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Zemaitis KJ, Fulcher JM, Kumar R, Degnan DJ, Lewis LA, Liao YC, Velickovic M, Williams SM, Moore RJ, Bramer LM, Velickovic D, Zhu Y, Zhou M, Pasa-Tolic L. Spatial top-down proteomics for the functional characterization of human kidney. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.580062. [PMID: 38405958 PMCID: PMC10888776 DOI: 10.1101/2024.02.13.580062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
BACKGROUND The Human Proteome Project has credibly detected nearly 93% of the roughly 20,000 proteins which are predicted by the human genome. However, the proteome is enigmatic, where alterations in amino acid sequences from polymorphisms and alternative splicing, errors in translation, and post-translational modifications result in a proteome depth estimated at several million unique proteoforms. Recently mass spectrometry has been demonstrated in several landmark efforts mapping the human proteoform landscape in bulk analyses. Herein, we developed an integrated workflow for characterizing proteoforms from human tissue in a spatially resolved manner by coupling laser capture microdissection, nanoliter-scale sample preparation, and mass spectrometry imaging. RESULTS Using healthy human kidney sections as the case study, we focused our analyses on the major functional tissue units including glomeruli, tubules, and medullary rays. After laser capture microdissection, these isolated functional tissue units were processed with microPOTS (microdroplet processing in one-pot for trace samples) for sensitive top-down proteomics measurement. This provided a quantitative database of 616 proteoforms that was further leveraged as a library for mass spectrometry imaging with near-cellular spatial resolution over the entire section. Notably, several mitochondrial proteoforms were found to be differentially abundant between glomeruli and convoluted tubules, and further spatial contextualization was provided by mass spectrometry imaging confirming unique differences identified by microPOTS, and further expanding the field-of-view for unique distributions such as enhanced abundance of a truncated form (1-74) of ubiquitin within cortical regions. CONCLUSIONS We developed an integrated workflow to directly identify proteoforms and reveal their spatial distributions. Where of the 20 differentially abundant proteoforms identified as discriminate between tubules and glomeruli by microPOTS, the vast majority of tubular proteoforms were of mitochondrial origin (8 of 10) where discriminate proteoforms in glomeruli were primarily hemoglobin subunits (9 of 10). These trends were also identified within ion images demonstrating spatially resolved characterization of proteoforms that has the potential to reshape discovery-based proteomics because the proteoforms are the ultimate effector of cellular functions. Applications of this technology have the potential to unravel etiology and pathophysiology of disease states, informing on biologically active proteoforms, which remodel the proteomic landscape in chronic and acute disorders.
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Hughes JW, Sisley EK, Hale OJ, Cooper HJ. Laser capture microdissection and native mass spectrometry for spatially-resolved analysis of intact protein assemblies in tissue. Chem Sci 2024; 15:5723-5729. [PMID: 38638209 PMCID: PMC11023061 DOI: 10.1039/d3sc04933g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 03/03/2024] [Indexed: 04/20/2024] Open
Abstract
Previously, we have shown that native ambient mass spectrometry imaging allows the spatial mapping of folded proteins and their complexes in thin tissue sections. Subsequent top-down native ambient mass spectrometry of adjacent tissue section enables protein identification. The challenges associated with protein identification by this approach are (i) the low abundance of proteins in tissue and associated long data acquisition timescales and (ii) irregular spatial distributions which hamper targeted sampling of the relevant tissue location. Here, we demonstrate that these challenges may be overcome through integration of laser capture microdissection in the workflow. We show identification of intact protein assemblies in rat liver tissue and apply the approach to identification of proteins in the granular layer of rat cerebellum.
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Affiliation(s)
- James W Hughes
- School of Biosciences, University of Birmingham Edgbaston Birmingham B15 2TT UK
| | - Emma K Sisley
- School of Biosciences, University of Birmingham Edgbaston Birmingham B15 2TT UK
| | - Oliver J Hale
- School of Biosciences, University of Birmingham Edgbaston Birmingham B15 2TT UK
| | - Helen J Cooper
- School of Biosciences, University of Birmingham Edgbaston Birmingham B15 2TT UK
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3
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Surface-sampling mass spectrometry to study proteins and protein complexes. Essays Biochem 2023; 67:229-241. [PMID: 36748325 PMCID: PMC10070487 DOI: 10.1042/ebc20220191] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 02/08/2023]
Abstract
This review aims to summarise the current capabilities of surface mass spectrometry (MS) approaches that offer intact protein analysis, and that of non-covalent complexes. Protein analysis is largely achieved via matrix-assisted laser desorption/ionisation (MALDI), which is in itself a surface analysis approach or solvent-based electrospray ionisation (ESI). Several surface sampling approaches have been developed based on ESI, and those that have been used for intact protein analysis will be discussed below. The extent of protein coverage, top-down elucidation, and probing of protein structure for native proteins and non-covalent complexes will be discussed for each approach. Strategies for improving protein analysis, ranging from sample preparation, and sampling methods to instrument modifications and the inclusion of ion mobility separation in the workflow will also be discussed. The relative benefits and drawbacks of each approach will be summarised, providing an overview of current capabilities.
