1
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Prell JS. Modeling collisional kinetic energy damping, heating, and cooling of ions in mass spectrometers: a tutorial perspective. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2024; 504:117290. [PMID: 39072228 PMCID: PMC11271708 DOI: 10.1016/j.ijms.2024.117290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Many powerful methods in mass spectrometry rely on activation of ions by high-energy collisions with gas particles. For example, multiple Collision Induced Dissociation (CID) has been used for many years to determine structural information for ions ranging from small organics to large, native-like protein complexes. More recently, Collision Induced Unfolding (CIU) has proved to be a very powerful method for understanding high-order protein structure and detecting differences between similar proteins. Quantifying the thermochemistry underlying dissociation/unfolding in these experiments can be quite challenging without reliable models of ion heating and cooling. Established physical models of CID are valuable in predicting ion heating but do not explicitly include mechanisms for cooling, which may play a large part in CID/CIU in modern instruments. Ab initio and Molecular Dynamics methods are extremely computationally expensive for modeling CID/CIU of large analytes such as biomolecular ions. In this tutorial perspective, limiting behaviors of ion kinetic energy damping, heating, and cooling set by "extreme" cases are explored, and an Improved Impulsive Collision Theory and associated software ("Ion Simulations of the Physics of Activation", IonSPA) are introduced that can model all of these for partially inelastic collisions. Finally, examples of modeled collisional activation of native-like protein ions under realistic experimental conditions are discussed, with an outlook toward the use of IonSPA in accessing the thermochemical information hidden in CID breakdown curves and CIU fingerprints.
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Affiliation(s)
- James S. Prell
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, OR, USA, 97403-1253
- Materials Science Institute, 1252 University of Oregon, OR, USA, 97403-1252
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2
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Oney-Hawthorne SD, Barondeau DP. Fe-S cluster biosynthesis and maturation: Mass spectrometry-based methods advancing the field. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119784. [PMID: 38908802 DOI: 10.1016/j.bbamcr.2024.119784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/25/2024] [Accepted: 06/10/2024] [Indexed: 06/24/2024]
Abstract
Iron‑sulfur (FeS) clusters are inorganic protein cofactors that perform essential functions in many physiological processes. Spectroscopic techniques have historically been used to elucidate details of FeS cluster type, their assembly and transfer, and changes in redox and ligand binding properties. Structural probes of protein topology, complex formation, and conformational dynamics are also necessary to fully understand these FeS protein systems. Recent developments in mass spectrometry (MS) instrumentation and methods provide new tools to investigate FeS cluster and structural properties. With the unique advantage of sampling all species in a mixture, MS-based methods can be utilized as a powerful complementary approach to probe native dynamic heterogeneity, interrogate protein folding and unfolding equilibria, and provide extensive insight into protein binding partners within an entire proteome. Here, we highlight key advances in FeS protein studies made possible by MS methodology and contribute an outlook for its role in the field.
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Affiliation(s)
| | - David P Barondeau
- Department of Chemistry, Texas A&M University, College Station, TX 77842, USA.
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3
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Zhao C, Slocum ST, Sherman DH, Ruotolo BT. Time-Resolved Ion Mobility-Mass Spectrometry Reveals Structural Transitions in the Disassembly of Modular Polyketide Syntheses. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:2136-2142. [PMID: 39038158 DOI: 10.1021/jasms.4c00181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
The type 1 polyketide synthase (PKS) assembly line uses its modular structure to produce polyketide natural products that form the basis of many pharmaceuticals. Currently, several cryoelectron microscopy (cryo-EM) structures of a multidomain PKS module have been constructed, but much remains to be learned. Here we utilize ion-mobility mass spectrometry (IM-MS) to record size and shape information and detect different conformational states of a 207 kDa didomain dimer comprised of ketosynthase (KS) and acyl transferase (AT), excised from full-length module. Furthermore, gas-phase stability differences between these different conformations are captured by collision induced unfolding (CIU) technology. Additionally, through tracking these forms as a function of time, we elucidate a detailed disassembly pathway for KS-AT dimers for the first time.
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Affiliation(s)
- Chunyi Zhao
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Samuel T Slocum
- Life Science Institute, Departments of Medicinal Chemistry, Chemistry and Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - David H Sherman
- Life Science Institute, Departments of Medicinal Chemistry, Chemistry and Microbiology & Immunology, 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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4
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Dai Z, Ben-Younis A, Vlachaki A, Raleigh D, Thalassinos K. Understanding the structural dynamics of human islet amyloid polypeptide: Advancements in and applications of ion-mobility mass spectrometry. Biophys Chem 2024; 312:107285. [PMID: 38941872 PMCID: PMC11260546 DOI: 10.1016/j.bpc.2024.107285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 05/30/2024] [Accepted: 06/23/2024] [Indexed: 06/30/2024]
Abstract
Human islet amyloid polypeptide (hIAPP) forms amyloid deposits that contribute to β-cell death in pancreatic islets and are considered a hallmark of Type II diabetes Mellitus (T2DM). Evidence suggests that the early oligomers of hIAPP formed during the aggregation process are the primary pathological agent in islet amyloid induced β-cell death. The self-assembly mechanism of hIAPP, however, remains elusive, largely due to limitations in conventional biophysical techniques for probing the distribution or capturing detailed structures of the early, structurally dynamic oligomers. The advent of Ion-mobility Mass Spectrometry (IM-MS) has enabled the characterisation of hIAPP early oligomers in the gas phase, paving the way towards a deeper understanding of the oligomerisation mechanism and the correlation of structural information with the cytotoxicity of the oligomers. The sensitivity and the rapid structural characterisation provided by IM-MS also show promise in screening hIAPP inhibitors, categorising their modes of inhibition through "spectral fingerprints". This review delves into the application of IM-MS to the dissection of the complex steps of hIAPP oligomerisation, examining the inhibitory influence of metal ions, and exploring the characterisation of hetero-oligomerisation with different hIAPP variants. We highlight the potential of IM-MS as a tool for the high-throughput screening of hIAPP inhibitors, and for providing insights into their modes of action. Finally, we discuss advances afforded by recent advancements in tandem IM-MS and the combination of gas phase spectroscopy with IM-MS, which promise to deliver a more sensitive and higher-resolution structural portrait of hIAPP oligomers. Such information may help facilitate a new era of targeted therapeutic strategies for islet amyloidosis in T2DM.
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Affiliation(s)
- Zijie Dai
- Institute of Structural and Molecular Biology, Division of Bioscience, University College London, London WC1E 6BT, UK
| | - Aisha Ben-Younis
- Institute of Structural and Molecular Biology, Division of Bioscience, University College London, London WC1E 6BT, UK
| | - Anna Vlachaki
- Department of Clinical Neurosciences, John van Geest Centre for Brain Repair, University of Cambridge, Forvie Site, Robinson Way, Cambridge CB2 0PY, UK
| | - Daniel Raleigh
- Institute of Structural and Molecular Biology, Division of Bioscience, University College London, London WC1E 6BT, UK; Department of Chemistry, Stony Brook University, 100 Nicolls Road, Stony Brook, New York 11794, United States.
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Bioscience, University College London, London WC1E 6BT, UK; Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, UK.
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5
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Yang HC, Scruggs SS, Chai M, Mathai G, Taylor JS, Gross ML. Distinguishing Isomeric Cyclobutane Thymidine Dimers by Ion Mobility and Tandem Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1768-1774. [PMID: 38952267 PMCID: PMC11305913 DOI: 10.1021/jasms.4c00133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
Irradiation of the major conformation of duplex DNA found in cells (B form) produces cyclobutane pyrimidine dimers (CPDs) from adjacent pyrimidines in a head-to-head orientation (syn) with the C5 substituents in a cis stereochemistry. These CPDs have crucial implications in skin cancer. Irradiation of G-quadruplexes and other non-B DNA conformations in vitro produces, however, CPDs between nonadjacent pyrimidines in nearby loops with syn and head-to-tail orientations (anti) with both cis and trans stereochemistry to yield a mixture of six possible isomers of the T=T dimer. This outcome is further complicated by formation of mixtures of nonadjacent CPDs of C=T, T=C, and C=C, and successful analysis depends on development of specific and sensitive methods. Toward meeting this need, we investigated whether ion mobility mass spectrometry (IMMS) and MS/MS can distinguish the cis,syn and trans,anti T=T CPDs. Ion mobility can afford baseline separation and give relative mobilities that are in accord with predicted cross sections. Complementing this ability to distinguish isomers is MS/MS collisional activation where fragmentation also distinguishes the two isomers and confirms conclusions drawn from ion mobility analysis. The observations offer early support that ion mobility and MS/MS can enable the distinction of DNA photoproduct isomers.
