indicate a rearrangement of higher-order structure in the asymmetric trimers that are believed to be stabilized by salt-bridge triads, which are absent from the symmetric trimers. Consequently, the symmetric trimers were found to be less stable in the gas phase, resulting in enhanced UVPD fragmentation overall and a notable difference in higher-order re-structuring based on the extent of hydrogen migration of protein fragments. The increased stability of the asymmetric trimers may justify their evolution and concomitant diversification of the TSF. Facilitating the classification of TSF members as symmetric or asymmetric trimers assists in delineating the evolutionary history of the TSF.
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Affiliation(s)
- Sarah N Sipe
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
| | - Emily B Lancaster
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Jamie P Butalewicz
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
| | - Christian P Whitman
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States.,Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
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6
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Snyder DT, Harvey SR, Wysocki VH. Surface-induced Dissociation Mass Spectrometry as a Structural Biology Tool. Chem Rev 2022; 122:7442-7487. [PMID: 34726898 PMCID: PMC9282826 DOI: 10.1021/acs.chemrev.1c00309] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Native mass spectrometry (nMS) is evolving into a workhorse for structural biology. The plethora of online and offline preparation, separation, and purification methods as well as numerous ionization techniques combined with powerful new hybrid ion mobility and mass spectrometry systems has illustrated the great potential of nMS for structural biology. Fundamental to the progression of nMS has been the development of novel activation methods for dissociating proteins and protein complexes to deduce primary, secondary, tertiary, and quaternary structure through the combined use of multiple MS/MS technologies. This review highlights the key features and advantages of surface collisions (surface-induced dissociation, SID) for probing the connectivity of subunits within protein and nucleoprotein complexes and, in particular, for solving protein structure in conjunction with complementary techniques such as cryo-EM and computational modeling. Several case studies highlight the significant role SID, and more generally nMS, will play in structural elucidation of biological assemblies in the future as the technology becomes more widely adopted. Cases are presented where SID agrees with solved crystal or cryoEM structures or provides connectivity maps that are otherwise inaccessible by "gold standard" structural biology techniques.
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Affiliation(s)
- Dalton T. Snyder
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
| | - Sophie R. Harvey
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
| | - Vicki H. Wysocki
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210,Corresponding author:
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7
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Vallejo DD, Rojas Ramírez C, Parson KF, Han Y, Gadkari VV, Ruotolo BT. Mass Spectrometry Methods for Measuring Protein Stability. Chem Rev 2022; 122:7690-7719. [PMID: 35316030 DOI: 10.1021/acs.chemrev.1c00857] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Mass spectrometry is a central technology in the life sciences, providing our most comprehensive account of the molecular inventory of the cell. In parallel with developments in mass spectrometry technologies targeting such assessments of cellular composition, mass spectrometry tools have emerged as versatile probes of biomolecular stability. In this review, we cover recent advancements in this branch of mass spectrometry that target proteins, a centrally important class of macromolecules that accounts for most biochemical functions and drug targets. Our efforts cover tools such as hydrogen-deuterium exchange, chemical cross-linking, ion mobility, collision induced unfolding, and other techniques capable of stability assessments on a proteomic scale. In addition, we focus on a range of application areas where mass spectrometry-driven protein stability measurements have made notable impacts, including studies of membrane proteins, heat shock proteins, amyloidogenic proteins, and biotherapeutics. We conclude by briefly discussing the future of this vibrant and fast-moving area of research.
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Affiliation(s)
- Daniel D Vallejo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Carolina Rojas Ramírez
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kristine F Parson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yilin Han
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Varun V Gadkari
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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8
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Surface-Induced Dissociation for Protein Complex Characterization. Methods Mol Biol 2022; 2500:211-237. [PMID: 35657596 DOI: 10.1007/978-1-0716-2325-1_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Native mass spectrometry (nMS) enables intact non-covalent complexes to be studied in the gas phase. nMS can provide information on composition, stoichiometry, topology, and, when coupled with surface-induced dissociation (SID), subunit connectivity. Here we describe the characterization of protein complexes by nMS and SID. Substructural information obtained using this method is consistent with the solved complex structure, when a structure exists. This provides confidence that the method can also be used to obtain substructural information for unknowns, providing insight into subunit connectivity and arrangements. High-energy SID can also provide information on proteoforms present. Previously SID has been limited to a few in-house modified instruments and here we focus on SID implemented within an in-house-modified Q Exactive UHMR. However, SID is currently commercially available within the Waters Select Series Cyclic IMS instrument. Projects are underway that involve the NIH-funded native MS resource (nativems.osu.edu), instrument vendors, and third-party vendors, with the hope of bringing the technology to more platforms and labs in the near future. Currently, nMS resource staff can perform SID experiments for interested research groups.
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9
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Snyder DT, Jones BJ, Lin YF, Cooper-Shepherd DA, Hewitt D, Wildgoose J, Brown JM, Langridge JI, Wysocki VH. Surface-induced dissociation of protein complexes on a cyclic ion mobility spectrometer. Analyst 2021; 146:6861-6873. [PMID: 34632987 PMCID: PMC8574189 DOI: 10.1039/d1an01407b] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We describe the implementation of a simple three-electrode surface-induced dissociation (SID) cell on a cyclic ion mobility spectrometer (cIMS) and demonstrate the utility of multipass mobility separations for resolving multiple conformations of protein complexes generated during collision-induced and surface-induced unfolding (CIU & SIU) experiments. In addition to CIU and SIU, SID of protein complexes is readily accomplished within the native instrument software and with no additional external power supplies by entering a single SID collision energy, a simplification in user experience compared to prior implementations. A set of cyclic homomeric protein complexes and a heterohexamer with known CID and SID behavior were analyzed to investigate mass and mobility resolution improvements, the latter of which improved by 20-50% (median: 33%) compared to a linear travelling wave device. Multiple passes of intact complexes, or their SID fragments, increased the mobility resolution by an average of 15% per pass, with the racetrack effect being observed after ∼3 or 4 passes, depending on the drift time spread of the analytes. Even with modest improvements to apparent mobility resolving power, multipass experiments were particularly useful for separating conformations produced from CIU and SIU experiments. We illustrate several examples where either (1) multipass experiments revealed multiple overlapping conformations previously unobserved or obscured due to limited mobility resolution, or (2) CIU or SIU conformations that appeared 'native' in a single pass experiment were actually slightly compacted or expanded, with the change only being measurable through multipass experiments. The work conducted here, the first utilization of multipass cyclic ion mobility for CIU, SIU, and SID of protein assemblies and a demonstration of a wholly integrated SIU/SID workflow, paves the way for widespread adoption of SID technology for native mass spectrometry and also improves our understanding of gas-phase protein complex CIU and SIU conformationomes.
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Affiliation(s)
- Dalton T Snyder
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, OH, USA 43210
| | - Benjamin J Jones
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, OH, USA 43210.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA 43210.
| | - Yu-Fu Lin
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, OH, USA 43210.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA 43210.
| | | | - Darren Hewitt
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, UK
| | - Jason Wildgoose
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, UK
| | - Jeffery M Brown
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, UK
| | - James I Langridge
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, UK
| | - Vicki H Wysocki
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, OH, USA 43210.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA 43210.