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Hirata T, Yang M, Khoo HH. Direct Analysis of Bio-Molecules in Solid Materials using Electrospray Ionisation Mass Spectrometry coupled with Laser Ablation and a Liquid Sampling Technique. Mass Spectrom (Tokyo) 2023; 12:A0121. [DOI: 10.5702/massspectrometry.a0121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 03/16/2023] [Indexed: 03/29/2023] Open
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5
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Villacob RA, Egbejiogu BC, Feizi N, Hogan C, Murray KK, Solouki T. Native Mass Spectrometry and Collision-Induced Unfolding of Laser-Ablated Proteins. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:2215-2225. [PMID: 36346890 DOI: 10.1021/jasms.2c00184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Infrared laser ablation sample transfer (LAST) was used to collect samples from solid surfaces for mass spectrometry under native spray conditions. Native mass spectrometry was utilized to probe the charge states and collision-induced unfolding (CIU) characteristics of bovine serum albumin (BSA), bovine hemoglobin (BHb), and jack-bean concanavalin A (ConA) via direct injection electrospray, after liquid extraction surface sampling, and after LAST. Each protein was deposited from solution on solid surfaces and laser-ablated for off-line analysis or sampled for online analysis. It was found that the protein ion gas-phase charge-state distributions were comparable for direct infusion, liquid extraction, and laser ablation experiments. Moreover, calculated average collision cross section (CCS) values from direct injection, liquid extraction, and laser ablation experiments were consistent with previously reported literature values. Additionally, an equivalent number of mobility features and conformational turnovers were identified from unfolding pathways from all three methods for all charge states of each protein analyzed in this work. The presented work suggests that laser ablation yields intact proteins (BSA, BHb, and ConA), is compatible with native mass spectrometry, and could be suitable for spatially resolved interrogation of unfolding pathways of proteins.
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Affiliation(s)
| | | | - Neda Feizi
- Baylor University, Waco, Texas 76706, United States
| | - Cole Hogan
- Baylor University, Waco, Texas 76706, United States
| | - Kermit K Murray
- Louisiana State University, Baton Rouge, Louisiana 70803, United States
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6
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Zemaitis KJ, Veličković D, Kew W, Fort KL, Reinhardt-Szyba M, Pamreddy A, Ding Y, Kaushik D, Sharma K, Makarov AA, Zhou M, Paša-Tolić L. Enhanced Spatial Mapping of Histone Proteoforms in Human Kidney Through MALDI-MSI by High-Field UHMR-Orbitrap Detection. Anal Chem 2022; 94:12604-12613. [PMID: 36067026 PMCID: PMC10064997 DOI: 10.1021/acs.analchem.2c01034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Core histones including H2A, H2B, H3, and H4 are key modulators of cellular repair, transcription, and replication within eukaryotic cells, playing vital roles in the pathogenesis of disease and cellular responses to environmental stimuli. Traditional mass spectrometry (MS)-based bottom-up and top-down proteomics allows for the comprehensive identification of proteins and of post-translational modification (PTM) harboring proteoforms. However, these methodologies have difficulties preserving near-cellular spatial distributions because they typically require laser capture microdissection (LCM) and advanced sample preparation techniques. Herein, we coupled a matrix-assisted laser desorption/ionization (MALDI) source with a Thermo Scientific Q Exactive HF Orbitrap MS upgraded with ultrahigh mass range (UHMR) boards for the first demonstration of complementary high-resolution accurate mass (HR/AM) measurements of proteoforms up to 16.5 kDa directly from tissues using this benchtop mass spectrometer. The platform achieved isotopic resolution throughout the detected mass range, providing confident assignments of proteoforms with low ppm mass error and a considerable increase in duty cycle over other Fourier transform mass analyzers. Proteoform mapping of core histones was demonstrated on sections of human kidney at near-cellular spatial resolution, with several key distributions of histone and other proteoforms noted within both healthy biopsy and a section from a renal cell carcinoma (RCC) containing nephrectomy. The use of MALDI-MS imaging (MSI) for proteoform mapping demonstrates several steps toward high-throughput accurate identification of proteoforms and provides a new tool for mapping biomolecule distributions throughout tissue sections in extended mass ranges.
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Affiliation(s)
- Kevin J Zemaitis
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Dušan Veličković
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - William Kew
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Kyle L Fort
- Thermo Fisher Scientific (Bremen) GmbH, 28199 Bremen, Germany
| | | | - Annapurna Pamreddy
- Center for Renal Precision Medicine, Department of Medicine, University of Texas Health, San Antonio, Texas 78284, United States
| | - Yanli Ding
- Department of Pathology and Laboratory Medicine, University of Texas Health, San Antonio, Texas 78284, United States
| | - Dharam Kaushik
- Department of Urology, University of Texas Health, San Antonio, Texas 78284, United States
| | - Kumar Sharma
- Center for Renal Precision Medicine, Department of Medicine, University of Texas Health, San Antonio, Texas 78284, United States.,Audie L. Murphy Memorial VA Hospital, South Texas Veterans Health Care System, San Antonio, Texas 78284, United States
| | - Alexander A Makarov
- Thermo Fisher Scientific (Bremen) GmbH, 28199 Bremen, Germany.,Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht 3584, The Netherlands
| | - Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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7
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Illes‐Toth E, Hale OJ, Hughes JW, Strittmatter N, Rose J, Clayton B, Sargeant R, Jones S, Dannhorn A, Goodwin RJA, Cooper HJ. Mass Spectrometry Detection and Imaging of a Non‐Covalent Protein–Drug Complex in Tissue from Orally Dosed Rats. Angew Chem Int Ed Engl 2022; 61:e202202075. [PMID: 35830332 PMCID: PMC9542108 DOI: 10.1002/anie.202202075] [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: 02/07/2022] [Indexed: 11/10/2022]
Abstract
Here, we demonstrate detection by mass spectrometry of an intact protein–drug complex directly from liver tissue from rats that had been orally dosed with the drug. The protein–drug complex comprised fatty acid binding protein 1, FABP1, non‐covalently bound to the small molecule therapeutic bezafibrate. Moreover, we demonstrate spatial mapping of the [FABP1+bezafibrate] complex across a thin section of liver by targeted mass spectrometry imaging. This work is the first demonstration of in situ mass spectrometry analysis of a non‐covalent protein–drug complex formed in vivo and has implications for early stage drug discovery by providing a route to target‐drug characterization directly from the physiological environment.