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Affiliation(s)
- Hsin-Chieh Yang
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130
| | - Savannah S. Scruggs
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130
| | - Mengqi Chai
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130
| | - George Mathai
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130
| | - John-Stephen Taylor
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130
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6
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Habibi SC, Bradford VR, Baird SC, Lucas SW, Chouinard CD, Nagy G. Development of a cyclic ion mobility spectrometry-mass spectrometry-based collision cross-section database of permethylated human milk oligosaccharides. JOURNAL OF MASS SPECTROMETRY : JMS 2024; 59:e5076. [PMID: 39041358 PMCID: PMC11283840 DOI: 10.1002/jms.5076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/28/2024] [Accepted: 06/28/2024] [Indexed: 07/24/2024]
Abstract
Human milk oligosaccharides (HMOs) are an important class of biomolecules responsible for the healthy development of the brain-gut axis of infants. Unfortunately, their accurate characterization is largely precluded due to a variety of reasons - there are over 200 possible HMO structures whereas only 10s of these are available as authentic analytical standards. Furthermore, their isomeric heterogeneity stemming from their many possible glycosidic linkage positions and corresponding α/β anomericities further complicates their analyses. While liquid chromatography coupled to tandem mass spectrometry remains the gold standard for HMO analyses, it often times cannot resolve all possible isomeric species and thus warrants the development of other orthogonal approaches. High-resolution ion mobility spectrometry coupled to mass spectrometry has emerged as a rapid alternative to condensed-phase separations but largely has remained limited to qualitative information related to the resolution of isomers. In this work, we have assessed the use of permethylation to improve both the resolution and sensitivity of HMO analyses with cyclic ion mobility separations coupled with mass spectrometry. In addition to this, we have developed the first-ever high-resolution collision cross-section database for permethylated HMOs using our previously established calibration protocol. We envision that this internal reference database generated from high-resolution cyclic ion mobility spectrometry-mass spectrometry will greatly aid in the accurate characterization of HMOs and provide a valuable, orthogonal, approach to existing liquid chromatography-tandem mass spectrometry-based methods.
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Affiliation(s)
- Sanaz C. Habibi
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Victoria R. Bradford
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Sophie C. Baird
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Shadrack Wilson Lucas
- Department of Chemistry, Clemson University, Clemson, South Carolina 29625, United States
| | | | - Gabe Nagy
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
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7
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Naylor CN, Nagy G. Recent advances in high-resolution traveling wave-based ion mobility separations coupled to mass spectrometry. MASS SPECTROMETRY REVIEWS 2024. [PMID: 39087820 DOI: 10.1002/mas.21902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 06/07/2024] [Accepted: 07/22/2024] [Indexed: 08/02/2024]
Abstract
Recently, ion mobility spectrometry-mass spectrometry (IMS-MS) has become more readily incorporated into various omics-based workflows. These growing applications are due to developments in instrumentation within the last decade that have enabled higher-resolution ion mobility separations. Two such platforms are the cyclic (cIMS) and structures for lossless ion manipulations (SLIM), both of which use traveling wave ion mobility spectrometry (TWIMS). High-resolution separations achieved with these techniques stem from the drastically increased pathlengths, on the order of 10 s of meters to >1 km, in both cIMS-MS and SLIM IMS-MS, respectively. Herein, we highlight recent developments and advances, for the period 2019-2023, in high-resolution traveling wave-based IMS-MS through instrumentation, calibration strategies, hyphenated techniques, and applications. Specifically, we will discuss applications including CCS calculations in multipass IMS-MS separations, coupling of IMS-MS with chromatography, imaging, and cryogenic infrared spectroscopy, and isomeric separations of glycans, lipids, and other small metabolites.
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Affiliation(s)
- Cameron N Naylor
- Department of Chemistry, University of Utah, Salt Lake City, Utah, USA
| | - Gabe Nagy
- Department of Chemistry, University of Utah, Salt Lake City, Utah, USA
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8
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Jobst KJ, Penney C, Burgers PC. Why are nH-perfluoroalkanoate ions more mobile than expected? Implications for identifying an emerging environmental pollutant. Chem Commun (Camb) 2024; 60:7894-7897. [PMID: 38979952 DOI: 10.1039/d4cc02762k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
nH-Perfluoroalkyl carboxylic acids (nH-PFCAs) are emerging pollutants. Their identification by ion mobility is frustrated by the nH-PFCAs having unexpectedly small collision cross sections (CCS). Theory and experiment agree that this is because nH-PFCA ions undergo internal hydrogen bridging, and this insight will help guide the creation of more accurate methods for pollutant identification.
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Affiliation(s)
- Karl J Jobst
- Department of Chemistry, Memorial University of Newfoundland, 45 Arctic Ave., St. John's A1C 5S7, NL, Canada.
| | - Chloe Penney
- Department of Chemistry, Memorial University of Newfoundland, 45 Arctic Ave., St. John's A1C 5S7, NL, Canada.
| | - Peter C Burgers
- Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands
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9
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Baines C, Sargeant J, Fage CD, Pugh H, Alkhalaf LM, Challis GL, Oldham NJ. Native ESI-MS and Collision-Induced Unfolding (CIU) of the Complex between Bacterial Elongation Factor-Tu and the Antibiotic Enacyloxin IIa. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1490-1496. [PMID: 38830009 PMCID: PMC11228974 DOI: 10.1021/jasms.4c00087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 05/09/2024] [Accepted: 05/20/2024] [Indexed: 06/05/2024]
Abstract
Collision-induced unfolding (CIU) of protein ions, monitored by ion mobility-mass spectrometry, can be used to assess the stability of their compact gas-phase fold and hence provide structural information. The bacterial elongation factor EF-Tu, a key protein for mRNA translation in prokaryotes and hence a promising antibiotic target, has been studied by CIU. The major [M + 12H]12+ ion of EF-Tu unfolded in collision with Ar atoms between 40 and 50 V, corresponding to an Elab energy of 480-500 eV. Binding of the cofactor analogue GDPNP and the antibiotic enacyloxin IIa stabilized the compact fold of EF-Tu, although dissociation of the latter from the complex diminished its stabilizing effect at higher collision energies. Molecular dynamics simulations of the [M + 12H]12+ EF-Tu ion showed similar qualitative behavior to the experimental results.
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Affiliation(s)
- Cameron Baines
- School
of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United
Kingdom
| | - Jacob Sargeant
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Christopher D. Fage
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Hannah Pugh
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Lona M. Alkhalaf
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Gregory L. Challis
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
- Warwick
Integrative Synthetic Biology Centre, University
of Warwick, Coventry CV4 7AL, United Kingdom
- Department
of Biochemistry and Molecular Biology, Biomedicine Discovery Institute,
Monash University, Clayton, Victoria 3800, Australia
- ARC
Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, Victoria 3800, Australia
| | - Neil J. Oldham
- School
of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United
Kingdom
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10
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Van Elzen R, Konijnenberg A, Van der Veken P, Edgeworth MJ, Scrivens JH, Fülöp V, Sobott F, Lambeir AM. Study of the Conformational Dynamics of Prolyl Oligopeptidase by Mass Spectrometry: Lessons Learned. J Med Chem 2024; 67:10436-10446. [PMID: 38783480 PMCID: PMC11215766 DOI: 10.1021/acs.jmedchem.4c00866] [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] [Received: 04/11/2024] [Revised: 05/14/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024]
Abstract
Ion mobility mass spectrometry (IM-MS) can be used to analyze native proteins according to their size and shape. By sampling individual molecules, it allows us to study mixtures of conformations, as long as they have different collision cross sections and maintain their native conformation after dehydration and vaporization in the mass spectrometer. Even though conformational heterogeneity of prolyl oligopeptidase has been demonstrated in solution, it is not detectable in IM-MS. Factors that affect the conformation in solution, binding of an active site ligand, the stabilizing Ser554Ala mutation, and acidification do not qualitatively affect the collision-induced unfolding pattern. However, measuring the protection of accessible cysteines upon ligand binding provides a principle for the development of MS-based ligand screening methods.