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10
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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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11
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Harvey SR, VanAernum ZL, Wysocki VH. Surface-Induced Dissociation of Anionic vs Cationic Native-Like Protein Complexes. J Am Chem Soc 2021; 143:7698-7706. [PMID: 33983719 DOI: 10.1021/jacs.1c00855] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Characterizing protein-protein interactions, stoichiometries, and subunit connectivity is key to understanding how subunits assemble into biologically relevant, multisubunit protein complexes. Native mass spectrometry (nMS) has emerged as a powerful tool to study protein complexes due to its low sample consumption and tolerance for heterogeneity. In nMS, positive mode ionization is routinely used and charge reduction, through the addition of solution additives, is often used, as the resulting lower charge states are often considered more native-like. When fragmented by surface-induced dissociation (SID), charge reduced complexes often give increased structural information over their "normal-charged" counterparts. A disadvantage of solution phase charge reduction is that increased adduction, and hence peak broadening, is often observed. Previous studies have shown that protein complexes ionized using negative mode generally form lower charge states relative to positive mode. Here we demonstrate that the lower charged protein complex anions activated by surface collisions fragment in a manner consistent with their solved structures, hence providing substructural information. Negative mode ionization in ammonium acetate offers the advantage of charge reduction without the peak broadening associated with solution phase charge reduction additives and provides direct structural information when coupled with SID. SID of 20S human proteasome (a 28-mer comprised of four stacked heptamer rings in an αββα formation), for example, provides information on both substructure (e.g., splitting into a 7α ring and the corresponding ββα 21-mer, and into α dimers and trimers to provide connectivity around the 7 α ring) and proteoform information on monomers.
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Affiliation(s)
- Sophie R Harvey
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Zachary L VanAernum
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
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12
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McCabe JW, Hebert MJ, Shirzadeh M, Mallis CS, Denton JK, Walker TE, Russell DH. THE IMS PARADOX: A PERSPECTIVE ON STRUCTURAL ION MOBILITY-MASS SPECTROMETRY. MASS SPECTROMETRY REVIEWS 2021; 40:280-305. [PMID: 32608033 PMCID: PMC7989064 DOI: 10.1002/mas.21642] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 06/03/2020] [Indexed: 05/06/2023]
Abstract
Studies of large proteins, protein complexes, and membrane protein complexes pose new challenges, most notably the need for increased ion mobility (IM) and mass spectrometry (MS) resolution. This review covers evolutionary developments in IM-MS in the authors' and key collaborators' laboratories with specific focus on developments that enhance the utility of IM-MS for structural analysis. IM-MS measurements are performed on gas phase ions, thus "structural IM-MS" appears paradoxical-do gas phase ions retain their solution phase structure? There is growing evidence to support the notion that solution phase structure(s) can be retained by the gas phase ions. It should not go unnoticed that we use "structures" in this statement because an important feature of IM-MS is the ability to deal with conformationally heterogeneous systems, thus providing a direct measure of conformational entropy. The extension of this work to large proteins and protein complexes has motivated our development of Fourier-transform IM-MS instruments, a strategy first described by Hill and coworkers in 1985 (Anal Chem, 1985, 57, pp. 402-406) that has proved to be a game-changer in our quest to merge drift tube (DT) and ion mobility and the high mass resolution orbitrap MS instruments. DT-IMS is the only method that allows first-principles determinations of rotationally averaged collision cross sections (CSS), which is essential for studies of biomolecules where the conformational diversities of the molecule precludes the use of CCS calibration approaches. The Fourier transform-IM-orbitrap instrument described here also incorporates the full suite of native MS/IM-MS capabilities that are currently employed in the most advanced native MS/IM-MS instruments. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Jacob W McCabe
- Department of Chemistry, Texas A&M University, College Station, TX, 77843
| | - Michael J Hebert
- Department of Chemistry, Texas A&M University, College Station, TX, 77843
| | - Mehdi Shirzadeh
- Department of Chemistry, Texas A&M University, College Station, TX, 77843
| | | | - Joanna K Denton
- Department of Chemistry, Texas A&M University, College Station, TX, 77843
| | - Thomas E Walker
- Department of Chemistry, Texas A&M University, College Station, TX, 77843
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, TX, 77843
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13
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Panczyk EM, Snyder DT, Ridgeway ME, Somogyi Á, Park MA, Wysocki VH. Surface-Induced Dissociation of Protein Complexes Selected by Trapped Ion Mobility Spectrometry. Anal Chem 2021; 93:5513-5520. [PMID: 33751887 DOI: 10.1021/acs.analchem.0c05373] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Native mass spectrometry (nMS), particularly in conjunction with gas-phase ion mobility spectrometry measurements, has proven useful as a structural biology tool for evaluating the stoichiometry, conformation, and topology of protein complexes. Here, we demonstrate the combination of trapped ion mobility spectrometry (TIMS) and surface-induced dissociation (SID) on a Bruker SolariX XR 15 T FT-ICR mass spectrometer for the structural analysis of protein complexes. We successfully performed SID on mobility-selected protein complexes, including the streptavidin tetramer and cholera toxin B with bound ligands. Additionally, TIMS-SID was employed on a mixture of the peptides desArg1 and desArg9 bradykinin to mobility-separate and identify the individual peptides. Importantly, results show that native-like conformations can be maintained throughout the TIMS analysis. The TIMS-SID spectra are analogous to SID spectra acquired using quadrupole mass selection, indicating little measurable, if any, structural rearrangement during mobility selection. Mobility parking was used on the ion or mobility of interest and 50-200 SID mass spectra were averaged. High-quality TIMS-SID spectra were acquired over a period of 2-10 min, comparable to or slightly longer than SID coupled with ion mobility on various instrument platforms in our laboratory. The ultrahigh resolving power of the 15 T FT-ICR allowed for the identification and relative quantification of overlapping SID fragments with the same nominal m/z based on isotope patterns, and it shows promise as a platform to probe small mass differences, such as protein/ligand binding or post-translational modifications. These results represent the potential of TIMS-SID-MS for the analysis of both protein complexes and peptides.
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Affiliation(s)
- Erin M Panczyk
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States.,Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Dalton T Snyder
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Mark E Ridgeway
- Bruker Daltonics Inc., Billerica, Massachusetts 01821, United States
| | - Árpád Somogyi
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States.,Campus Chemical Instrument Center, Mass Spectrometry and Proteomics, The Ohio State University, Columbus, Ohio 43210, United States
| | - Melvin A Park
- Bruker Daltonics Inc., Billerica, Massachusetts 01821, United States
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States.,Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States.,Campus Chemical Instrument Center, Mass Spectrometry and Proteomics, The Ohio State University, Columbus, Ohio 43210, United States
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14
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Snyder DT, Lin YF, Somogyi A, Wysocki V. Tandem surface-induced dissociation of protein complexes on an ultrahigh resolution platform. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2021; 461:116503. [PMID: 33889055 PMCID: PMC8057730 DOI: 10.1016/j.ijms.2020.116503] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We describe instrumentation for conducting tandem surface-induced dissociation (tSID) of native protein complexes on an ultrahigh resolution Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. The two stages of SID are accomplished with split lenses replacing the entrance lenses of the quadrupole mass filter (stage 1, referred to herein as SID-Q) and the collision cell (stage 2, Q-SID). After SID-Q, the scattered projectile ions and subcomplexes formed in transit traverse the 20 mm pre-filter prior to the mass-selecting quadrupole, providing preliminary insights into the SID fragmentation kinetics of noncovalent protein complexes. The isolated SID fragments (subcomplexes) are then fragmented by SID in the collision cell entrance lens (Q-SID), generating subcomplexes of subcomplexes. We show that the ultrahigh resolution of the FT-ICR can be used for deconvolving species overlapping in m/z, which are particularly prominent in tandem SID spectra due to the combination of symmetric charge partitioning and narrow product ion charge state distributions. Various protein complex topologies are explored, including homotetramers, homopentamers, a homohexamer, and a heterohexamer.