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Affiliation(s)
- Eva Illes‐Toth
- School of Biosciences University of Birmingham Edgbaston Birmingham B15 2TT UK
| | - Oliver J. Hale
- School of Biosciences University of Birmingham Edgbaston Birmingham B15 2TT UK
| | - James W. Hughes
- School of Biosciences University of Birmingham Edgbaston Birmingham B15 2TT UK
| | - Nicole Strittmatter
- Imaging & Data Analytics Clinical Pharmacology & Safety Sciences Biopharmaceuticals R&D, AstraZeneca Cambridge CB4 0WG UK
| | - Jonathan Rose
- Animal Sciences & Technologies Clinical Pharmacology & Safety Sciences, AstraZeneca Babraham Research Campus Babraham Cambridge, CB22 3AT UK
| | - Ben Clayton
- Animal Sciences & Technologies Clinical Pharmacology & Safety Sciences, AstraZeneca Babraham Research Campus Babraham Cambridge, CB22 3AT UK
| | - Rebecca Sargeant
- Imaging & Data Analytics Clinical Pharmacology & Safety Sciences Biopharmaceuticals R&D, AstraZeneca Cambridge CB4 0WG UK
| | - Stewart Jones
- Imaging & Data Analytics Clinical Pharmacology & Safety Sciences Biopharmaceuticals R&D, AstraZeneca Cambridge CB4 0WG UK
| | - Andreas Dannhorn
- Imaging & Data Analytics Clinical Pharmacology & Safety Sciences Biopharmaceuticals R&D, AstraZeneca Cambridge CB4 0WG UK
| | - Richard J. A. Goodwin
- Imaging & Data Analytics Clinical Pharmacology & Safety Sciences Biopharmaceuticals R&D, AstraZeneca Cambridge CB4 0WG UK
| | - Helen J. Cooper
- School of Biosciences University of Birmingham Edgbaston Birmingham B15 2TT UK
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8
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Illes‐Toth E, Hale OJ, Hughes JW, Strittmatter N, Rose J, Clayton B, Sargeant R, Jones S, Dannhorn A, Goodwin RJA, Cooper HJ. Mass Spectrometry Detection and Imaging of a Non-Covalent Protein-Drug Complex in Tissue from Orally Dosed Rats. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 134:e202202075. [PMID: 38505542 PMCID: PMC10946869 DOI: 10.1002/ange.202202075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Indexed: 11/07/2022]
Abstract
Here, we demonstrate detection by mass spectrometry of an intact protein-drug complex directly from liver tissue from rats that had been orally dosed with the drug. The protein-drug complex comprised fatty acid binding protein 1, FABP1, non-covalently bound to the small molecule therapeutic bezafibrate. Moreover, we demonstrate spatial mapping of the [FABP1+bezafibrate] complex across a thin section of liver by targeted mass spectrometry imaging. This work is the first demonstration of in situ mass spectrometry analysis of a non-covalent protein-drug complex formed in vivo and has implications for early stage drug discovery by providing a route to target-drug characterization directly from the physiological environment.
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Affiliation(s)
- Eva Illes‐Toth
- School of BiosciencesUniversity of BirminghamEdgbastonBirmingham B15 2TTUK
| | - Oliver J. Hale
- School of BiosciencesUniversity of BirminghamEdgbastonBirmingham B15 2TTUK
| | - James W. Hughes
- School of BiosciencesUniversity of BirminghamEdgbastonBirmingham B15 2TTUK
| | - Nicole Strittmatter
- Imaging & Data AnalyticsClinical Pharmacology & Safety SciencesBiopharmaceuticals R&D, AstraZenecaCambridgeCB4 0WGUK
| | - Jonathan Rose
- Animal Sciences & TechnologiesClinical Pharmacology & Safety Sciences, AstraZenecaBabraham Research CampusBabrahamCambridge, CB22 3ATUK
| | - Ben Clayton
- Animal Sciences & TechnologiesClinical Pharmacology & Safety Sciences, AstraZenecaBabraham Research CampusBabrahamCambridge, CB22 3ATUK
| | - Rebecca Sargeant
- Imaging & Data AnalyticsClinical Pharmacology & Safety SciencesBiopharmaceuticals R&D, AstraZenecaCambridgeCB4 0WGUK
| | - Stewart Jones
- Imaging & Data AnalyticsClinical Pharmacology & Safety SciencesBiopharmaceuticals R&D, AstraZenecaCambridgeCB4 0WGUK
| | - Andreas Dannhorn
- Imaging & Data AnalyticsClinical Pharmacology & Safety SciencesBiopharmaceuticals R&D, AstraZenecaCambridgeCB4 0WGUK
| | - Richard J. A. Goodwin
- Imaging & Data AnalyticsClinical Pharmacology & Safety SciencesBiopharmaceuticals R&D, AstraZenecaCambridgeCB4 0WGUK
| | - Helen J. Cooper
- School of BiosciencesUniversity of BirminghamEdgbastonBirmingham B15 2TTUK
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9
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Comparison of methods for quantitative analysis of ranibizumab and bevacizumab in human plasma using various bioanalytical techniques, including microfluidic immunoassay, triple quadrupole, and high-resolution liquid chromatography-tandem mass spectrometry approaches. J Pharm Biomed Anal 2022; 217:114823. [DOI: 10.1016/j.jpba.2022.114823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 04/05/2022] [Accepted: 05/05/2022] [Indexed: 11/20/2022]
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10
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Hale OJ, Cooper HJ. Native Ambient Mass Spectrometry of an Intact Membrane Protein Assembly and Soluble Protein Assemblies Directly from Lens Tissue. Angew Chem Int Ed Engl 2022; 61:e202201458. [PMID: 35665580 PMCID: PMC9401010 DOI: 10.1002/anie.202201458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Indexed: 11/16/2022]