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Affiliation(s)
- Roos Van Elzen
- Laboratory
of Medical Biochemistry, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Albert Konijnenberg
- Laboratory
of Biomolecular & Analytical Mass Spectrometry, Department of
Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
| | - Pieter Van der Veken
- Laboratory
of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Matthew J. Edgeworth
- Waters/Warwick
Centre for BioMedical Mass Spectrometry and Proteomics, School of
Life Sciences, University of Warwick, Coventry CV4 7AL, U.K.
| | - James H. Scrivens
- Waters/Warwick
Centre for BioMedical Mass Spectrometry and Proteomics, School of
Life Sciences, University of Warwick, Coventry CV4 7AL, U.K.
| | - Vilmos Fülöp
- School
of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K.
- Institute
of Biochemistry and Medical Chemistry, Medical School, University of Pécs, 7624 Pécs, Hungary
| | - Frank Sobott
- Laboratory
of Biomolecular & Analytical Mass Spectrometry, Department of
Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
- Astbury
Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
- School
of Molecular and Cellular Biology, University
of Leeds, Leeds LS2 9JT, U.K.
| | - Anne-Marie Lambeir
- Laboratory
of Medical Biochemistry, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
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11
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Huang S, Righetti L, Claassen FW, Krishna A, Ma M, van Beek TA, Chen B, Zuilhof H, Salentijn GIJ. Ultrafast, Selective, and Highly Sensitive Nonchromatographic Analysis of Fourteen Cannabinoids in Cannabis Extracts, Δ8-Tetrahydrocannabinol Synthetic Mixtures, and Edibles by Cyclic Ion Mobility Spectrometry-Mass Spectrometry. Anal Chem 2024; 96:10170-10181. [PMID: 38862388 PMCID: PMC11209660 DOI: 10.1021/acs.analchem.3c05879] [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] [Received: 12/22/2023] [Revised: 05/28/2024] [Accepted: 05/30/2024] [Indexed: 06/13/2024]
Abstract
The diversity of cannabinoid isomers and complexity of Cannabis products pose significant challenges for analytical methodologies. In this study, we developed a method to analyze 14 different cannabinoid isomers in diverse samples within milliseconds by leveraging the unique adduct-forming behavior of silver ions in advanced cyclic ion mobility spectrometry-mass spectrometry. The developed method achieved the separation of isomers from four groups of cannabinoids: Δ3-tetrahydrocannabinol (THC) (1), Δ8-THC (2), Δ9-THC (3), cannabidiol (CBD) (4), Δ8-iso-THC (5), and Δ(4)8-iso-THC (6) (all MW = 314); 9α-hydroxyhexahydrocannabinol (7), 9β-hydroxyhexahydrocannabinol (8), and 8-hydroxy-iso-THC (9) (all MW = 332); tetrahydrocannabinolic acid (THCA) (10) and cannabidiolic acid (CBDA) (11) (both MW = 358); Δ8-tetrahydrocannabivarin (THCV) (12), Δ8-iso-THCV (13), and Δ9-THCV (14) (all MW = 286). Moreover, experimental and theoretical traveling wave collision cross section values in nitrogen (TWCCSN2) of cannabinoid-Ag(I) species were obtained for the first time with an average error between experimental and theoretical values of 2.6%. Furthermore, a workflow for the identification of cannabinoid isomers in Cannabis and Cannabis-derived samples was established based on three identification steps (m/z and isotope pattern of Ag(I) adducts, TWCCSN2, and MS/MS fragments). Afterward, calibration curves of three major cannabinoids were established with a linear range of 1-250 ng·ml-1 for Δ8-THC (2) (R2 = 0.9999), 0.1-25 ng·ml-1 for Δ9-THC (3) (R2 = 0.9987), and 0.04-10 ng·ml-1 for CBD (4) (R2 = 0.9986) as well as very low limits of detection (0.008-0.2 ng·ml-1). Finally, relative quantification of Δ8-THC (2), Δ9-THC (3), and CBD (4) in eight complex acid-treated CBD mixtures was achieved without chromatographic separation. The results showed good correspondence (R2 = 0.999) with those obtained by gas chromatography-flame ionization detection/mass spectrometry.
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Affiliation(s)
- Si Huang
- Key
Laboratory of Phytochemical R&D of Hunan Province and Key Laboratory
of Chemical Biology & Traditional Chinese Medicine Research of
Ministry of Education, Hunan Normal University, No.36, Lushan Road, Changsha 410081, China
- Laboratory
of Organic Chemistry, Wageningen University, Stippeneng 4, Wageningen 6708 WE, The
Netherlands
| | - Laura Righetti
- Laboratory
of Organic Chemistry, Wageningen University, Stippeneng 4, Wageningen 6708 WE, The
Netherlands
- Wageningen
Food Safety Research (WFSR), Wageningen
University & Research, P.O. Box 230, Wageningen 6700 AE, The Netherlands
| | - Frank W. Claassen
- Laboratory
of Organic Chemistry, Wageningen University, Stippeneng 4, Wageningen 6708 WE, The
Netherlands
| | - Akash Krishna
- Laboratory
of Organic Chemistry, Wageningen University, Stippeneng 4, Wageningen 6708 WE, The
Netherlands
| | - Ming Ma
- Key
Laboratory of Phytochemical R&D of Hunan Province and Key Laboratory
of Chemical Biology & Traditional Chinese Medicine Research of
Ministry of Education, Hunan Normal University, No.36, Lushan Road, Changsha 410081, China
| | - Teris A. van Beek
- Laboratory
of Organic Chemistry, Wageningen University, Stippeneng 4, Wageningen 6708 WE, The
Netherlands
| | - Bo Chen
- Key
Laboratory of Phytochemical R&D of Hunan Province and Key Laboratory
of Chemical Biology & Traditional Chinese Medicine Research of
Ministry of Education, Hunan Normal University, No.36, Lushan Road, Changsha 410081, China
| | - Han Zuilhof
- Key
Laboratory of Phytochemical R&D of Hunan Province and Key Laboratory
of Chemical Biology & Traditional Chinese Medicine Research of
Ministry of Education, Hunan Normal University, No.36, Lushan Road, Changsha 410081, China
- Laboratory
of Organic Chemistry, Wageningen University, Stippeneng 4, Wageningen 6708 WE, The
Netherlands
| | - Gert IJ. Salentijn
- Laboratory
of Organic Chemistry, Wageningen University, Stippeneng 4, Wageningen 6708 WE, The
Netherlands
- Wageningen
Food Safety Research (WFSR), Wageningen
University & Research, P.O. Box 230, Wageningen 6700 AE, The Netherlands
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12
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Villafuerte-Vega RC, Li HW, Bergman AE, Slaney TR, Chennamsetty N, Chen G, Tao L, Ruotolo BT. Ion Mobility-Mass Spectrometry and Collision-Induced Unfolding Rapidly Characterize the Structural Polydispersity and Stability of an Fc-Fusion Protein. Anal Chem 2024; 96:10003-10012. [PMID: 38853531 DOI: 10.1021/acs.analchem.4c01408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Fc-fusion proteins are an emerging class of protein therapeutics that combine the properties of biological ligands with the unique properties of the fragment crystallizable (Fc) domain of an immunoglobulin G (IgG). Due to their diverse higher-order structures (HOSs), Fc-fusion proteins remain challenging characterization targets within biopharmaceutical pipelines. While high-resolution biophysical tools are available for HOS characterization, they frequently demand extended time frames and substantial quantities of purified samples, rendering them impractical for swiftly screening candidate molecules. Herein, we describe the development of ion mobility-mass spectrometry (IM-MS) and collision-induced unfolding (CIU) workflows that aim to fill this technology gap, where we focus on probing the HOS of a model Fc-Interleukin-10 (Fc-IL-10) fusion protein engineered using flexible glycine-serine linkers. We evaluate the ability of these techniques to probe the flexibility of Fc-IL-10 in the absence of bulk solvent relative to other proteins of similar size, as well as localize structural changes of low charge state Fc-IL-10 ions to specific Fc and IL-10 unfolding events during CIU. We subsequently apply these tools to probe the local effects of glycine-serine linkers on the HOS and stability of IL-10 homodimer, which is the biologically active form of IL-10. Our data reveals that Fc-IL-10 produces significantly more structural transitions during CIU and broader IM profiles when compared to a wide range of model proteins, indicative of its exceptional structural dynamism. Furthermore, we use a combination of enzymatic approaches to annotate these intricate CIU data and localize specific transitions to the unfolding of domains within Fc-IL-10. Finally, we detect a strong positive, quadratic relationship between average linker mass and fusion protein stability, suggesting a cooperative influence between glycine-serine linkers and overall fusion protein stability. This is the first reported study on the use of IM-MS and CIU to characterize HOS of Fc-fusion proteins, illustrating the practical applicability of this approach.