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Affiliation(s)
- Dalton T. Snyder
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus OH, USA 43210
| | - Yu-Fu Lin
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus OH, USA 43210
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus OH, USA 43210
| | - Arpad Somogyi
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus OH, USA 43210
| | - Vicki Wysocki
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus OH, USA 43210
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus OH, USA 43210
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15
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Sever AIM, Yin V, Konermann L. Interrogating the Quaternary Structure of Noncanonical Hemoglobin Complexes by Electrospray Mass Spectrometry and Collision-Induced Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:270-280. [PMID: 33124417 DOI: 10.1021/jasms.0c00320] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Various activation methods are available for the fragmentation of gaseous protein complexes produced by electrospray ionization (ESI). Such experiments can potentially yield insights into quaternary structure. Collision-induced dissociation (CID) is the most widely used fragmentation technique. Unfortunately, CID of protein complexes is dominated by the ejection of highly charged monomers, a process that does not yield any structural insights. Using hemoglobin (Hb) as a model system, this work examines under what conditions CID generates structurally informative subcomplexes. Native ESI mainly produced tetrameric Hb ions. In addition, "noncanonical" hexameric and octameric complexes were observed. CID of all these species [(αβ)2, (αβ)3, and (αβ)4] predominantly generated highly charged monomers. In addition, we observed hexamer → tetramer + dimer dissociation, implying that hexamers have a tetramer··dimer architecture. Similarly, the observation of octamer → two tetramer dissociation revealed that octamers have a tetramer··tetramer composition. Gas-phase candidate structures of Hb assemblies were produced by molecular dynamics (MD) simulations. Ion mobility spectrometry was used to identify the most likely candidates. Our data reveal that the capability of CID to produce structurally informative subcomplexes depends on the fate of protein-protein interfaces after transfer into the gas phase. Collapse of low affinity interfaces conjoins the corresponding subunits and favors CID via monomer ejection. Structurally informative subcomplexes are formed only if low affinity interfaces do not undergo a major collapse. However, even in these favorable cases CID is still dominated by monomer ejection, requiring careful analysis of the experimental data for the identification of structurally informative subcomplexes.
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Affiliation(s)
- Alexander I M Sever
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Victor Yin
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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16
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Zhou M, Lantz C, Brown KA, Ge Y, Paša-Tolić L, Loo JA, Lermyte F. Higher-order structural characterisation of native proteins and complexes by top-down mass spectrometry. Chem Sci 2020; 11:12918-12936. [PMID: 34094482 PMCID: PMC8163214 DOI: 10.1039/d0sc04392c] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 10/05/2020] [Indexed: 12/11/2022] Open
Abstract
In biology, it can be argued that if the genome contains the script for a cell's life cycle, then the proteome constitutes an ensemble cast of actors that brings these instructions to life. Their interactions with each other, co-factors, ligands, substrates, and so on, are key to understanding nearly any biological process. Mass spectrometry is well established as the method of choice to determine protein primary structure and location of post-translational modifications. In recent years, top-down fragmentation of intact proteins has been increasingly combined with ionisation of noncovalent assemblies under non-denaturing conditions, i.e., native mass spectrometry. Sequence, post-translational modifications, ligand/metal binding, protein folding, and complex stoichiometry can thus all be probed directly. Here, we review recent developments in this new and exciting field of research. While this work is written primarily from a mass spectrometry perspective, it is targeted to all bioanalytical scientists who are interested in applying these methods to their own biochemistry and chemical biology research.
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Affiliation(s)
- Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory Richland WA 99354 USA
| | - Carter Lantz
- Department of Chemistry and Biochemistry, Department of Biological Chemistry, University of California-Los Angeles Los Angeles CA 90095 USA
| | - Kyle A Brown
- Department of Chemistry, University of Wisconsin-Madison Madison WI 53706 USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison Madison WI 53706 USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison Madison WI 53706 USA
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory Richland WA 99354 USA
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, Department of Biological Chemistry, University of California-Los Angeles Los Angeles CA 90095 USA
| | - Frederik Lermyte
- Department of Chemistry, Institute of Chemistry and Biochemistry, Technical University of Darmstadt 64287 Darmstadt Germany
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège 4000 Liège Belgium
- School of Engineering, University of Warwick Coventry CV4 7AL UK
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17
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Snyder DT, Panczyk EM, Somogyi A, Kaplan DA, Wysocki V. Simple and Minimally Invasive SID Devices for Native Mass Spectrometry. Anal Chem 2020; 92:11195-11203. [PMID: 32700898 DOI: 10.1021/acs.analchem.0c01657] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We describe a set of simple devices for surface-induced dissociation of proteins and protein complexes on three instrument platforms. All of the devices use a novel yet simple split lens geometry that is minimally invasive (requiring a few millimeters along the ion path axis) and is easier to operate than prior generations of devices. The split lens is designed to be small enough to replace the entrance lens of a Bruker FT-ICR collision cell, the dynamic range enhancement (DRE) lens of a Waters Q-IM-TOF, or the exit lens of a transfer multipole of a Thermo Scientific Extended Mass Range (EMR) Orbitrap. Despite the decrease in size and reduction in number of electrodes to 3 (from 10 to 12 in Gen 1 and ∼6 in Gen 2), we show sensitivity improvement in a variety of cases across all platforms while also maintaining SID capabilities across a wide mass and energy range. The coupling of SID, high resolution, and ion mobility is demonstrated for a variety of protein complexes of varying topologies.
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18
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Allison TM, Barran P, Benesch JLP, Cianferani S, Degiacomi MT, Gabelica V, Grandori R, Marklund EG, Menneteau T, Migas LG, Politis A, Sharon M, Sobott F, Thalassinos K. Software Requirements for the Analysis and Interpretation of Native Ion Mobility Mass Spectrometry Data. Anal Chem 2020; 92:10881-10890. [PMID: 32649184 DOI: 10.1021/acs.analchem.9b05792] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The past few years have seen a dramatic increase in applications of native mass and ion mobility spectrometry, especially for the study of proteins and protein complexes. This increase has been catalyzed by the availability of commercial instrumentation capable of carrying out such analyses. As in most fields, however, the software to process the data generated from new instrumentation lags behind. Recently, a number of research groups have started addressing this by developing software, but further improvements are still required in order to realize the full potential of the data sets generated. In this perspective, we describe practical aspects as well as challenges in processing native mass spectrometry (MS) and ion mobility-MS data sets and provide a brief overview of currently available tools. We then set out our vision of future developments that would bring the community together and lead to the development of a common platform to expedite future computational developments, provide standardized processing approaches, and serve as a location for the deposition of data for this emerging field. This perspective has been written by members of the European Cooperation in Science and Technology Action on Native MS and Related Methods for Structural Biology (EU COST Action BM1403) as an introduction to the software tools available in this area. It is intended to serve as an overview for newcomers and to stimulate discussions in the community on further developments in this field, rather than being an in-depth review. Our complementary perspective (http://dx.doi.org/10.1021/acs.analchem.9b05791) focuses on computational approaches used in this field.