Abstract
Membrane proteins constitute around two‐thirds of therapeutic targets but present a significant challenge for structural analysis due to their low abundance and solubility. Existing methods for structural analysis rely on over‐expression and/or purification of the membrane protein, thus removing any links back to actual physiological environment. Here, we demonstrate mass spectrometry analysis of an intact oligomeric membrane protein directly from tissue. Aquaporin‐0 exists as a 113 kDa tetramer, with each subunit featuring six transmembrane helices. We report the characterisation of the intact assembly directly from a section of sheep eye lens without sample pre‐treatment. Protein identity was confirmed by mass measurement of the tetramer and subunits, together with top‐down mass spectrometry, and the spatial distribution was determined by mass spectrometry imaging. Our approach allows simultaneous analysis of soluble protein assemblies in the tissue.
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Affiliation(s)
- Oliver J. Hale
- School of Biosciences University of Birmingham Edgbaston B15 2TT UK
| | - Helen J. Cooper
- School of Biosciences University of Birmingham Edgbaston B15 2TT UK
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11
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Hale OJ, Cooper HJ. Native Ambient Mass Spectrometry of an Intact Membrane Protein Assembly and Soluble Protein Assemblies Directly from Lens Tissue. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 134:e202201458. [PMID: 38505128 PMCID: PMC10946450 DOI: 10.1002/ange.202201458] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Indexed: 12/16/2022]
Abstract
Membrane proteins constitute around two-thirds of therapeutic targets but present a significant challenge for structural analysis due to their low abundance and solubility. Existing methods for structural analysis rely on over-expression and/or purification of the membrane protein, thus removing any links back to actual physiological environment. Here, we demonstrate mass spectrometry analysis of an intact oligomeric membrane protein directly from tissue. Aquaporin-0 exists as a 113 kDa tetramer, with each subunit featuring six transmembrane helices. We report the characterisation of the intact assembly directly from a section of sheep eye lens without sample pre-treatment. Protein identity was confirmed by mass measurement of the tetramer and subunits, together with top-down mass spectrometry, and the spatial distribution was determined by mass spectrometry imaging. Our approach allows simultaneous analysis of soluble protein assemblies in the tissue.
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Affiliation(s)
- Oliver J. Hale
- School of BiosciencesUniversity of BirminghamEdgbastonB15 2TTUK
| | - Helen J. Cooper
- School of BiosciencesUniversity of BirminghamEdgbastonB15 2TTUK
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12
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Nagornov KO, Kozhinov AN, Gasilova N, Menin L, Tsybin YO. Characterization of the Time-Domain Isotopic Beat Patterns of Monoclonal Antibodies in Fourier Transform Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1113-1125. [PMID: 35638743 DOI: 10.1021/jasms.1c00336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The time-domain transients in the Fourier transform mass spectrometry (FTMS) analysis of monoclonal antibodies (mAbs) are known to exhibit characteristic isotopic beat patterns. These patterns are defined by the isotopic distributions of all gaseous mAb ions present in the FTMS mass analyzer, originating from single or multiple charge states, and from single or multiple proteoforms. For an isolated charge state of a single proteoform, the mAb isotopic beat pattern resembles narrow splashes of signal amplitude (beats), spaced periodically in the time-domain transient, with broad (often exceeding 1 s) "valleys" between them. Here, we reinforce the importance of isotopic beat patterns for the accurate interpretation and presentation of FTMS data in the analysis of mAbs and other large biopolymers. An updated, mAb-grade version of the transient-mediated FTMS data simulation and visualization tool, FTMS Simulator is introduced and benchmarked. We then apply this tool to evaluate the charge-state dependent characteristics of isotopic beats in mAbs analyses with modern models of Orbitrap and ion cyclotron resonance (ICR) FTMS instruments, including detection of higher-order harmonics. We demonstrate the impact of the isotopic beat patterns on the analytical characteristics of the resulting mass spectra of individual and overlapping mAb proteoforms. The results reported here detail highly nonlinear dependences of resolution and signal-to-noise ratio on the time-domain transient period, absorption or magnitude mode spectra representation, and apodization functions. The provided description and the demonstrated ability to routinely conduct accurate simulations of FTMS data for large biopolymers should aid the end-users of Orbitrap and ICR FTMS instruments in the analysis of mAbs and other biopolymers, including viruses.