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Affiliation(s)
| | - Henry W Li
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Addison E Bergman
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Thomas R Slaney
- Analytical Development and Attribute Sciences, Biologics Development, Global Product Development and Supply, Bristol Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - Naresh Chennamsetty
- Analytical Development and Attribute Sciences, Biologics Development, Global Product Development and Supply, Bristol Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - Guodong Chen
- Analytical Development and Attribute Sciences, Biologics Development, Global Product Development and Supply, Bristol Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - Li Tao
- Analytical Development and Attribute Sciences, Biologics Development, Global Product Development and Supply, Bristol Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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13
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Williams-Pavlantos K, Mokarizadeh AH, Curole BJ, Grayson SM, Tsige M, Wesdemiotis C. Elucidation of Dithiol-yne Comb Polymer Architectures by Tandem Mass Spectrometry and Ion Mobility Techniques. Polymers (Basel) 2024; 16:1665. [PMID: 38932016 PMCID: PMC11207239 DOI: 10.3390/polym16121665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 06/02/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
Polymers have a wide range of applications depending on their composition, size, and architecture. Varying any of these three characteristics can greatly impact the resulting chemical, physical, and mechanical properties. While many techniques are available to determine polymer composition and size, determining the exact polymer architecture is more challenging. Herein, tandem mass spectrometry (MS/MS) and ion mobility mass spectrometry (IM-MS) methods are utilized to derive crucial architectural information about dithiol-yne comb polymers. Based on their unique fragmentation products and IM drift times, dithiol-yne oligomers with distinct architectures were successfully differentiated and characterized. Additionally, experimental collision cross-sections (Ω) derived via IM-MS were compared to theoretically extracted Ω values from molecular dynamics simulated structures to deduce the architectural motif of these comb oligomers. Overall, this work demonstrates the benefits of combining various mass spectrometry techniques in order to gain a complete understanding of a complex polymer mixture.
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Affiliation(s)
| | - Abdol Hadi Mokarizadeh
- School of Polymer Science and Polymer Engineering, University of Akron, Akron, OH 44325, USA; (A.H.M.); (M.T.)
| | - Brennan J. Curole
- Department of Chemistry, Tulane University, New Orleans, LA 70118, USA;
| | - Scott M. Grayson
- Department of Chemistry, Tulane University, New Orleans, LA 70118, USA;
| | - Mesfin Tsige
- School of Polymer Science and Polymer Engineering, University of Akron, Akron, OH 44325, USA; (A.H.M.); (M.T.)
| | - Chrys Wesdemiotis
- Department of Chemistry, University of Akron, Akron, OH 44325, USA;
- School of Polymer Science and Polymer Engineering, University of Akron, Akron, OH 44325, USA; (A.H.M.); (M.T.)
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14
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Benoit F, Wang X, Dai J, Geue N, England RM, Bristow AWT, Barran PE. Exploring the Conformational Landscape of Poly(l-lysine) Dendrimers Using Ion Mobility Mass Spectrometry. Anal Chem 2024; 96:9390-9398. [PMID: 38812282 PMCID: PMC11170554 DOI: 10.1021/acs.analchem.4c00099] [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] [Received: 01/05/2024] [Revised: 05/22/2024] [Accepted: 05/22/2024] [Indexed: 05/31/2024]
Abstract
Ion mobility mass spectrometry (IM-MS) measures the mass, size, and shape of ions in the same experiment, and structural information is provided via collision cross-section (CCS) values. The majority of commercially available IM-MS instrumentation relies on the use of CCS calibrants, and here, we present data from a family of poly(l-lysine) dendrimers and explore their suitability for this purpose. In order to test these compounds, we employed three different IM-MS platforms (Agilent 6560 IM-QToF, Waters Synapt G2, and a home-built variable temperature drift tube IM-MS) and used them to investigate six different generations of dendrimers in two buffer gases (helium and nitrogen). Each molecule gives a highly discrete CCS distribution suggestive of single conformers for each m/z value. The DTCCSN2 values of this series of molecules (molecular weight: 330-16,214 Da) range from 182 to 2941 Å2, which spans the CCS range that would be found by many synthetic molecules including supramolecular compounds and many biopolymers. The CCS values for each charge state were highly reproducible in day-to-day analysis on each instrument, although we found small variations in the absolute CCS values between instruments. The rigidity of each dendrimer was probed using collisionally activated and high-temperature IM-MS experiments, where no evidence for a significant CCS change ensued. Taken together, this data indicates that these polymers are candidates for CCS calibration and could also help to reconcile differences found in CCS measurements on different instrument geometries.
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Affiliation(s)
- Florian Benoit
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
of Biotechnology, Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Xudong Wang
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
of Biotechnology, Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Junxiao Dai
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
of Biotechnology, Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Niklas Geue
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
of Biotechnology, Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Richard M. England
- Advanced
Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Macclesfield SK10 2NA, U.K.
| | - Anthony W. T. Bristow
- Chemical
Development, Pharmaceutical Technology and Development, Operations, AstraZeneca, Macclesfield SK10 2NA, U.K.
| | - Perdita E. Barran
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
of Biotechnology, Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
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15
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Grifnée E, Kune C, Delvaux C, Tilmant T, Quinton L, Matagne A, Mazzucchelli G, Far J, De Pauw E. Investigation of Structure-Stabilizing Elements in Proteins by Ion Mobility Mass Spectrometry and Collision-Induced Unfolding. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1076-1088. [PMID: 38660944 DOI: 10.1021/jasms.3c00398] [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: 04/26/2024]
Abstract
A recently developed proteolytic reactor, designed for protein structural investigation, was coupled to ion mobility mass spectrometry to monitor collisional cross section (CCS) evolution of model proteins undergoing trypsin-mediated mono enzymatic digestion. As peptides are released during digestion, the CCS of the remaining protein structure may deviate from the classical 2/3 power of the CCS-mass relationship for spherical structures. The classical relationship between CCS and mass (CCS = A × M2/3) for spherical structures, assuming a globular shape in the gas phase, may deviate as stabilizing elements are lost during digestion. In addition, collision-induced unfolding (CIU) experiments on partially digested proteins provided insights into the CCS resilience in the gas phase to ion activation, potentially due to the presence of stabilizing elements. The study initially investigated a model peptide ModBea (3 kDa), assessing the impact of disulfide bridges on CCS resilience in both reduced and oxidized forms. Subsequently, β-lactoglobulin (2 disulfide bridges), calmodulin (Ca2+ coordination cation), and cytochrome c (heme) were selected to investigate the influence of common structuring elements on CCS resilience. CIU experiments probed the unfolding process, evaluating the effect of losing specific peptides on the energy landscapes of partially digested proteins. Comparisons of the TWCCSN2→He to trend curves describing the CCS/mass relationship revealed that proteins with structure-stabilizing elements consistently exhibit TWCCSN2→He and greater resilience toward CIU compared to proteins lacking these elements. The integration of online digestion, ion mobility, and CIU provides a valuable tool for identifying structuring elements in biopolymers in the gas phase.
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Affiliation(s)
- Elodie Grifnée
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
| | - Christopher Kune
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
| | - Cédric Delvaux
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
| | - Thomas Tilmant
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
| | - Loïc Quinton
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
| | - André Matagne
- Laboratory of Enzymology and Protein Folding, Center for Protein Engineering, InBioS Research Unit, University of Liège, B-4000 Liège, Belgium
| | - Gabriel Mazzucchelli
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
| | - Johann Far
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
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16
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Benzenberg LR, Katzberger P, Wu R, Metternich JB, Riniker S, Zenobi R. Probing the Stability of a β-Hairpin Scaffold after Desolvation. J Phys Chem Lett 2024; 15:5041-5046. [PMID: 38700091 DOI: 10.1021/acs.jpclett.4c00920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Probing the structural characteristics of biomolecular ions in the gas phase following native mass spectrometry (nMS) is of great interest, because noncovalent interactions, and thus native fold features, are believed to be largely retained upon desolvation. However, the conformation usually depends heavily on the charge state of the species investigated. In this study, we combine transition metal ion Förster resonance energy transfer (tmFRET) and ion mobility-mass spectrometry (IM-MS) with molecular dynamics (MD) simulations to interrogate the β-hairpin structure of GB1p in vacuo. Fluorescence lifetime values and collisional cross sections suggest an unfolding of the β-hairpin motif for higher charge states. MD simulations are consistent with experimental constraints, yet intriguingly provide an alternative structural interpretation: preservation of the β-hairpin is not only predicted for 2+ but also for 4+ charged species, which is unexpected given the substantial Coulomb repulsion for small secondary structure scaffolds.