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Affiliation(s)
- Timothy M Allison
- School of Physical and Chemical Sciences, Biomolecular Interaction Centre, University of Canterbury, Christchurch 8140, New Zealand
| | - Perdita Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Justin L P Benesch
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, South Parks Road, Oxford OX1 3TA, United Kingdom
| | - Sarah Cianferani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Matteo T Degiacomi
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, South Parks Road, Oxford OX1 3TA, United Kingdom.,Department of Physics, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - Valerie Gabelica
- University of Bordeaux, INSERM and CNRS, ARNA Laboratory, IECB site, 2 Rue Robert Escarpit, 33600 Pessac, France
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy
| | - Erik G Marklund
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | - Thomas Menneteau
- Division of Biosciences, Institute of Structural and Molecular Biology, University College of London, Gower Street, London WC1E 6BT, United Kingdom
| | - Lukasz G Migas
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Argyris Politis
- Department of Chemistry, King's College London, 7 Trinity Street, London SE1 1DB, United Kingdom
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry, Department of Chemistry, University of Antwerp, 2020 Antwerp, Belgium.,School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Konstantinos Thalassinos
- Division of Biosciences, Institute of Structural and Molecular Biology, University College of London, Gower Street, London WC1E 6BT, United Kingdom.,Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, Malet Street, London WC1E 7HX, United Kingdom
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19
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Aliyari E, Konermann L. Formation of Gaseous Proteins via the Ion Evaporation Model (IEM) in Electrospray Mass Spectrometry. Anal Chem 2020; 92:10807-10814. [DOI: 10.1021/acs.analchem.0c02290] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Elnaz Aliyari
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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20
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Panczyk EM, Gilbert JD, Jagdale GS, Stiving AQ, Baker LA, Wysocki VH. Ion Mobility and Surface Collisions: Submicrometer Capillaries Can Produce Native-like Protein Complexes. Anal Chem 2020; 92:2460-2467. [PMID: 31909984 DOI: 10.1021/acs.analchem.9b03666] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The use of submicrometer capillaries for nanoelectrospray ionization of native proteins and protein complexes effectively reduces the number of nonspecific salt adducts to biological molecules, therefore increasing the apparent resolution of a mass spectrometer without any further instrument modifications or increased ion activation. However, the increased interaction between proteins and the surface of the capillary has been shown to promote protein expansion and therefore loss of native structure. Here, we compare the effect of micrometer and submicrometer sized capillaries on the native structures of the protein complexes streptavidin, concanavalin A, and C-reactive protein under charge reducing conditions. We observe that the use of submicrometer capillaries did not result in a significantly higher charge state distribution, indicative of expansion, when compared to micrometer sized capillaries for complexes in 100 mM ammonium acetate and 100 mM triethylammonium acetate and for streptavidin in 200 mM ammonium acetate with no charge reduction. Additionally, no significant differences in collision cross sections were observed using ion mobility mass spectrometry. Finally, the dissociation behaviors of protein complexes ionized using micrometer and submicrometer capillaries were compared to determine if any structural perturbation occurred during ionization. Protein complexes from both capillary sizes displayed similar surface-induced dissociation patterns at similar activation energies. The results suggest that submicrometer capillaries do not result in significant changes to protein complex structure under charge reducing conditions and may be used for native mass spectrometry experiments. Submicrometer capillaries can be used to resolve small mass differences of biological systems on a QTOF platform; however, a laser tip puller is required for pulling reproducible submicrometer capillaries, and disruption in spray due to clogging was observed for larger protein complexes.
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Affiliation(s)
- Erin M Panczyk
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States.,Resource for Native Mass Spectrometry Guided Structural Biology , The Ohio State University , Columbus , Ohio 43210 , United States
| | - Joshua D Gilbert
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States
| | - Gargi S Jagdale
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Alyssa Q Stiving
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States.,Resource for Native Mass Spectrometry Guided Structural Biology , The Ohio State University , Columbus , Ohio 43210 , United States
| | - Lane A Baker
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States.,Resource for Native Mass Spectrometry Guided Structural Biology , The Ohio State University , Columbus , Ohio 43210 , United States
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21
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Shen X, Yang Z, McCool EN, Lubeckyj RA, Chen D, Sun L. Capillary zone electrophoresis-mass spectrometry for top-down proteomics. Trends Analyt Chem 2019; 120:115644. [PMID: 31537953 PMCID: PMC6752746 DOI: 10.1016/j.trac.2019.115644] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Mass spectrometry (MS)-based top-down proteomics characterizes complex proteomes at the intact proteoform level and provides an accurate picture of protein isoforms and protein post-translational modifications in the cell. The progress of top-down proteomics requires novel analytical tools with high peak capacity for proteoform separation and high sensitivity for proteoform detection. The requirements have made capillary zone electrophoresis (CZE)-MS an attractive approach for advancing large-scale top-down proteomics. CZE has achieved a peak capacity of 300 for separation of complex proteoform mixtures. CZE-MS has shown drastically better sensitivity than commonly used reversed-phase liquid chromatography (RPLC)-MS for proteoform detection. The advanced CZE-MS identified 6,000 proteoforms of nearly 1,000 proteoform families from a complex proteome sample, which represents one of the largest top-down proteomic datasets so far. In this review, we focus on the recent progress in CZE-MS-based top-down proteomics and provide our perspectives about its future directions.
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Affiliation(s)
- Xiaojing Shen
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Zhichang Yang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Elijah N. McCool
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Rachele A. Lubeckyj
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Daoyang Chen
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
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22
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Snyder DT, Panczyk E, Stiving AQ, Gilbert JD, Somogyi A, Kaplan D, Wysocki V. Design and Performance of a Second-Generation Surface-Induced Dissociation Cell for Fourier Transform Ion Cyclotron Resonance Mass Spectrometry of Native Protein Complexes. Anal Chem 2019; 91:14049-14057. [PMID: 31584811 DOI: 10.1021/acs.analchem.9b03746] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A second-generation ("Gen 2") device capable of surface-induced dissociation (SID) and collision-induced dissociation (CID) for Fourier transform ion cyclotron resonance mass spectrometry of protein complexes has been designed, simulated, fabricated, and experimentally compared to a first-generation device ("Gen 1"). The primary goals of the redesign were to (1) simplify SID by reducing the number of electrodes, (2) increase CID and SID sensitivity by lengthening the collision cell, and (3) increase the mass range of the device for analysis of larger multimeric proteins, all while maintaining the normal instrument configuration and operation. Compared to Gen 1, Gen 2 exhibits an approximately 10× increase in sensitivity in flythrough mode, 7× increase in CID sensitivity for protonated leucine enkephalin (m/z 556), and 14× increase of CID sensitivity of 53 kDa streptavidin tetramer. It also approximately doubles the useful mass range (from m/z 8000 to m/z 15 000) using a rectilinear ion trap with a smaller inscribed radius or triples it (to m/z 22 000) using a hexapole collision cell and yields a 3-10× increase in SID sensitivity. We demonstrate the increased mass range and sensitivity on a variety of model molecules spanning nearly 3 orders of magnitude in absolute mass and present examples where the high resolution of the FT-ICR is advantageous for deconvoluting overlapping SID fragments.