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Affiliation(s)
| | | | - Natalia Gasilova
- Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Laure Menin
- Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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13
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DelGuidice CE, Ismaiel OA, Mylott WR, Yuan M, Halquist MS. Intact quantitative bioanalytical method development and fit-for-purpose validation of a monoclonal antibody and its related fab fragment in human vitreous and aqueous humor using LC-HRMS. Anal Bioanal Chem 2022; 414:4189-4202. [PMID: 35451621 DOI: 10.1007/s00216-022-04071-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 03/27/2022] [Accepted: 04/06/2022] [Indexed: 11/29/2022]
Abstract
Ranibizumab is an FDA-approved drug used to treat wet age-related macular degeneration (AMD), diabetic retinopathy, macular edema, and myopic choroidal neovascularization. Bevacizumab is another drug often used off-label to treat wet AMD. In order to reduce unwanted angiogenesis, ranibizumab and bevacizumab target circulating VEGF-A in the eye. Concentration levels in human vitreous and aqueous humor can be used to provide valuable efficacy information. However, vitreous and aqueous humor's aqueous environment, and vitreous humor's viscosity, as well as the stickiness of the analytes can provide bioanalytical challenges. In this manuscript, we describe the development, optimization, and fit-for-purpose validation of an LC-HRMS method designed for intact quantitative bioanalysis of ranibizumab and bevacizumab in human vitreous and aqueous humor following intravitreal administration. In order to fully develop this method, evaluations were conducted to optimize the conditions, including the data processing model (extracted ion chromatograms (XICs) vs deconvolution), carryover mitigation, sample preparation scheme optimization for surrogate and primary matrices, use of internal standard/immunocapture/deglycosylation, and optimization of the extraction and dilution procedure, as well as optimization of the liquid chromatography and mass spectrometry conditions. Once the method was fully optimized, a fit-for-purpose validation was conducted, including matrix parallelism, with a linear calibration range of 10 to 200 µg/mL. The development of this intact quantitative method using LC-HRMS provides a proof-of-concept template for challenging, but valuable new and exciting bioanalytical techniques.
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Affiliation(s)
- Catherine E DelGuidice
- Department of Pharmaceutics, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, USA. .,PPD Laboratories, Richmond, VA, USA.
| | - Omnia A Ismaiel
- Department of Analytical Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
| | | | | | - Matthew S Halquist
- Department of Pharmaceutics, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, USA
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14
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Hale O, Hughes JW, Sisley EK, Cooper HJ. Native Ambient Mass Spectrometry Enables Analysis of Intact Endogenous Protein Assemblies up to 145 kDa Directly from Tissue. Anal Chem 2022; 94:5608-5614. [PMID: 35358391 PMCID: PMC9008691 DOI: 10.1021/acs.analchem.1c05353] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 02/22/2022] [Indexed: 02/07/2023]
Abstract
Untargeted label-free interrogation of proteins in their functional form directly from their physiological environment promises to transform life sciences research by providing unprecedented insight into their transient interactions with other biomolecules and xenobiotics. Native ambient mass spectrometry (NAMS) shows great potential for the structural analysis of endogenous protein assemblies directly from tissues; however, to date, this has been limited to assemblies of low molecular weight (<20 kDa) or very high abundance (hemoglobin tetramer in blood vessels, RidA homotrimer in kidney cortex tissues). The present work constitutes a step change for NAMS of protein assemblies: we demonstrate the detection and identification of a range of intact endogenous protein assemblies with various stoichiometries (dimer, trimer, and tetramer) from a range of tissue types (brain, kidney, liver) by the use of multiple NAMS techniques. Crucially, we demonstrate a greater than twofold increase in accessible molecular weight (up to 145 kDa). In addition, spatial distributions of protein assemblies up to 94 kDa were mapped in brain and kidney by nanospray desorption electrospray ionization (nano-DESI) mass spectrometry imaging.
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Affiliation(s)
- Oliver
J. Hale
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K.
| | - James W. Hughes
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K.
| | - Emma K. Sisley
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K.
| | - Helen J. Cooper
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K.
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15
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Klykov O, Kopylov M, Carragher B, Heck AJ, Noble AJ, Scheltema RA. Label-free visual proteomics: Coupling MS- and EM-based approaches in structural biology. Mol Cell 2022; 82:285-303. [PMID: 35063097 PMCID: PMC8842845 DOI: 10.1016/j.molcel.2021.12.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/14/2021] [Accepted: 12/20/2021] [Indexed: 01/22/2023]
Abstract
Combining diverse experimental structural and interactomic methods allows for the construction of comprehensible molecular encyclopedias of biological systems. Typically, this involves merging several independent approaches that provide complementary structural and functional information from multiple perspectives and at different resolution ranges. A particularly potent combination lies in coupling structural information from cryoelectron microscopy or tomography (cryo-EM or cryo-ET) with interactomic and structural information from mass spectrometry (MS)-based structural proteomics. Cryo-EM/ET allows for sub-nanometer visualization of biological specimens in purified and near-native states, while MS provides bioanalytical information for proteins and protein complexes without introducing additional labels. Here we highlight recent achievements in protein structure and interactome determination using cryo-EM/ET that benefit from additional MS analysis. We also give our perspective on how combining cryo-EM/ET and MS will continue bridging gaps between molecular and cellular studies by capturing and describing 3D snapshots of proteomes and interactomes.