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Affiliation(s)
- Lukas R Benzenberg
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences ETH Zurich, Vladimir-Prelog-Weg 3, CH-8093 Zurich, Switzerland
| | - Paul Katzberger
- Institute of Molecular Physical Science, Department of Chemistry and Applied Biosciences ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Ri Wu
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences ETH Zurich, Vladimir-Prelog-Weg 3, CH-8093 Zurich, Switzerland
| | - Jonas B Metternich
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences ETH Zurich, Vladimir-Prelog-Weg 3, CH-8093 Zurich, Switzerland
| | - Sereina Riniker
- Institute of Molecular Physical Science, Department of Chemistry and Applied Biosciences ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Renato Zenobi
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences ETH Zurich, Vladimir-Prelog-Weg 3, CH-8093 Zurich, Switzerland
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17
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Zimnicka MM. Structural studies of supramolecular complexes and assemblies by ion mobility mass spectrometry. MASS SPECTROMETRY REVIEWS 2024; 43:526-559. [PMID: 37260128 DOI: 10.1002/mas.21851] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 04/26/2023] [Accepted: 05/10/2023] [Indexed: 06/02/2023]
Abstract
Recent advances in instrumentation and development of computational strategies for ion mobility mass spectrometry (IM-MS) studies have contributed to an extensive growth in the application of this analytical technique to comprehensive structural description of supramolecular systems. Apart from the benefits of IM-MS for interrogation of intrinsic properties of noncovalent aggregates in the experimental gas-phase environment, its merits for the description of native structural aspects, under the premises of having maintained the noncovalent interactions innate upon the ionization process, have attracted even more attention and gained increasing interest in the scientific community. Thus, various types of supramolecular complexes and assemblies relevant for biological, medical, material, and environmental sciences have been characterized so far by IM-MS supported by computational chemistry. This review covers the state-of-the-art in this field and discusses experimental methods and accompanying computational approaches for assessing the reliable three-dimensional structural elucidation of supramolecular complexes and assemblies by IM-MS.
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Affiliation(s)
- Magdalena M Zimnicka
- Mass Spectrometry Group, Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
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18
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Webb IK. Perspective: The complex relationship between charge, mobility, and gas-phase protein structure. JOURNAL OF MASS SPECTROMETRY : JMS 2024; 59:e5013. [PMID: 38605450 DOI: 10.1002/jms.5013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/07/2024] [Accepted: 02/21/2024] [Indexed: 04/13/2024]
Abstract
Ion mobility spectrometry coupled to mass spectrometry (IMS/MS) is a widely used tool for biomolecular separations and structural elucidation. The application of IMS/MS has resulted in exciting developments in structural proteomics and genomics. This perspective gives a brief background of the field, addresses some of the important issues in making structural measurements, and introduces complementary techniques.
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Affiliation(s)
- Ian K Webb
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana, USA
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19
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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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20
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Wörner TP, Thurman HA, Makarov AA, Shvartsburg AA. Expanding Differential Ion Mobility Separations into the MegaDalton Range. Anal Chem 2024; 96:5392-5398. [PMID: 38526848 DOI: 10.1021/acs.analchem.3c05012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Along with mass spectrometry (MS), ion mobility separations (IMS) are advancing to ever larger biomolecules. The emergence of electrospray ionization (ESI) and native MS enabled the IMS/MS analyses of proteins up to ∼100 kDa in the 1990s and whole protein complexes and viruses up to ∼10 MDa since the 2000s. Differential IMS (FAIMS) is substantially orthogonal to linear IMS based on absolute mobility K and offers exceptional resolution, unique selectivity, and steady filtering readily compatible with slower analytical methods such as electron capture or transfer dissociation (ECD/ETD). However, the associated MS stages had limited FAIMS to ions with m/z < 8000 and masses under ∼300 kDa. Here, we integrate high-definition FAIMS with the Q-Exactive Orbitrap UHMR mass spectrometer that can handle m/z up to 80,000 and MDa-size ions in the native ESI regime. In the initial evaluation, the oligomers of monoclonal antibody adalimumab (148 kDa) are size-selected up to at least the nonamers (1.34 MDa) with m/z values up to ∼17,000. This demonstrates the survival and efficient separation of noncovalent MDa assemblies in the FAIMS process, opening the door to novel analyses of the heaviest macromolecules.
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Affiliation(s)
- Tobias P Wörner
- Thermo Fisher Scientific, Hanna-Kunath Strasse 11, Bremen 28199, Germany
| | - Hayden A Thurman
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Alexander A Makarov
- Thermo Fisher Scientific, Hanna-Kunath Strasse 11, Bremen 28199, Germany
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Alexandre A Shvartsburg
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
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21
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Critch-Doran O, Jenkins K, Hashemihedeshi M, Mommers AA, Green MK, Dorman FL, Jobst KJ. Toward Part-per-Million Precision in the Determination of an Ion's Collision Cross Section Using Multipass Cyclic Ion Mobility. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:775-783. [PMID: 38498916 DOI: 10.1021/jasms.4c00003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
In cyclic ion mobility (cIMS), ions are permitted to travel multiple passes around the drift cell, increasing the distance traveled and the relative separation between ions. This study tests the hypothesis that multiple passes around the cell can also result in improved precision when measuring an ion's mobility and the collision cross section (TWCCS) derived therefrom. Experiments were performed with a diverse set of compounds, including 16 polycyclic aromatic hydrocarbons using gas chromatographic atmospheric pressure chemical ionization and a set of drug molecules by direct infusion electrospray ionization. The average periodic drift time, viz., the average time required for the ion to travel around the cIMS cell once, shifts dramatically, approaching part-per-million (ppm) precision as the number of passes increases to ∼100. Extrapolation of the precision of the CCS values with respect to the number of passes led to the prediction that the precision will reach 1000 ppm after 50 passes, 100 ppm after 100 passes, and <10 ppm after 150 passes. Experiments wherein the number of passes exceeded 100 produced TWCCS values having within-run precisions ranging between 15 and 117 ppm. The improved precision with an increasing number of passes may be a consequence of mitigating space-charge effects by allowing the ions to occupy a larger region of the cIMS cell. A method is proposed to enable practical measurements of TWCCS with ppm precision and is demonstrated to characterize an unknown drug mixture.
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Affiliation(s)
- Olivia Critch-Doran
- Department of Chemistry, Memorial University of Newfoundland, 45 Arctic Ave., St. John's, Newfoundland and Labrador A1C 5S7, Canada
| | - Kevin Jenkins
- Department of Chemistry, Memorial University of Newfoundland, 45 Arctic Ave., St. John's, Newfoundland and Labrador A1C 5S7, Canada
| | - Mahin Hashemihedeshi
- Department of Chemistry, Memorial University of Newfoundland, 45 Arctic Ave., St. John's, Newfoundland and Labrador A1C 5S7, Canada
| | - Alexander A Mommers
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - M Kirk Green
- Department of Chemistry & Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Frank L Dorman
- Department of Chemistry, Dartmouth College, Hannover, New Hampshire 03755, United States
- Waters Corporation, 34 Maple St., Milford, Massachusetts 01757, United States
| | - Karl J Jobst
- Department of Chemistry, Memorial University of Newfoundland, 45 Arctic Ave., St. John's, Newfoundland and Labrador A1C 5S7, Canada
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22
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Buzitis NW, Clowers BH. Development of a Modular, Open-Source, Reduced-Pressure, Drift Tube Ion Mobility Spectrometer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:804-813. [PMID: 38512132 DOI: 10.1021/jasms.4c00057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Toward the goal of minimizing construction costs while maintaining high performance, a new, reduced-pressure, drift tube ion mobility system is coupled with an ion trap mass analyzer through a custom ion shuttle. The availability of reduced-pressure ion mobility systems remains limited due to comparatively expensive commercial options and limited shared design features in the open literature. This report details the complete design and benchmarking characteristics of a reduced-pressure ion mobility system. The system is constructed from FR4 PCB electrodes and encased in a PTFE vacuum enclosure with custom torque-tightened couplers to utilize standard KF40 bulkheads. The PTFE enclosure directly minimizes the overall system expenses, and the implementation of threaded brass inserts allows for facile attachments to the vacuum enclosure without damaging the thermoplastic housing. Front and rear ion funnels maximize ion transmission and help mitigate the effects of radial ion diffusion. A custom planar ion shuttle transports ions from the exit of the rear ion funnel into the ion optics of an ion trap mass analyzer. The planar ion shuttle can couple the IM system to any contemporary Thermo Scientific ion trap mass analyzer. Signal stability and ion intensity remain unchanging following the implementation of the planar ion shuttle when compared to the original stacked ring ion guide. The constructed IM system showed resolving powers up to 85 for various small molecules and proteins using the Fourier transform from a ∼1 m drift tube. Recorded mobilities derived from first principles agree with published literature results with an average error of 1.1% and an average error toward literature values using single field calibration of <1.3%.