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Affiliation(s)
| | | | | | | | | | - Desmond Kaplan
- KapScience LLC , Tewksbury , Massachusetts 01876 , United States
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23
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Seffernick J, Harvey SR, Wysocki VH, Lindert S. Predicting Protein Complex Structure from Surface-Induced Dissociation Mass Spectrometry Data. ACS CENTRAL SCIENCE 2019; 5:1330-1341. [PMID: 31482115 PMCID: PMC6716128 DOI: 10.1021/acscentsci.8b00912] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Indexed: 05/23/2023]
Abstract
Recently, mass spectrometry (MS) has become a viable method for elucidation of protein structure. Surface-induced dissociation (SID), colliding multiply charged protein complexes or other ions with a surface, has been paired with native MS to provide useful structural information such as connectivity and topology for many different protein complexes. We recently showed that SID gives information not only on connectivity and topology but also on relative interface strengths. However, SID has not yet been coupled with computational structure prediction methods that could use the sparse information from SID to improve the prediction of quaternary structures, i.e., how protein subunits interact with each other to form complexes. Protein-protein docking, a computational method to predict the quaternary structure of protein complexes, can be used in combination with subunit structures from X-ray crystallography and NMR in situations where it is difficult to obtain an experimental structure of an entire complex. While de novo structure prediction can be successful, many studies have shown that inclusion of experimental data can greatly increase prediction accuracy. In this study, we show that the appearance energy (AE, defined as 10% fragmentation) extracted from SID can be used in combination with Rosetta to successfully evaluate protein-protein docking poses. We developed an improved model to predict measured SID AEs and incorporated this model into a scoring function that combines the RosettaDock scoring function with a novel SID scoring term, which quantifies agreement between experiments and structures generated from RosettaDock. As a proof of principle, we tested the effectiveness of these restraints on 57 systems using ideal SID AE data (AE determined from crystal structures using the predictive model). When theoretical AEs were used, the RMSD of the selected structure improved or stayed the same in 95% of cases. When experimental SID data were incorporated on a different set of systems, the method predicted near-native structures (less than 2 Å root-mean-square deviation, RMSD, from native) for 6/9 tested cases, while unrestrained RosettaDock (without SID data) only predicted 3/9 such cases. Score versus RMSD funnel profiles were also improved when SID data were included. Additionally, we developed a confidence measure to evaluate predicted model quality in the absence of a crystal structure.
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24
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Lee JH, Pollert K, Konermann L. Testing the Robustness of Solution Force Fields for MD Simulations on Gaseous Protein Ions. J Phys Chem B 2019; 123:6705-6715. [DOI: 10.1021/acs.jpcb.9b04014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Justin H. Lee
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Katja Pollert
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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25
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Donor MT, Mroz AM, Prell JS. Experimental and theoretical investigation of overall energy deposition in surface-induced unfolding of protein ions. Chem Sci 2019; 10:4097-4106. [PMID: 31049192 PMCID: PMC6471915 DOI: 10.1039/c9sc00644c] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 03/06/2019] [Indexed: 12/15/2022] Open
Abstract
Recent advances in native mass spectrometry have enabled its use to probe the structure of and interactions within biomolecular complexes. Surface-induced dissociation, in which inter- and intramolecular interactions are disrupted following an energetic ion-surface collision, is a method that can directly interrogate the topology of protein complexes. However, a quantitative relationship between the ion kinetic energy at the moment of surface collision and the internal energy deposited into the ion has not yet been established for proteins. The factors affecting energy deposition in surface-induced unfolding (SIU) of protein monomers were investigated and a calibration relating laboratory-frame kinetic energy to internal energy developed. Protein monomers were unfolded by SIU and by collision-induced unfolding (CIU). CIU and SIU cause proteins to undergo the same unfolding transitions at different values of laboratory-frame kinetic energy. There is a strong correlation between the SIU and CIU energies, demonstrating that SIU, like CIU, can largely be understood as a thermal process. The change in internal energy in CIU was modeled using a Monte Carlo approach and theory. Computed values of the overall efficiency were found to be approximately 25% and used to rescale the CIU energy axis and relate nominal SIU energies to internal energy. The energy deposition efficiency in SIU increases with mass and kinetic energy from a low of ∼20% to a high of ∼68%, indicating that the effective mass of the surface increases along with the mass of the ion. The effect of ion structure on energy deposition was probed using multiple stages of ion activation. Energy deposition in SIU strongly depends on structure, decreasing as the protein is elongated, due to decreased effective protein-surface collisional cross section and increased transfer to rotational modes.
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Affiliation(s)
- Micah T Donor
- Department of Chemistry and Biochemistry , 1253 University of Oregon , Eugene , OR 97403-1253 , USA
| | - Austin M Mroz
- Department of Chemistry and Biochemistry , 1253 University of Oregon , Eugene , OR 97403-1253 , USA
| | - James S Prell
- Department of Chemistry and Biochemistry , 1253 University of Oregon , Eugene , OR 97403-1253 , USA
- Materials Science Institute , University of Oregon , 1252 University of Oregon , Eugene , OR 97403-1252 , USA . ; ; Tel: +1 541 346 2597
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26
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Relative interfacial cleavage energetics of protein complexes revealed by surface collisions. Proc Natl Acad Sci U S A 2019; 116:8143-8148. [PMID: 30944216 DOI: 10.1073/pnas.1817632116] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
To fulfill their biological functions, proteins must interact with their specific binding partners and often function as large assemblies composed of multiple proteins or proteins plus other biomolecules. Structural characterization of these complexes, including identification of all binding partners, their relative binding affinities, and complex topology, is integral for understanding function. Understanding how proteins assemble and how subunits in a complex interact is a cornerstone of structural biology. Here we report a native mass spectrometry (MS)-based method to characterize subunit interactions in globular protein complexes. We demonstrate that dissociation of protein complexes by surface collisions, at the lower end of the typical surface-induced dissociation (SID) collision energy range, consistently cleaves the weakest protein:protein interfaces, producing products that are reflective of the known structure. We present here combined results for multiple complexes as a training set, two validation cases, and four computational models. We show that SID appearance energies can be predicted from structures via a computationally derived expression containing three terms (number of residues in a given interface, unsatisfied hydrogen bonds, and a rigidity factor).