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Affiliation(s)
- Oleg Klykov
- National Center for In-situ Tomographic Ultramicroscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Mykhailo Kopylov
- National Center for In-situ Tomographic Ultramicroscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Bridget Carragher
- National Center for In-situ Tomographic Ultramicroscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Albert J.R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CH Utrecht, The Netherlands,Netherlands Proteomics Center, 3584 CH Utrecht, The Netherlands
| | - Alex J Noble
- National Center for In-situ Tomographic Ultramicroscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA,Corresponding author for cryo-EM/ET/FIB-SEM: Alex J. Noble, tel: (+1) 212-939-0660;
| | - Richard A. Scheltema
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CH Utrecht, The Netherlands,Netherlands Proteomics Center, 3584 CH Utrecht, The Netherlands,Corresponding author for MS: Richard A. Scheltema, tel: (+31) 30 253 6804;
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Otsuka Y. Direct Liquid Extraction and Ionization Techniques for Understanding Multimolecular Environments in Biological Systems (Secondary Publication). Mass Spectrom (Tokyo) 2021; 10:A0095. [PMID: 34249586 PMCID: PMC8246329 DOI: 10.5702/massspectrometry.a0095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 11/23/2022] Open
Abstract
A combination of direct liquid extraction using a small volume of solvent and electrospray ionization allows the rapid measurement of complex chemical components in biological samples and visualization of their distribution in tissue sections. This review describes the development of such techniques and their application to biological research since the first reports in the early 2000s. An overview of electrospray ionization, ion suppression in samples, and the acceleration of specific chemical reactions in charged droplets is also presented. Potential future applications for visualizing multimolecular environments in biological systems are discussed.
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Affiliation(s)
- Yoichi Otsuka
- Graduate School of Science, Osaka University, 1–1 Machikaneyama-cho, Toyonaka, Osaka 560–0043, Japan
- JST, PRESTO, 4–1–8 Honcho, Kawaguchi, Saitama 332–0012, Japan
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18
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Sakamoto W, Azegami N, Konuma T, Akashi S. Single-Cell Native Mass Spectrometry of Human Erythrocytes. Anal Chem 2021; 93:6583-6588. [PMID: 33871982 DOI: 10.1021/acs.analchem.1c00588] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Native mass spectrometry (MS) enables the determination of the molecular mass of protein complexes. Generally, samples for native MS are isolated, purified, and prepared in volatile solutions. However, to understand the function of proteins in living cells, it is essential to characterize the protein complex as is, without isolation/purification of the protein, using the smallest possible amount of the sample. In the present study, we modified the "live single-cell MS" method, which has mainly been used in metabolomics, and applied it to observe hemoglobin directly sampled from human erythrocytes. By optimizing the experimental methods and conditions, we obtained native mass spectra of hemoglobin using only a single erythrocyte, which was directly sampled into a nanoelectrospray ionization emitter using a micromanipulator and microinjector system. That is, our method enables the analysis of ∼0.45 fmol of hemoglobin directly sampled from an erythrocyte. To our knowledge, this is the first report of native MS for endogenous proteins using a single intact human cell.
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Abstract
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Previously, we have
demonstrated native mass spectrometry imaging
(native MSI) in which the spatial distribution of proteins maintained
in their native-like, folded conformations was determined using liquid
extraction surface analysis (LESA). While providing an excellent testbed
for proof of principle, the spatial resolution of LESA is currently
limited for imaging primarily by the physical size of the sampling
pipette tip. Here, we report the adoption of nanospray-desorption
electrospray ionization (nano-DESI) for native MSI, delivering substantial
improvements in resolution versus native LESA MSI. In addition, native
nano-DESI may be used for location-targeted top–down proteomics
analysis directly from tissue. Proteins, including a homodimeric complex
not previously detected by native MSI, were identified through a combination
of collisional activation, high-resolution MS and proton transfer
charge reduction.
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Affiliation(s)
- Oliver J Hale
- School of Biosciences, University of Birmingham, Edgbaston B15 2TT, U.K
| | - Helen J Cooper
- School of Biosciences, University of Birmingham, Edgbaston B15 2TT, U.K
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20
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Yan B, Bunch J. Probing Folded Proteins and Intact Protein Complexes by Desorption Electrospray Ionization Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:690-699. [PMID: 33605725 DOI: 10.1021/jasms.0c00417] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Native mass spectrometry (MS) enables the study of intact proteins as well as noncovalent protein-protein and protein-ligand complexes in their biological state. In this work, we present the application of a Waters desorption electrospray ionization (DESI) source with a prototype spray emitter for rapid surface measurements of folded and native protein structures. A comparison of DESI spray solvent shows that adding 50% methanol to 200 mM ammonium acetate solution does not reduce its performance in preserving folded protein structures. Instead, improved signal-to-noise (S/N) ratio is obtained, and less adducted peaks are detected by using this uncommon native MS solvent system. The standard DESI design with an inlet tube allows optimization of sampling temperature conditions to improve desolvation and therefore S/N ratio. Furthermore, tuning the inlet temperature enables the control and study of unfolding behavior of proteins from surface samples. The optimized condition for native DESI has been applied to several selected proteins and protein complexes with the molecular weight ranging from 8.6 to 66.4 kDa. Ions of folded proteins with narrow charge state distribution (CSD), or peaks showing noncovalent-bond-assembled intact protein complexes, are observed in the spectra. Evidence for the structural refolding of denatured proteins and protein complexes sampled with native solvent highlights the need for care when interpreting DESI native MS data, particularly for proteins with stable native structures.
