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Makey DM, Gadkari VV, Kennedy RT, Ruotolo BT. Cyclic Ion Mobility-Mass Spectrometry and Tandem Collision Induced Unfolding for Quantification of Elusive Protein Biomarkers. Anal Chem 2024; 96:6021-6029. [PMID: 38557001 PMCID: PMC11081454 DOI: 10.1021/acs.analchem.4c00477] [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: 04/04/2024]
Abstract
Sensitive analytical techniques that are capable of detecting and quantifying disease-associated biomolecules are indispensable in our efforts to understand disease mechanisms and guide therapeutic intervention through early detection, accurate diagnosis, and effective monitoring of disease. Parkinson's Disease (PD), for example, is one of the most prominent neurodegenerative disorders in the world, but the diagnosis of PD has primarily been based on the observation of clinical symptoms. The protein α-synuclein (α-syn) has emerged as a promising biomarker candidate for PD, but a lack of analytical methods to measure complex disease-associated variants of α-syn has prevented its widespread use as a biomarker. Antibody-based methods such as immunoassays and mass spectrometry-based approaches have been used to measure a limited number of α-syn forms; however, these methods fail to differentiate variants of α-syn that display subtle differences in only the sequence and structure. In this work, we developed a cyclic ion mobility-mass spectrometry method that combines multiple stages of activation and timed ion selection to quantify α-syn variants using both mass- and structure-based measurements. This method can allow for the quantification of several α-syn variants present at physiological levels in biological fluid. Taken together, this approach can be used to galvanize future efforts aimed at understanding the underlying mechanisms of PD and serves as a starting point for the development of future protein-structure-based diagnostics and therapeutic interventions.
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Affiliation(s)
- Devin M Makey
- 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
| | - Robert T Kennedy
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Pharmacology, 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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2
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Juliano BR, Keating JW, Li HW, Anders AG, Xie Z, Ruotolo BT. Development of an Automated, High-Throughput Methodology for Native Mass Spectrometry and Collision-Induced Unfolding. Anal Chem 2023; 95:16717-16724. [PMID: 37924308 PMCID: PMC11081713 DOI: 10.1021/acs.analchem.3c03788] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2023]
Abstract
Native ion mobility mass spectrometry (nIM-MS) has emerged as a useful technology for the rapid evaluation of biomolecular structures. When combined with collisional activation in a collision-induced unfolding (CIU) experiment, nIM-MS experimentation can be leveraged to gain greater insight into biomolecular conformation and stability. However, nIM-MS and CIU remain throughput limited due to nonautomated sample preparation and introduction. Here, we explore the use of a RapidFire robotic sample handling system to develop an automated, high-throughput methodology for nMS and CIU. We describe native RapidFire-MS (nRapidFire-MS) capable of performing online desalting and sample introduction in as little as 10 s per sample. When combined with CIU, our nRapidFire-MS approach can be used to collect CIU fingerprints in 30 s following desalting by using size exclusion chromatography cartridges. When compared to nMS and CIU data collected using standard approaches, ion signals recorded by nRapidFire-MS exhibit identical ion collision cross sections, indicating that the same conformational populations are tracked by the two approaches. Our data further suggest that nRapidFire-MS can be extended to study a variety of biomolecular classes, including proteins and protein complexes ranging from 5 to 300 kDa and oligonucleotides. Furthermore, nRapidFire-MS data acquired for biotherapeutics suggest that nRapidFire-MS has the potential to enable high-throughput nMS analyses of biopharmaceutical samples. We conclude by discussing the potential of nRapidFire-MS for enabling the development of future CIU assays capable of catalyzing breakthroughs in protein engineering, inhibitor discovery, and formulation development for biotherapeutics.
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Affiliation(s)
- Brock R Juliano
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Joseph W Keating
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Henry W Li
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Anna G Anders
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Zhuoer Xie
- Attribute Sciences, Process Development, Amgen, Thousand Oaks, California 91320, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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3
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Zheng Z, Ma M, Jia Y, Cui Y, Zhao R, Li S, Wenthur C, Li L, Li G. Expedited Evaluation of Conformational Stability-Heterogeneity Associations for Crude Polyclonal Antibodies in Response to Conjugate Vaccines. Anal Chem 2023; 95:10895-10902. [PMID: 37433088 PMCID: PMC10695093 DOI: 10.1021/acs.analchem.3c00223] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Abstract
Conjugate vaccines have been demonstrated to be a promising strategy for immunotherapeutic intervention in substance use disorder, wherein a hapten structurally similar to the target drug is conjugated to an immunogenic carrier protein. The antibodies generated following immunization with these species can provide long-lasting protection against overdose through sequestration of the abused drug in the periphery, which mitigates its ability to cross the blood-brain barrier. However, these antibodies exhibit a high degree of heterogeneity in structure. The resultant variations in chemical and structural compositions have not yet been clearly linked to the stability that directly affects their in vivo functional performance. In this work, we describe a rapid mass-spectrometry-based analytical workflow capable of simultaneous and comprehensive interrogation of the carrier protein-dependent heterogeneity and stability of crude polyclonal antibodies in response to conjugate vaccines. Quantitative collision-induced unfolding-ion mobility-mass spectrometry with an all-ion mode is adapted to rapidly assess the conformational heterogeneity and stability of crude serum antibodies collected from four different vaccine conditions, in an unprecedented manner. A series of bottom-up glycoproteomic experiments was performed to reveal the driving force underlying these observed heterogeneities. Overall, this study not only presents a generally applicable workflow for fast assessment of crude antibody conformational stability and heterogeneity at the intact protein level but also leverages carrier protein optimization as a simple solution to antibody quality control.