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27
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VanAernum ZL, Gilbert JD, Belov ME, Makarov AA, Horning SR, Wysocki VH. Surface-Induced Dissociation of Noncovalent Protein Complexes in an Extended Mass Range Orbitrap Mass Spectrometer. Anal Chem 2019; 91:3611-3618. [PMID: 30688442 PMCID: PMC6516482 DOI: 10.1021/acs.analchem.8b05605] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Native mass spectrometry continues to develop as a significant complement to traditional structural biology techniques. Within native mass spectrometry (MS), surface-induced dissociation (SID) has been shown to be a powerful activation method for the study of noncovalent complexes of biological significance. High-resolution mass spectrometers have become increasingly adapted to the analysis of high-mass ions and have demonstrated their importance in understanding how small mass changes can affect the overall structure of large biomolecular complexes. Herein we demonstrate the first adaptation of surface-induced dissociation in a modified high-mass-range, high-resolution Orbitrap mass spectrometer. The SID device was designed to be installed in the Q Exactive series of Orbitrap mass spectrometers with minimal disruption of standard functions. The performance of the SID-Orbitrap instrument has been demonstrated with several protein complex and ligand-bound protein complex systems ranging from 53 to 336 kDa. We also address the effect of ion source temperature on native protein-ligand complex ions as assessed by SID. Results are consistent with previous findings on quadrupole time-of-flight instruments and suggest that SID coupled to high-resolution MS is well-suited to provide information on the interface interactions within protein complexes and ligand-bound protein complexes.
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28
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Bakhtiari M, Konermann L. Protein Ions Generated by Native Electrospray Ionization: Comparison of Gas Phase, Solution, and Crystal Structures. J Phys Chem B 2019; 123:1784-1796. [DOI: 10.1021/acs.jpcb.8b12173] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Maryam Bakhtiari
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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29
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Stiving AQ, VanAernum ZL, Busch F, Harvey SR, Sarni SH, Wysocki VH. Surface-Induced Dissociation: An Effective Method for Characterization of Protein Quaternary Structure. Anal Chem 2019; 91:190-209. [PMID: 30412666 PMCID: PMC6571034 DOI: 10.1021/acs.analchem.8b05071] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Alyssa Q. Stiving
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
| | - Zachary L. VanAernum
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
| | - Florian Busch
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH 43210
| | - Sophie R. Harvey
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH 43210
| | - Samantha H. Sarni
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210
- The Center for RNA Biology, The Ohio State University, Columbus, OH 43210
| | - Vicki H. Wysocki
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH 43210
- The Center for RNA Biology, The Ohio State University, Columbus, OH 43210
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30
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Shen X, Kou Q, Guo R, Yang Z, Chen D, Liu X, Hong H, Sun L. Native Proteomics in Discovery Mode Using Size-Exclusion Chromatography-Capillary Zone Electrophoresis-Tandem Mass Spectrometry. Anal Chem 2018; 90:10095-10099. [PMID: 30085653 PMCID: PMC6156775 DOI: 10.1021/acs.analchem.8b02725] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Native proteomics aims to characterize complex proteomes under native conditions and ultimately produces a full picture of endogenous protein complexes in cells. It requires novel analytical platforms for high-resolution and liquid-phase separation of protein complexes prior to native mass spectrometry (MS) and MS/MS. In this work, size-exclusion chromatography (SEC)-capillary zone electrophoresis (CZE)-MS/MS was developed for native proteomics in discovery mode, resulting in the identification of 144 proteins, 672 proteoforms, and 23 protein complexes from the Escherichia coli proteome. The protein complexes include four protein homodimers, 16 protein-metal complexes, two protein-[2Fe-2S] complexes, and one protein-glutamine complex. Half of them have not been reported in the literature. This work represents the first example of online liquid-phase separation-MS/MS for the characterization of a complex proteome under the native condition, offering the proteomics community an efficient and simple platform for native proteomics.
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Affiliation(s)
- Xiaojing Shen
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI 48824 USA
| | - Qiang Kou
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, 719 Indiana Avenue, Indianapolis, IN 46202 USA
| | - Ruiqiong Guo
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI 48824 USA
| | - Zhichang Yang
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI 48824 USA
| | - Daoyang Chen
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI 48824 USA
| | - Xiaowen Liu
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, 719 Indiana Avenue, Indianapolis, IN 46202 USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 410 W. 10th Street, Indianapolis, IN 46202 USA
| | - Heedeok Hong
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI 48824 USA
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI 48824 USA
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31
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Metwally H, Duez Q, Konermann L. Chain Ejection Model for Electrospray Ionization of Unfolded Proteins: Evidence from Atomistic Simulations and Ion Mobility Spectrometry. Anal Chem 2018; 90:10069-10077. [DOI: 10.1021/acs.analchem.8b02926] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Haidy Metwally
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Quentin Duez
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
- Organic Synthesis and Mass Spectrometry Laboratory, University of Mons, Place du Parc, 23, Mons 7000, Belgium
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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32
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Duez Q, Metwally H, Konermann L. Electrospray Ionization of Polypropylene Glycol: Rayleigh-Charged Droplets, Competing Pathways, and Charge State-Dependent Conformations. Anal Chem 2018; 90:9912-9920. [DOI: 10.1021/acs.analchem.8b02115] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Quentin Duez
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
- Organic Synthesis and Mass Spectrometry Laboratory, University of Mons, Place du Parc, 23, Mons, 7000, Belgium
| | - Haidy Metwally
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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33
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Konermann L, Metwally H, McAllister RG, Popa V. How to run molecular dynamics simulations on electrospray droplets and gas phase proteins: Basic guidelines and selected applications. Methods 2018; 144:104-112. [DOI: 10.1016/j.ymeth.2018.04.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 04/10/2018] [Accepted: 04/12/2018] [Indexed: 12/13/2022] Open
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34
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Gadkari VV, Harvey SR, Raper AT, Chu WT, Wang J, Wysocki VH, Suo Z. Investigation of sliding DNA clamp dynamics by single-molecule fluorescence, mass spectrometry and structure-based modeling. Nucleic Acids Res 2018; 46:3103-3118. [PMID: 29529283 PMCID: PMC5888646 DOI: 10.1093/nar/gky125] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 01/23/2018] [Accepted: 02/12/2018] [Indexed: 12/20/2022] Open
Abstract
Proliferating cell nuclear antigen (PCNA) is a trimeric ring-shaped clamp protein that encircles DNA and interacts with many proteins involved in DNA replication and repair. Despite extensive structural work to characterize the monomeric, dimeric, and trimeric forms of PCNA alone and in complex with interacting proteins, no structure of PCNA in a ring-open conformation has been published. Here, we use a multidisciplinary approach, including single-molecule Förster resonance energy transfer (smFRET), native ion mobility-mass spectrometry (IM-MS), and structure-based computational modeling, to explore the conformational dynamics of a model PCNA from Sulfolobus solfataricus (Sso), an archaeon. We found that Sso PCNA samples ring-open and ring-closed conformations even in the absence of its clamp loader complex, replication factor C, and transition to the ring-open conformation is modulated by the ionic strength of the solution. The IM-MS results corroborate the smFRET findings suggesting that PCNA dynamics are maintained in the gas phase and further establishing IM-MS as a reliable strategy to investigate macromolecular motions. Our molecular dynamic simulations agree with the experimental data and reveal that ring-open PCNA often adopts an out-of-plane left-hand geometry. Collectively, these results implore future studies to define the roles of PCNA dynamics in DNA loading and other PCNA-mediated interactions.