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Affiliation(s)
- Bin Yan
- National Centre of Excellence in Mass Spectrometry Imaging, National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
| | - Josephine Bunch
- National Centre of Excellence in Mass Spectrometry Imaging, National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
- Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, London SW7 2AZ, U.K
- Rosalind Franklin Institute, Harwell Campus, Didcot OX11 0FA, U.K
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21
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DelGuidice CE, Ismaiel OA, Mylott WR, Halquist MS. Optimization and method validation for the quantitative analysis of a monoclonal antibody and its related fab fragment in human plasma after intravitreal administration, using LC-MS/MS. J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1164:122474. [PMID: 33508760 DOI: 10.1016/j.jchromb.2020.122474] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 11/19/2020] [Accepted: 11/23/2020] [Indexed: 01/07/2023]
Abstract
As biologic based drugs become an increasingly important sector of the pharmaceutical industry, accurate and precision techniques for bioanalysis are required to support clinical trials and beyond. Ranibizumab, a fab therapeutic, is an FDA approved drug to treat wet age-related macular degeneration (AMD), as well as other eye related diseases. Ranibizumab's mAb counterpart, bevacizumab, is often also used off-label to treat wet AMD. Ranibizumab and bevacizumab target circulating VEGF-A in the eye, reducing unwanted angiogenesis. Since these drugs are designed for local intravitreal administration, concentration levels in human plasma are expected to be significantly lower compared to vitreous fluid concentrations, presenting bioanalytical challenges. However, this is important for assessment of drug toxicity. In this manuscript, we describe the development, optimization, and validation of an LC-MS/MS method designed for quantitative bioanalysis of ranibizumab and bevacizumab in human plasma following intravitreal administration. In order to fully develop this method, evaluations were conducted to optimize the conditions, including selection of the surrogate peptide by in-silico experiments, optimizations of the immunocapture, denaturation, reduction, alkylation, and digestion extraction steps, as well as optimization of the LC-MS/MS conditions, and evaluation of a dissociation step to determine if there was interference from VEGF or ADAs. Once the method was fully optimized, it was then validated, following the 2018 FDA guidance on bioanalytical method validations. This method is now available for use during clinical trials and precision medicine, for the quantitative evaluation of systemic exposure of ranibizumab or bevacizumab in human plasma after intravitreal administration, with a linear calibration range of 0.300-100 ng/mL.
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Affiliation(s)
- Catherine E DelGuidice
- Department of Pharmaceutics, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, USA; PPD Laboratories, Richmond, VA, USA.
| | - Omnia A Ismaiel
- PPD Laboratories, Richmond, VA, USA; Department of Analytical Chemistry, Faculty of Pharmacy, Zagazig University, Egypt
| | | | - Matthew S Halquist
- Department of Pharmaceutics, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, USA.
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Affiliation(s)
- James E. Keener
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Guozhi Zhang
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Michael T. Marty
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
- Bio5 Institute, University of Arizona, Tucson, AZ 85721, USA
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23
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Hale OJ, Cooper HJ. Native Mass Spectrometry Imaging and In Situ Top-Down Identification of Intact Proteins Directly from Tissue. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2531-2537. [PMID: 32822168 DOI: 10.1021/jasms.0c00226] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Mass spectrometry imaging (MSI) provides information on the spatial distribution of molecules within a biological substrate without the requirement for labeling. Its broad specificity, i.e., the capability to spatially profile any analyte ion detected, constitutes a major advantage over other imaging techniques. A separate branch of mass spectrometry, native mass spectrometry, provides information relating to protein structure through retention of solution-phase interactions in the gas phase. Integration of MSI and native mass spectrometry ("native MSI") affords opportunities for simultaneous acquisition of spatial and structural information on proteins directly from their physiological environment. Here, we demonstrate significant improvements in native MSI and associated protein identification of intact proteins and protein assemblies in thin sections of rat kidney by use of liquid extraction surface analysis on a state-of-the-art Orbitrap mass spectrometer optimized for intact protein analysis. Proteins of up to 47 kDa, including a trimeric protein complex, were imaged and identified.
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Affiliation(s)
- Oliver J Hale
- School of Biosciences, University of Birmingham, Edgbaston B15 2TT, U.K
| | - Helen J Cooper
- School of Biosciences, University of Birmingham, Edgbaston B15 2TT, U.K
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Abstract
Analysis of intact proteins by native mass spectrometry has emerged as a powerful tool for obtaining insight into subunit diversity, post-translational modifications, stoichiometry, structural arrangement, stability, and overall architecture. Typically, such an analysis is performed following protein purification procedures, which are time consuming, costly, and labor intensive. As this technology continues to move forward, advances in sample handling and instrumentation have enabled the investigation of intact proteins in situ and in crude samples, offering rapid analysis and improved conservation of the biological context. This emerging field, which involves various ion source platforms such as matrix-assisted laser desorption ionization (MALDI) and electrospray ionization (ESI) for both spatial imaging and solution-based analysis, is expected to impact many scientific fields, including biotechnology, pharmaceuticals, and clinical sciences. In this Perspective, we discuss the information that can be retrieved by such experiments as well as the current advantages and technical challenges associated with the different sampling strategies. Furthermore, we present future directions of these MS-based methods, including current limitations and efforts that should be made to make these approaches more accessible. Considering the vast progress we have witnessed in recent years, we anticipate that the advent of further innovations enabling minimal handling of MS samples will make this field more robust, user friendly, and widespread.