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Affiliation(s)
- Nathan W Buzitis
- Department of Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Brian H Clowers
- Department of Chemistry, Washington State University, Pullman, Washington 99164, United States
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23
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Wang N, Dixit SM, Lee T, DeFiglia SA, Ruotolo BT, Håkansson K. Salt-Bridged Peptide Anion Gaseous Structures Enable Efficient Negative Ion Electron Capture Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:784-792. [PMID: 38489759 DOI: 10.1021/jasms.4c00030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/17/2024]
Abstract
We previously discovered that electron attachment to gaseous peptide anions can occur within a relatively narrow electron energy range. The resulting charge-increased radical ions undergo dissociation analogous to conventional cation electron capture/transfer dissociation (ECD/ETD), thus enabling a novel tandem mass spectrometry (MS/MS) technique that we termed negative ion electron capture dissociation (niECD). We proposed that gaseous zwitterionic structures are required for niECD with electron capture either occurring at or being directed by a positively charged site. Here, we further evaluate this zwitterion mechanism by performing niECD of peptides derivatized to alter their ability to form zwitterionic gaseous structures. Introduction of a fixed positive charge tag, a highly basic guanidino group, or a highly acidic sulfonate group to promote zwitterionic structures in singly charged anions, rescued the niECD ability of a peptide refractory to niECD in its unmodified form. We also performed a systematic study of five sets of synthetic peptides with decreasing zwitterion propensity and found that niECD efficiency decreased accordingly, further supporting the zwitterion mechanism. However, traveling-wave ion mobility-mass spectrometry experiments, performed to gain further insight into the gas-phase structures of peptides showing high niECD efficiency, exhibited an inverse correlation between the orientationally averaged collision cross sections and niECD efficiency. These results indicate that compact salt-bridged structures are also a requirement for effective niECD.
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Affiliation(s)
- Ning Wang
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Sugyan M Dixit
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Teresa Lee
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Steven A DeFiglia
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Kristina Håkansson
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
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24
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Bechtella L, Chunsheng J, Fentker K, Ertürk GR, Safferthal M, Polewski Ł, Götze M, Graeber SY, Vos GM, Struwe WB, Mall MA, Mertins P, Karlsson NG, Pagel K. Ion mobility-tandem mass spectrometry of mucin-type O-glycans. Nat Commun 2024; 15:2611. [PMID: 38521783 PMCID: PMC10960840 DOI: 10.1038/s41467-024-46825-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 03/12/2024] [Indexed: 03/25/2024] Open
Abstract
The dense O-glycosylation of mucins plays an important role in the defensive properties of the mucus hydrogel. Aberrant glycosylation is often correlated with inflammation and pathology such as COPD, cancer, and Crohn's disease. The inherent complexity of glycans and the diversity in the O-core structure constitute fundamental challenges for the analysis of mucin-type O-glycans. Due to coexistence of multiple isomers, multidimensional workflows such as LC-MS are required. To separate the highly polar carbohydrates, porous graphitized carbon is often used as a stationary phase. However, LC-MS workflows are time-consuming and lack reproducibility. Here we present a rapid alternative for separating and identifying O-glycans released from mucins based on trapped ion mobility mass spectrometry. Compared to established LC-MS, the acquisition time is reduced from an hour to two minutes. To test the validity, the developed workflow was applied to sputum samples from cystic fibrosis patients to map O-glycosylation features associated with disease.
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Affiliation(s)
- Leïla Bechtella
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Altensteinstraße 23A, 14195, Berlin, Germany
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4‑6, 14195, Berlin, Germany
| | - Jin Chunsheng
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Kerstin Fentker
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Altensteinstraße 23A, 14195, Berlin, Germany
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Güney R Ertürk
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Altensteinstraße 23A, 14195, Berlin, Germany
| | - Marc Safferthal
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Altensteinstraße 23A, 14195, Berlin, Germany
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4‑6, 14195, Berlin, Germany
| | - Łukasz Polewski
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Altensteinstraße 23A, 14195, Berlin, Germany
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4‑6, 14195, Berlin, Germany
| | - Michael Götze
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Altensteinstraße 23A, 14195, Berlin, Germany
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4‑6, 14195, Berlin, Germany
| | - Simon Y Graeber
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine and Cystic Fibrosis Center, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Center for Lung Research (DZL), associated partner site, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Gaël M Vos
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Altensteinstraße 23A, 14195, Berlin, Germany
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4‑6, 14195, Berlin, Germany
| | - Weston B Struwe
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, OX1 3QU, UK
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Marcus A Mall
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine and Cystic Fibrosis Center, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Center for Lung Research (DZL), associated partner site, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Philipp Mertins
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany
- Berlin Institute of Health, 10178, Berlin, Germany
| | - Niclas G Karlsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Life Sciences and Health, Faculty of Health Sciences, Oslo Metropolitan University, Oslo, Norway
| | - Kevin Pagel
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Altensteinstraße 23A, 14195, Berlin, Germany.
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4‑6, 14195, Berlin, Germany.
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25
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Redding MJ, Grayson SM, Charles L. Mass spectrometry of dendrimers. MASS SPECTROMETRY REVIEWS 2024. [PMID: 38504498 DOI: 10.1002/mas.21876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 11/14/2023] [Accepted: 03/06/2024] [Indexed: 03/21/2024]
Abstract
Mass spectrometry (MS) has become an essential technique to characterize dendrimers as it proved efficient at tackling analytical challenges raised by their peculiar onion-like structure. Owing to their chemical diversity, this review covers benefits of MS methods as a function of dendrimer classes, discussing advantages and limitations of ionization techniques, tandem mass spectrometry (MS/MS) strategies to determine the structure of defective species, as well as most recently demonstrated capabilities of ion mobility spectrometry (IMS) in the field. Complementarily, the well-defined structure of these macromolecules offers major advantages in the development of MS-based method, as reported in a second section reviewing uses of dendrimers as MS and IMS calibration standards and as multifunctional charge inversion reagents in gas phase ion/ion reactions.
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Affiliation(s)
- McKenna J Redding
- Department of Chemistry, Tulane University, New Orleans, Los Angeles, USA
| | - Scott M Grayson
- Department of Chemistry, Tulane University, New Orleans, Los Angeles, USA
| | - Laurence Charles
- Aix Marseille Université, CNRS, Institut de Chimie Radicalaire, Marseille, France
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26
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Harvey SR, Gadkari VV, Ruotolo BT, Russell DH, Wysocki VH, Zhou M. Expanding Native Mass Spectrometry to the Masses. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:646-652. [PMID: 38303101 DOI: 10.1021/jasms.3c00352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
At the 33rd ASMS Sanibel Meeting, on Membrane Proteins and Their Complexes, a morning roundtable discussion was held discussing the current challenges facing the field of native mass spectrometry and approaches to expanding the field to nonexperts. This Commentary summarizes the discussion and current initiatives to address these challenges.