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Affiliation(s)
- Zhen Zheng
- State Key Laboratory of Pharmaceutical Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Science, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, China
- School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Min Ma
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Yifei Jia
- State Key Laboratory of Pharmaceutical Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Science, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Yusi Cui
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Rui Zhao
- State Key Laboratory of Pharmaceutical Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Science, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Shuangshuang Li
- School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Cody Wenthur
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Gongyu Li
- State Key Laboratory of Pharmaceutical Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Science, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
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4
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West CP, Mesa Sanchez D, Morales AC, Hsu YJ, Ryan J, Darmody A, Slipchenko LV, Laskin J, Laskin A. Molecular and Structural Characterization of Isomeric Compounds in Atmospheric Organic Aerosol Using Ion Mobility-Mass Spectrometry. J Phys Chem A 2023; 127:1656-1674. [PMID: 36763810 DOI: 10.1021/acs.jpca.2c06459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Secondary organic aerosol (SOA) formed through multiphase atmospheric chemistry makes up a large fraction of airborne particles. The chemical composition and molecular structures of SOA constituents vary between different emission sources and aging processes in the atmosphere, which complicates their identification. In this work, we employ drift tube ion mobility spectrometry with quadrupole time-of-flight mass spectrometry (IM-MS) detection for rapid gas-phase separation and multidimensional characterization of isomers in two biogenic SOAs produced from ozonolysis of isomeric monoterpenes, d-limonene (LSOA) and α-pinene (PSOA). SOA samples were ionized using electrospray ionization (ESI) and characterized using IM-MS in both positive and negative ionization modes. The IM-derived collision cross sections in nitrogen gas (DTCCSN2 ) for individual SOA components were obtained using multifield and single-field measurements. A novel application of IM multiplexing/high-resolution demultiplexing methodology was employed to increase sensitivity, improve peak shapes, and augment mobility baseline resolution, which revealed several isomeric structures for the measured ions. For LSOA and PSOA samples, we report significant structural differences of the isomer structures. Molecular structural calculations using density functional theory combined with the theoretical modeling of CCS values provide insights into the structural differences between LSOA and PSOA constituents. The average DTCCSN2 values for monomeric SOA components observed as [M + Na]+ ions are 3-6% higher than those of their [M - H]- counterparts. Meanwhile, dimeric and trimeric isomer components in both samples showed an inverse trend with the relevant values of [M - H]- ions being 3-7% higher than their [M + Na]+ counterparts, respectively. The results indicate that the structures of Na+-coordinated oligomeric ions are more compact than those of the corresponding deprotonated species. The coordination with Na+ occurs on the oxygen atoms of the carbonyl groups leading to a compact configuration. Meanwhile, deprotonated molecules have higher DTCCSN2 values due to their elongated structures in the gas phase. Therefore, DTCCSN2 values of isomers in SOA mixtures depend strongly on the mode of ionization in ESI. Additionally, PSOA monomers and dimers exhibit larger DTCCSN2 values (1-4%) than their LSOA counterparts owing to more rigid structures. A cyclobutane ring is present with functional groups pointing in opposite directions in PSOA compounds, as compared to noncyclic flexible LSOA structures, forming more compact ions in the gas phase. Lastly, we investigated the effects of direct photolysis on the chemical transformations of selected individual PSOA components. We use IM-MS to reveal structural changes associated with aerosol aging by photolysis. This study illustrates the detailed molecular and structural descriptors for the detection and annotation of structural isomers in complex SOA mixtures.