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Affiliation(s)
- Shay Vimer
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Gili Ben-Nissan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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Hale OJ, Illes-Toth E, Mize TH, Cooper HJ. High-Field Asymmetric Waveform Ion Mobility Spectrometry and Native Mass Spectrometry: Analysis of Intact Protein Assemblies and Protein Complexes. Anal Chem 2020; 92:6811-6816. [PMID: 32343119 PMCID: PMC7304667 DOI: 10.1021/acs.analchem.0c00649] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
![]()
High-field asymmetric
waveform ion mobility spectrometry (FAIMS)
enables the separation of ions on the basis of their differential
mobility in an asymmetric oscillating electric field. We, and others,
have previously demonstrated the benefits of FAIMS for the analysis
of peptides and denatured proteins. To date, FAIMS has not been integrated
with native mass spectrometry of folded proteins and protein complexes,
largely due to concerns over the heating effects associated with the
high electric fields employed. Here, we demonstrate the newly introduced
cylindrical FAIMS Pro device coupled with an Orbitrap Eclipse enables
analysis of intact protein assemblies up to 147 kDa. No evidence for
dissociation was detected suggesting that any field heating is insufficient
to disrupt the noncovalent interactions governing these assemblies.
Moreover, the FAIMS device was integrated into native liquid extraction
surface analysis (LESA) MS of protein assemblies directly from thin
tissue sections. Intact tetrameric hemoglobin (64 kDa) and trimeric
reactive intermediate deiminase A (RidA, 43 kDa) were detected. Improvements
in signal-to-noise of between 1.5× and 12× were observed
for these protein assemblies on integration of FAIMS.
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Affiliation(s)
- Oliver J Hale
- School of Biosciences, University of Birmingham, Edgbaston B15 2TT, U.K
| | - Eva Illes-Toth
- School of Biosciences, University of Birmingham, Edgbaston B15 2TT, U.K
| | - Todd H Mize
- School of Biosciences, University of Birmingham, Edgbaston B15 2TT, U.K
| | - Helen J Cooper
- School of Biosciences, University of Birmingham, Edgbaston B15 2TT, U.K
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Hale OJ, Sisley EK, Griffiths RL, Styles IB, Cooper HJ. Native LESA TWIMS-MSI: Spatial, Conformational, and Mass Analysis of Proteins and Protein Complexes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:873-879. [PMID: 32159346 PMCID: PMC7147347 DOI: 10.1021/jasms.9b00122] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 02/13/2020] [Accepted: 02/18/2020] [Indexed: 05/18/2023]
Abstract
We have previously demonstrated native liquid extraction surface analysis (LESA) mass spectrometry imaging of small intact proteins in thin tissue sections. We also showed calculation of collision cross sections for specific proteins extracted from discrete locations in tissue by LESA traveling wave ion mobility spectrometry (TWIMS). Here, we demonstrate an integrated native LESA TWIMS mass spectrometry imaging (MSI) workflow, in which ion mobility separation is central to the imaging experiment and which provides spatial, conformational, and mass information on endogenous proteins in a single experiment. The approach was applied to MSI of a thin tissue section of mouse kidney. The results show that the benefits of integration of TWIMS include improved specificity of the ion images and the capacity to calculate collision cross sections for any protein or protein complex detected in any pixel (without a priori knowledge of the presence of the protein).
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Affiliation(s)
- Oliver J. Hale
- School of Biosciences, University of
Birmingham, Edgbaston B15 2TT, U.K.
| | - Emma K. Sisley
- School of Biosciences, University of
Birmingham, Edgbaston B15 2TT, U.K.
| | - Rian L. Griffiths
- School of Biosciences, University of
Birmingham, Edgbaston B15 2TT, U.K.
| | - Iain B. Styles
- School of Computer Science, University of
Birmingham, Edgbaston B15 2TT, U.K.
| | - Helen J. Cooper
- School of Biosciences, University of
Birmingham, Edgbaston B15 2TT, U.K.
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Hale OJ, Cooper HJ. In situ mass spectrometry analysis of intact proteins and protein complexes from biological substrates. Biochem Soc Trans 2020; 48:317-326. [PMID: 32010951 PMCID: PMC7054757 DOI: 10.1042/bst20190793] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/09/2020] [Accepted: 01/09/2020] [Indexed: 12/15/2022]
Abstract
Advances in sample preparation, ion sources and mass spectrometer technology have enabled the detection and characterisation of intact proteins. The challenges associated include an appropriately soft ionisation event, efficient transmission and detection of the often delicate macromolecules. Ambient ion sources, in particular, offer a wealth of strategies for analysis of proteins from solution environments, and directly from biological substrates. The last two decades have seen rapid development in this area. Innovations include liquid extraction surface analysis, desorption electrospray ionisation and nanospray desorption electrospray ionisation. Similarly, developments in native mass spectrometry allow protein-protein and protein-ligand complexes to be ionised and analysed. Identification and characterisation of these large ions involves a suite of hyphenated mass spectrometry techniques, often including the coupling of ion mobility spectrometry and fragmentation techniques. The latter include collision, electron and photon-induced methods, each with their own characteristics and benefits for intact protein identification. In this review, recent developments for in situ protein analysis are explored, with a focus on ion sources and tandem mass spectrometry techniques used for identification.
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Affiliation(s)
- Oliver J. Hale
- School of Biosciences, University of Birmingham, Edgbaston B15 2TT, U.K
| | - Helen J. Cooper
- School of Biosciences, University of Birmingham, Edgbaston B15 2TT, U.K
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