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Affiliation(s)
- Sophie R Harvey
- Department of Chemistry and Biochemistry, Native Mass Spectrometry Guided Structural Biology Center, The Ohio State University, Columbus, Ohio, 43210, United States
| | - Varun V Gadkari
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77844, United States
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, Native Mass Spectrometry Guided Structural Biology Center, The Ohio State University, Columbus, Ohio, 43210, United States
| | - Mowei Zhou
- Department of Chemistry, Zhejiang University, Hangzhou, Zhejiang 310058, China
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27
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Schweipert M, Nehls T, Frühauf A, Debarnot C, Kumar A, Knapp S, Lermyte F, Meyer‐Almes F. The catalytic domain of free or ligand bound histone deacetylase 4 occurs in solution predominantly in closed conformation. Protein Sci 2024; 33:e4917. [PMID: 38358265 PMCID: PMC10868454 DOI: 10.1002/pro.4917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/16/2024]
Abstract
Human histone deacetylase 4 (HDAC4) is a key epigenetic regulator involved in a number of important cellular processes. This makes HDAC4 a promising target for the treatment of several cancers and neurodegenerative diseases, in particular Huntington's disease. HDAC4 is highly regulated by phosphorylation and oxidation, which determine its nuclear or cytosolic localization, and exerts its function through multiple interactions with other proteins, forming multiprotein complexes of varying composition. The catalytic domain of HDAC4 is known to interact with the SMRT/NCOR corepressor complex when the structural zinc-binding domain (sZBD) is intact and forms a closed conformation. Crystal structures of the HDAC4 catalytic domain have been reported showing an open conformation of HDAC4 when bound to certain ligands. Here, we investigated the relevance of this HDAC4 conformation under physiological conditions in solution. We show that proper zinc chelation in the sZBD is essential for enzyme function. Loss of the structural zinc ion not only leads to a massive decrease in enzyme activity, but it also has serious consequences for the overall structural integrity and stability of the protein. However, the Zn2+ free HDAC4 structure in solution is incompatible with the open conformation. In solution, the open conformation of HDAC4 was also not observed in the presence of a variety of structurally divergent ligands. This suggests that the open conformation of HDAC4 cannot be induced in solution, and therefore cannot be exploited for the development of HDAC4-specific inhibitors.
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Affiliation(s)
- Markus Schweipert
- Department of Chemical Engineering and BiotechnologyUniversity of Applied SciencesDarmstadtGermany
| | - Thomas Nehls
- Department of ChemistryClemens‐Schöpf‐Institute of Chemistry and Biochemistry, Technical University of DarmstadtDarmstadtGermany
| | - Anton Frühauf
- Department of Chemical Engineering and BiotechnologyUniversity of Applied SciencesDarmstadtGermany
| | - Cecilé Debarnot
- Department of Chemical Engineering and BiotechnologyUniversity of Applied SciencesDarmstadtGermany
| | - Adarsh Kumar
- Fachbereich Biochemie, Chemie und PharmazieInstitut für Pharmazeutische Chemie, Goethe‐University FrankfurtFrankfurt Am MainGermany
| | - Stefan Knapp
- Fachbereich Biochemie, Chemie und PharmazieInstitut für Pharmazeutische Chemie, Goethe‐University FrankfurtFrankfurt Am MainGermany
| | - Frederik Lermyte
- Department of ChemistryClemens‐Schöpf‐Institute of Chemistry and Biochemistry, Technical University of DarmstadtDarmstadtGermany
| | - Franz‐Josef Meyer‐Almes
- Department of Chemical Engineering and BiotechnologyUniversity of Applied SciencesDarmstadtGermany
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28
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Anders AG, Tidwell ED, Gadkari VV, Koutmos M, Ruotolo BT. Collision-Induced Unfolding Reveals Disease-Associated Stability Shifts in Mitochondrial Transfer Ribonucleic Acids. J Am Chem Soc 2024; 146:4412-4420. [PMID: 38329282 DOI: 10.1021/jacs.3c09230] [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: 02/09/2024]
Abstract
Ribonucleic acids (RNAs) remain challenging targets for structural biology, creating barriers to understanding their vast functions in cellular biology and fully realizing their applications in biotechnology. The inherent dynamism of RNAs creates numerous obstacles in capturing their biologically relevant higher-order structures (HOSs), and as a result, many RNA functions remain unknown. In this study, we describe the development of native ion mobility-mass spectrometry and collision-induced unfolding (CIU) for the structural characterization of a variety of RNAs. We evaluate the ability of these techniques to preserve native structural features in the gas phase across a wide range of functional RNAs. Finally, we apply these tools to study the elusive mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes-associated A3243G mutation. Our data demonstrate that our experimentally determined conditions preserve some solution-state memory of RNAs via the correlated complexity of CIU fingerprints and RNA HOS, the observation of predicted stability shifts in the control RNA samples, and the retention of predicted magnesium binding events in gas-phase RNA ions. Significant differences in collision cross section and stability are observed as a function of the A3243G mutation across a subset of the mitochondrial tRNA maturation pathway. We conclude by discussing the potential application of CIU for the development of RNA-based biotherapeutics and, more broadly, transcriptomic characterization.
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Affiliation(s)
- Anna G Anders
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Elizabeth D Tidwell
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Varun V Gadkari
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Markos Koutmos
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Biophysics, 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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29
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Chung NA, May JC, Robinson RAS, McLean JA. Solvent Composition Can Have a Measurable Influence on the Ion Mobility-Derived Collision Cross Section of Small Molecules. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:234-243. [PMID: 38082535 DOI: 10.1021/jasms.3c00338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
Ion mobility (IM) is an important analytical technique for increasing identification coverage of metabolites in untargeted studies, especially when integrated into traditional liquid chromatography-mass spectrometry workflows. While there has been extensive work surrounding best practices to obtain and standardize collision cross section (CCS) measurements necessary for comparing across different IM techniques and laboratories, there has been little investigation into experimental factors beyond the mobility separation region that could potentially influence CCS measurements. The first-principles derived CCS of 15 chemical standards were evaluated across 27 aqueous:organic solvent compositions using a high-precision drift tube instrument. A small but measurable dependency of the CCS on the solvent composition was observed, with the larger analytes from this study (m/z > 400) exhibiting a characteristic increase in CCS at the intermediate (40-60%) solvent compositions. Parallels to the behavior of solvent viscosity and protonation site tautomers (protomers) were noted, although the origin of these solvent-dependent CCS trends is as yet unclear. Taken together, these findings document a solvent dependency on CCS, which, while minor (<0.5%), identifies an important need for reporting the solvent system when utilizing CCS in comparative ion mobility studies.
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Affiliation(s)
- Nadjali A Chung
- Center for Innovative Technology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Jody C May
- Center for Innovative Technology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - John A McLean
- Center for Innovative Technology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
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30
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Kwantwi-Barima P, Garimella SVB, Attah IK, Zheng X, Ibrahim YM, Smith RD. Accumulation of Large Ion Populations with High Ion Densities and Effects Due to Space Charge in Traveling Wave-Based Structures for Lossless Ion Manipulations (SLIM) IMS-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:365-377. [PMID: 38175933 PMCID: PMC10853970 DOI: 10.1021/jasms.3c00389] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 11/19/2023] [Accepted: 12/13/2023] [Indexed: 01/06/2024]
Abstract
The accumulation of very large ion populations in traveling wave (TW)-based Structures for Lossless ion Manipulations (SLIM) has been studied to better understand aspects of "in-SLIM" ion accumulation, and particularly its use in conjunction with ion mobility spectrometry (IMS). A linear SLIM ion path was implemented that had a "gate" for blocking and accumulating ions for arbitrary time periods. Removing the gate potential caused ions to exit, and the spatial distributions of accumulated ions examined. The ion populations for a set of peptides increased approximately linearly with increased accumulation times until space change effects became significant, after which the peptide precursor ion populations decreased due to growing space charge-related ion activation, reactions, and losses. Ion activation increased with added storage times and the TW amplitude. Lower amplitude TWs in the accumulation/storage region prevented or minimized ion losses or ion heating effects that can also lead to fragmentation. Our results supported the use of an accumulation region close to the SLIM entrance for speeding accumulation, minimizing ion heating, and avoiding ion population profiles that result in IMS peak tailing. Importantly, space charge-driven separations were observed for large populations of accumulated species and attributed to the opposing effects of space charge and the TW. In these separations, ion species form distributions or peaks, sometimes moving against the TW, and are ordered in the SLIM based on their mobilities. Only the highest mobility ions located closest to the gate in the trapped ion population (and where the highest ion densities were achieved) were significantly activated. The observed separations may offer utility for ion prefractionation of ions and increasing the dynamic range measurements, increasing the resolving power of IMS separations by decreasing peak widths for accumulated ion populations, and other purposes benefiting from separations of extremely large ion populations.