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Affiliation(s)
- Christopher P West
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Daniela Mesa Sanchez
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ana C Morales
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Yun-Jung Hsu
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jackson Ryan
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Andrew Darmody
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States.,Department of Aeronautics and Aerospace Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Lyudmila V Slipchenko
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Julia Laskin
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Alexander Laskin
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States.,Department of Earth, Atmospheric & Planetary Sciences, Purdue University, West Lafayette, Indiana 47907, United States
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5
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Gadkari VV, Juliano BR, Mallis CS, May JC, Kurulugama RT, Fjeldsted JC, McLean JA, Russell DH, Ruotolo BT. Performance evaluation of in-source ion activation hardware for collision-induced unfolding of proteins and protein complexes on a drift tube ion mobility-mass spectrometer. Analyst 2023; 148:391-401. [PMID: 36537590 PMCID: PMC10103148 DOI: 10.1039/d2an01452a] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Native ion mobility-mass spectrometry (IM-MS) has emerged as an information-rich technique for gas phase protein structure characterization; however, IM resolution is currently insufficient for the detection of subtle structural differences in large biomolecules. This challenge has spurred the development of collision-induced unfolding (CIU) which utilizes incremental gas phase activation to unfold a protein in order to expand the number of measurable descriptors available for native protein ions. Although CIU is now routinely used in native mass spectrometry studies, the interlaboratory reproducibility of CIU has not been established. Here we evaluate the reproducibility of the CIU data produced across three laboratories (University of Michigan, Texas A&M University, and Vanderbilt University). CIU data were collected for a variety of protein ions ranging from 8.6-66 kDa. Within the same laboratory, the CIU fingerprints were found to be repeatable with root mean square deviation (RMSD) values of less than 5%. Collision cross section (CCS) values of the CIU intermediates were consistent across the laboratories, with most features exhibiting an interlaboratory reproducibility of better than 1%. In contrast, the activation potentials required to induce protein CIU transitions varied between the three laboratories. To address these differences, three source assemblies were constructed with an updated ion activation hardware design utilizing higher mechanical tolerance specifications. The production-grade assemblies were found to produce highly consistent CIU data for intact antibodies, exhibiting high precision ion CCS and CIU transition values, thus opening the door to establishing databases of CIU fingerprints to support future biomolecular classification efforts.
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Affiliation(s)
- Varun V Gadkari
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA.
| | - Brock R Juliano
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA.
| | - Christopher S Mallis
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, USA
| | - Jody C May
- Center for Innovative Technology, Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, USA
| | | | | | - John A McLean
- Center for Innovative Technology, Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, USA
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA.
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6
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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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7
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Dai Y, Sun L, Han S, Xu S, Wang L, Ding Y. Proteomic Study on the Reproductive Toxicity of Tripterygium Glycosides in Rats. Front Pharmacol 2022; 13:888968. [PMID: 35668950 PMCID: PMC9163711 DOI: 10.3389/fphar.2022.888968] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 05/02/2022] [Indexed: 12/02/2022] Open
Abstract
Tripterygium glycoside tablet (TGT) is a common clinically used and effective non-steroidal immunosuppressant. However, its reproductive toxicity limits its application in pediatric immune diseases, warranting the study of the molecular mechanism behind its reproductive toxicity. In the present study, 4-week-old male Sprague Dawley (SD) rats were provided TGT through continuous gavage with a clinically equivalent dose of 12 mg/kg for 12 weeks. The reproductive toxicity of TGT was recorded, and its toxicity mechanism was verified through experimental validation and proteomics analyses. Our results demonstrated that TGT could significantly reduce the testosterone level in the serum as well as the concentration and survival rate of sperms. Pathological sections of the testis revealed that TGT could reduce spermatocytes at different levels and make the convoluted meridians vacuolated. Based on tandem mass tag (TMT)-labeled quantitative rats testicular tissue proteomics, 34 differential proteins were screened, involving protein digestion and absorption, PPAR signaling pathway, PI3K-Akt, and other pathways, among which PI3K-Akt plays an important role in the study of reproductive injury. Western blotting results revealed that TGT could significantly downregulate the Col1A1, Col1A2, p-PI3K, and p-Akt expressions and inhibit the expression of proteins related to the PI3K-Akt signaling pathway. In summary, the clinically equivalent dose of TGT induced reproductive toxicity of 4-week-old male SD rats, possibly in relation to the inhibition of the PI3K-Akt pathway expression.
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Affiliation(s)
- Yanlin Dai
- Pediatric Medical College, Henan University of Traditional Chinese Medicine, Zhengzhou, China
| | - Lihui Sun
- Pediatric Medical College, Henan University of Traditional Chinese Medicine, Zhengzhou, China
| | - Shanshan Han
- Pediatric Medical College, Henan University of Traditional Chinese Medicine, Zhengzhou, China
- Department of Pediatrics, The First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, China
- *Correspondence: Shanshan Han, ; Ying Ding,
| | - Shanshan Xu
- Pediatric Medical College, Henan University of Traditional Chinese Medicine, Zhengzhou, China
| | - Long Wang
- Pediatric Medical College, Henan University of Traditional Chinese Medicine, Zhengzhou, China
| | - Ying Ding
- Pediatric Medical College, Henan University of Traditional Chinese Medicine, Zhengzhou, China
- Department of Pediatrics, The First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, China
- *Correspondence: Shanshan Han, ; Ying Ding,
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