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Affiliation(s)
- Varun V Gadkari
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Sophie R Harvey
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK
| | - Austin T Raper
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Wen-Ting Chu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P.R. China
| | - Jin Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P.R. China
- Department of Chemistry and Physics, State University of New York at Stony Brook, Stony Brook, NY 11794-3400, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Zucai Suo
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
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35
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Metwally H, Konermann L. Crown Ether Effects on the Location of Charge Carriers in Electrospray Droplets: Implications for the Mechanism of Protein Charging and Supercharging. Anal Chem 2018; 90:4126-4134. [DOI: 10.1021/acs.analchem.8b00099] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Haidy Metwally
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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36
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Ben-Nissan G, Sharon M. The application of ion-mobility mass spectrometry for structure/function investigation of protein complexes. Curr Opin Chem Biol 2018; 42:25-33. [PMID: 29128665 PMCID: PMC5796646 DOI: 10.1016/j.cbpa.2017.10.026] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 10/19/2017] [Accepted: 10/24/2017] [Indexed: 12/16/2022]
Abstract
Ion-mobility mass spectrometry (IM-MS) is an approach that can provide information on the stoichiometry, composition, protein contacts and topology of protein complexes. The power of this approach lies not only in its sensitivity and speed of analysis, but also in the fact that it is a technique that can capture the repertoire of conformational states adopted by protein assemblies. Here, we describe the array of available IM-MS based tools, and demonstrate their application to the structural characterization of various protein complexes, including challenging systems as amyloid aggregates and membrane proteins. We also discuss recent studies in which IM-MS was applied towards investigations of conformational transitions and stabilization effects induced by protein interactions.
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Affiliation(s)
- Gili Ben-Nissan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel.
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37
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Boeri Erba E, Signor L, Oliva MF, Hans F, Petosa C. Characterizing Intact Macromolecular Complexes Using Native Mass Spectrometry. Methods Mol Biol 2018; 1764:133-151. [PMID: 29605913 DOI: 10.1007/978-1-4939-7759-8_9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Native mass spectrometry (MS) enables the characterization of macromolecular assemblies with high sensitivity. It can reveal the stoichiometry of subunits as well as their two-dimensional interaction network and provide information regarding the dynamic behavior of macromolecular complexes. Here, we describe the workflow to perform native MS experiments. In addition, we illustrate the quality control analysis of proteins using MS in denaturing conditions.
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Affiliation(s)
- Elisabetta Boeri Erba
- Institut de Biologie Structurale (IBS), Université de Grenoble Alpes, CEA, CNRS, Grenoble, France.
| | - Luca Signor
- Institut de Biologie Structurale (IBS), Université de Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Mizar F Oliva
- Institut de Biologie Structurale (IBS), Université de Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Fabienne Hans
- Institut de Biologie Structurale (IBS), Université de Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Carlo Petosa
- Institut de Biologie Structurale (IBS), Université de Grenoble Alpes, CEA, CNRS, Grenoble, France
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38
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D'Atri V, Causon T, Hernandez-Alba O, Mutabazi A, Veuthey JL, Cianferani S, Guillarme D. Adding a new separation dimension to MS and LC-MS: What is the utility of ion mobility spectrometry? J Sep Sci 2017; 41:20-67. [PMID: 29024509 DOI: 10.1002/jssc.201700919] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 09/19/2017] [Accepted: 09/19/2017] [Indexed: 12/12/2022]
Abstract
Ion mobility spectrometry is an analytical technique known for more than 100 years, which entails separating ions in the gas phase based on their size, shape, and charge. While ion mobility spectrometry alone can be useful for some applications (mostly security analysis for detecting certain classes of narcotics and explosives), it becomes even more powerful in combination with mass spectrometry and high-performance liquid chromatography. Indeed, the limited resolving power of ion mobility spectrometry alone can be tackled when combining this analytical strategy with mass spectrometry or liquid chromatography with mass spectrometry. Over the last few years, the hyphenation of ion mobility spectrometry to mass spectrometry or liquid chromatography with mass spectrometry has attracted more and more interest, with significant progresses in both technical advances and pioneering applications. This review describes the theoretical background, available technologies, and future capabilities of these techniques. It also highlights a wide range of applications, from small molecules (natural products, metabolites, glycans, lipids) to large biomolecules (proteins, protein complexes, biopharmaceuticals, oligonucleotides).
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Affiliation(s)
- Valentina D'Atri
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Tim Causon
- Division of Analytical Chemistry, Department of Chemistry, University of Natural Resources and Life Sciences (BOKU Vienna), Vienna, Austria
| | - Oscar Hernandez-Alba
- BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC, Université de Strasbourg, CNRS, Strasbourg, France
| | - Aline Mutabazi
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Jean-Luc Veuthey
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Sarah Cianferani
- BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC, Université de Strasbourg, CNRS, Strasbourg, France
| | - Davy Guillarme
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
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39
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Yefremova Y, Opuni KFM, Danquah BD, Thiesen HJ, Glocker MO. Intact Transition Epitope Mapping (ITEM). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1612-1622. [PMID: 28616748 DOI: 10.1007/s13361-017-1654-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 03/06/2017] [Accepted: 03/07/2017] [Indexed: 06/07/2023]
Abstract
Intact transition epitope mapping (ITEM) enables rapid and accurate determination of protein antigen-derived epitopes by either epitope extraction or epitope excision. Upon formation of the antigen peptide-containing immune complex in solution, the entire mixture is electrosprayed to translate all constituents as protonated ions into the gas phase. There, ions from antibody-peptide complexes are separated from unbound peptide ions according to their masses, charges, and shapes either by ion mobility drift or by quadrupole ion filtering. Subsequently, immune complexes are dissociated by collision induced fragmentation and the ion signals of the "complex-released peptides," which in effect are the epitope peptides, are recorded in the time-of-flight analyzer of the mass spectrometer. Mixing of an antibody solution with a solution in which antigens or antigen-derived peptides are dissolved is, together with antigen proteolysis, the only required in-solution handling step. Simplicity of sample handling and speed of analysis together with very low sample consumption makes ITEM faster and easier to perform than other experimental epitope mapping methods. Graphical Abstract ᅟ.
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Affiliation(s)
- Yelena Yefremova
- Proteome Center Rostock, University Medicine Rostock, Schillingallee 69, 18057, Rostock, Germany
| | - Kwabena F M Opuni
- Proteome Center Rostock, University Medicine Rostock, Schillingallee 69, 18057, Rostock, Germany
| | - Bright D Danquah
- Proteome Center Rostock, University Medicine Rostock, Schillingallee 69, 18057, Rostock, Germany
| | - Hans-Juergen Thiesen
- Institute of Immunology, University Medicine Rostock, Schillingallee 70, 18057, Rostock, Germany
| | - Michael O Glocker
- Proteome Center Rostock, University Medicine Rostock, Schillingallee 69, 18057, Rostock, Germany.
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40
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Abstract
In this review, we focus on an important aspect of ion mobility (IM) research, namely the reporting of quantitative ion mobility measurements in the form of the gas-phase collision cross section (CCS), which has provided a common basis for comparison across different instrument platforms and offers a unique form of structural information, namely size and shape preferences of analytes in the absence of bulk solvent. This review surveys the over 24,000 CCS values reported from IM methods spanning the era between 1975 to 2015, which provides both a historical and analytical context for the contributions made thus far, as well as insight into the future directions that quantitative ion mobility measurements will have in the analytical sciences. The analysis was conducted in 2016, so CCS values reported in that year are purposely omitted. In another few years, a review of this scope will be intractable, as the number of CCS values which will be reported in the next three to five years is expected to exceed the total amount currently published in the literature.
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Affiliation(s)
- Jody C May
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute for Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University , Nashville, Tennessee 37235, United States
| | - Caleb B Morris
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute for Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University , Nashville, Tennessee 37235, United States
| | - John A McLean
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute for Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University , Nashville, Tennessee 37235, United States
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41
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Yan J, Zhou M, Gilbert JD, Wolff JJ, Somogyi Á, Pedder RE, Quintyn RS, Morrison LJ, Easterling ML, Paša-Tolić L, Wysocki VH. Surface-Induced Dissociation of Protein Complexes in a Hybrid Fourier Transform Ion Cyclotron Resonance Mass Spectrometer. Anal Chem 2016; 89:895-901. [DOI: 10.1021/acs.analchem.6b03986] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jing Yan
- Department
of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Mowei Zhou
- Environmental
Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Joshua D. Gilbert
- Department
of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | | | - Árpád Somogyi
- OSU
Mass Spectrometry and Proteomics Facility, The Ohio State University, Columbus, Ohio 43210, United States
| | | | - Royston S. Quintyn
- Department
of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Lindsay J. Morrison
- Department
of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | | | - Ljiljana Paša-Tolić
- Environmental
Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Vicki H. Wysocki
- Department
of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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42
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Schachel TD, Metwally H, Popa V, Konermann L. Collision-Induced Dissociation of Electrosprayed NaCl Clusters: Using Molecular Dynamics Simulations to Visualize Reaction Cascades in the Gas Phase. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1846-1854. [PMID: 27631502 DOI: 10.1007/s13361-016-1468-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/28/2016] [Accepted: 07/29/2016] [Indexed: 06/06/2023]
Abstract
Infusion of NaCl solutions into an electrospray ionization (ESI) source produces [Na(n+1)Cl n ]+ and other gaseous clusters. The n = 4, 13, 22 magic number species have cuboid ground state structures and exhibit elevated abundance in ESI mass spectra. Relatively few details are known regarding the mechanisms whereby these clusters undergo collision-induced dissociation (CID). The current study examines to what extent molecular dynamics (MD) simulations can be used to garner insights into the sequence of events taking place during CID. Experiments on singly charged clusters reveal that the loss of small neutrals is the dominant fragmentation pathway. MD simulations indicate that the clusters undergo extensive structural fluctuations prior to decomposition. Consistent with the experimentally observed behavior, most of the simulated dissociation events culminate in ejection of small neutrals ([NaCl] i , with i = 1, 2, 3). The MD data reveal that the prevalence of these dissociation channels is linked to the presence of short-lived intermediates where a relatively compact core structure carries a small [NaCl] i protrusion. The latter can separate from the parent cluster via cleavage of a single Na-Cl contact. Fragmentation events of this type are kinetically favored over other dissociation channels that would require the quasi-simultaneous rupture of multiple electrostatic contacts. The CID behavior of NaCl cluster ions bears interesting analogies to that of collisionally activated protein complexes. Overall, it appears that MD simulations represent a valuable tool for deciphering the dissociation of noncovalently bound systems in the gas phase. Graphical Abstract ᅟ.
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Affiliation(s)
- Tilo D Schachel
- Department of Chemistry, The University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Haidy Metwally
- Department of Chemistry, The University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Vlad Popa
- Department of Chemistry, The University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, ON, N6A 5B7, Canada.
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43
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Morrison LJ, Brodbelt JS. 193 nm Ultraviolet Photodissociation Mass Spectrometry of Tetrameric Protein Complexes Provides Insight into Quaternary and Secondary Protein Topology. J Am Chem Soc 2016; 138:10849-59. [PMID: 27480400 DOI: 10.1021/jacs.6b03905] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein-protein interfaces and architecture are critical to the function of multiprotein complexes. Mass spectrometry-based techniques have emerged as powerful strategies for characterization of protein complexes, particularly for heterogeneous mixtures of structures. In the present study, activation and dissociation of three tetrameric protein complexes (streptavidin, transthyretin, and hemoglobin) in the gas phase was undertaken by 193 nm ultraviolet photodissociation (UVPD) for the characterization of higher order structure. High pulse energy UVPD resulted in the production of dimers and low charged monomers exhibiting symmetrical charge partitioning among the subunits (the so-called symmetrical dissociation pathways), consistent with the subunit organization of the complexes. In addition, UVPD promoted backbone cleavages of the monomeric subunits, the abundances of which corresponded to the more flexible loop regions of the proteins.
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Affiliation(s)
- Lindsay J Morrison
- Department of Chemistry, University of Texas , Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas , Austin, Texas 78712, United States
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44
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Thachuk M, Fegan SK, Raheem N. Description and control of dissociation channels in gas-phase protein complexes. J Chem Phys 2016. [DOI: 10.1063/1.4960615] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Mark Thachuk
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Sarah K. Fegan
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Nigare Raheem
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
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Bartman CE, Metwally H, Konermann L. Effects of Multidentate Metal Interactions on the Structure of Collisionally Activated Proteins: Insights from Ion Mobility Spectrometry and Molecular Dynamics Simulations. Anal Chem 2016; 88:6905-13. [DOI: 10.1021/acs.analchem.6b01627] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Claire E. Bartman
- Department
of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Haidy Metwally
- Department
of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department
of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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Popa V, Trecroce DA, McAllister RG, Konermann L. Collision-Induced Dissociation of Electrosprayed Protein Complexes: An All-Atom Molecular Dynamics Model with Mobile Protons. J Phys Chem B 2016; 120:5114-24. [DOI: 10.1021/acs.jpcb.6b03035] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Vlad Popa
- Department
of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Danielle A. Trecroce
- Department
of Chemistry, The University of Western Ontario, London, ON N6A 5B7, Canada
| | - Robert G. McAllister
- Department
of Chemistry, The University of Western Ontario, London, ON N6A 5B7, Canada
| | - Lars Konermann
- Department
of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
- Department
of Chemistry, The University of Western Ontario, London, ON N6A 5B7, Canada
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Cleary SP, Thompson AM, Prell JS. Fourier Analysis Method for Analyzing Highly Congested Mass Spectra of Ion Populations with Repeated Subunits. Anal Chem 2016; 88:6205-13. [DOI: 10.1021/acs.analchem.6b01088] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Sean P. Cleary
- Department
of Chemistry and
Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
| | - Avery M. Thompson
- 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
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48
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Affiliation(s)
- Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
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49
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Harvey SR, Yan J, Brown JM, Hoyes E, Wysocki VH. Extended Gas-Phase Trapping Followed by Surface-Induced Dissociation of Noncovalent Protein Complexes. Anal Chem 2015; 88:1218-21. [DOI: 10.1021/acs.analchem.5b03479] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Sophie R. Harvey
- Department
of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- School
of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Jing Yan
- Department
of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jeffery M. Brown
- Waters Corporation, Altrincham
Road, Wilmslow, SK9 4AX, United Kingdom
| | - Emmy Hoyes
- Waters Corporation, Altrincham
Road, Wilmslow, SK9 4AX, United Kingdom
| | - Vicki H. Wysocki
- Department
of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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