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Affiliation(s)
- Pearl Kwantwi-Barima
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Sandilya V. B. Garimella
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Isaac K. Attah
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Xueyun Zheng
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Yehia M. Ibrahim
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
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31
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Zhao H, Wijerathna AMSD, Dong Q, Bai Q, Jiang Z, Yuan J, Wang J, Chen M, Zirnheld M, Li R, Liu D, Wang P, Zhang Y, Li Y. Adjusting the Architecture of Heptagonal Metallo-Macrocycles by Embedding Metal Nodes into the Backbone. Angew Chem Int Ed Engl 2024; 63:e202318029. [PMID: 38087428 DOI: 10.1002/anie.202318029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Indexed: 12/30/2023]
Abstract
Coordination-driven self-assembly has been extensively employed for the bottom-up construction of discrete metallo-macrocycles. However, the prevalent use of benzene rings as the backbone limits the formation of large metallo-macrocycles with more than six edges. Herein, by embedding metal nodes into the ligand backbone, we successfully regulated the ligand arm angle and assembled two giant heptagonal metallo-macrocycles with precise control. The angle between two arms at position 4 of the central terpyridine (tpy) extended after complexation with metal ions, leading to ring expansion of the metallo-macrocycle. The assembled structures were straightforwardly identified through multi-dimensional NMR spectroscopy (1 H, COSY, NOESY), multidimensional mass spectrometry analysis (ESI-MS and TWIM-MS), transmission electron microscopy (TEM), as well as scanning tunneling microscopy (STM). In addition, the catalytic performances of metallo-macrocycles in the oxidation of thioanisole were studied, with both supramolecules exhibiting good conversion rates. Furthermore, fiber-like nanostructures were observed from single-molecule heptagons by hierarchical self-assembly.
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Affiliation(s)
- He Zhao
- Department of Organic and Polymer Chemistry, Hunan Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan, 410083, China
| | | | - Qiangqiang Dong
- Department of Organic and Polymer Chemistry, Hunan Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan, 410083, China
| | - Qixia Bai
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou Key Laboratory for Clean Energy and Materials, Guangzhou University, Guangzhou, 510006, China
| | - Zhiyuan Jiang
- Department of Organic and Polymer Chemistry, Hunan Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan, 410083, China
| | - Jie Yuan
- School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Jun Wang
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou Key Laboratory for Clean Energy and Materials, Guangzhou University, Guangzhou, 510006, China
| | - Mingzhao Chen
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou Key Laboratory for Clean Energy and Materials, Guangzhou University, Guangzhou, 510006, China
| | - Markus Zirnheld
- Department of Physics, Old Dominion University, Norfolk, VA 23529, USA
| | - Rockwell Li
- Department of Physics, Old Dominion University, Norfolk, VA 23529, USA
| | - Die Liu
- Department of Organic and Polymer Chemistry, Hunan Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan, 410083, China
| | - Pingshan Wang
- Department of Organic and Polymer Chemistry, Hunan Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan, 410083, China
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou Key Laboratory for Clean Energy and Materials, Guangzhou University, Guangzhou, 510006, China
| | - Yuan Zhang
- Department of Physics, Old Dominion University, Norfolk, VA 23529, USA
| | - Yiming Li
- Department of Organic and Polymer Chemistry, Hunan Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan, 410083, China
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32
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Habeck T, Maciel EVS, Kretschmer K, Lermyte F. Charge site manipulation to enhance top-down fragmentation efficiency. Proteomics 2024; 24:e2300082. [PMID: 37043727 DOI: 10.1002/pmic.202300082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/05/2023] [Accepted: 04/06/2023] [Indexed: 04/14/2023]
Abstract
In recent years, top-down mass spectrometry has become a widely used approach to study proteoforms; however, improving sequence coverage remains an important goal. Here, two different proteins, α-synuclein and bovine carbonic anhydrase, were subjected to top-down collision-induced dissociation (CID) after electrospray ionisation. Two high-boiling solvents, DMSO and propylene carbonate, were added to the protein solution in low concentration (2%) and the effects on the top-down fragmentation patterns of the proteins were systematically investigated. Each sample was measured in triplicate, which revealed highly reproducible differences in the top-down CID fragmentation patterns in the presence of a solution additive, even if the same precursor charge state was isolated in the quadrupole of the instrument. Further investigation supports the solution condition-dependent selective formation of different protonation site isomers as the underlying cause of these differences. Higher sequence coverage was often observed in the presence of additives, and the benefits of this approach became even more evident when datasets from different solution conditions were combined, as increases up to 35% in cleavage coverage were obtained. Overall, this approach therefore represents a promising opportunity to increase top-down fragmentation efficiency.
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Affiliation(s)
- Tanja Habeck
- Department of Chemistry, Clemens-Schöpf-Institute of Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Hessen, Germany
| | - Edvaldo Vasconcelos Soares Maciel
- Department of Chemistry, Clemens-Schöpf-Institute of Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Hessen, Germany
| | - Kevin Kretschmer
- Department of Chemistry, Clemens-Schöpf-Institute of Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Hessen, Germany
| | - Frederik Lermyte
- Department of Chemistry, Clemens-Schöpf-Institute of Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Hessen, Germany
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33
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Villacob RA, Feizi N, Beno SC, Solouki T. Collision-Induced Unfolding, Tandem MS, Bottom-up Proteomics, and Interactomics for Identification of Protein Complexes in Native Surface Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:13-30. [PMID: 38095581 DOI: 10.1021/jasms.3c00261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
Endogenously occurring salts and nonvolatile matrix components in untreated biological surfaces can suppress protein ionization and promote adduct formation, challenging protein identification. Characterization of labile proteins within biological specimens is particularly demanding because additional purification or sample treatment steps can be time-intensive and can disrupt noncovalent interactions. It is demonstrated that the combined use of collision-induced unfolding, tandem mass spectrometry, and bottom-up proteomics improves protein characterization in native surface mass spectrometry (NSMS). This multiprong analysis is achieved by acquiring NSMS, MS/MS, ion mobility (IM), and bottom-up proteomics data from a single surface extracted sample. The validity of this multiprong approach was confirmed by the successful characterization of nine surface-deposited proteins, with molecular weights ranging from 8 to 147 kDa, in two separate mixtures. Bottom-up proteomics provided a list of proteins to match against observed proteins in NSMS and their detected subunits in tandem MS. The method was applied to characterize endogenous proteins from untreated chicken liver samples. The subcapsular liver sampling for NSMS analysis allowed for the detection of endogenous proteins with molecular weights of up to ∼220 kDa. Moreover, using IM-MS, collision cross sections and collision-induced unfolding pathways of enzymatic proteins and protein complexes of up to 145 kDa were obtained.
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Affiliation(s)
- Raul A Villacob
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Neda Feizi
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Sarah C Beno
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Touradj Solouki
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
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34
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Ibáñez-Ibáñez L, Mollar-Cuni A, Apaloo-Messan E, Sharma AK, Mata JA, Maseras F, Vicent C. Ion mobility mass spectrometry uncovers regioselectivity in the carboxylate-assisted C-H activation of palladium N-heterocyclic carbene complexes. Dalton Trans 2024; 53:656-665. [PMID: 38073605 DOI: 10.1039/d3dt02793g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Carboxylate-assisted Pd-catalyzed C-H bond activation constitutes a mild and versatile synthetic tool to efficiently and selectively cleave inert C-H bonds. Herein, we demonstrate a simple method to experimentally evaluate both reactivity and selectivity in such systems using mass spectrometry (MS) methods. The N-heterocyclic carbene (NHC) cations [(NHC)PdX]+, bearing as X- ligand bases commonly used to promote the C-H activation (carboxylates and bicarbonate), are generated in the gas-phase by ESI-MS. Their C-H bond activation at the N-bound groups of the NHC is then studied using Collision Induced Dissociation (CID) experiments. Ion Mobility Spectrometry (IM)-MS is exploited to identify a number of regioisomers associated with the distinctive site selective C-H activations. It is demonstrated that such C-H activation concomitant with acetic acid release occurs from a mixture of activated [(NHC-H)Pd(CH3CO2H)]+ and non-activated [(NHC)Pd(CH3CO2)]+ complexes. The identity of the X-type ligands (X = Cl-, carboxylates and bicarbonate) has a significant impact on the regioisomer branching ratio upon CID conditions. IM-MS in conjunction with a DFT mechanistic study is presented for the acetate-assisted C-H activation of the [(NHC)Pd(CH3CO2)]+ cation featuring butyl and aryl as N-donor groups.
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Affiliation(s)
- Laura Ibáñez-Ibáñez
- Institute of Advanced Materials (INAM), Net of organometallic chemistry for sustainable solutions (OASIS), Universitat Jaume I, Avda. Sos Baynat s/n, 12071, Castellón, Spain.
| | - Andres Mollar-Cuni
- Institute of Advanced Materials (INAM), Net of organometallic chemistry for sustainable solutions (OASIS), Universitat Jaume I, Avda. Sos Baynat s/n, 12071, Castellón, Spain.
| | - Edmond Apaloo-Messan
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), The Barcelona Institute of Science and Technology, Avgda. Països Catalans, 16, 43007 Tarragona, Spain.
| | - Akhilesh K Sharma
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), The Barcelona Institute of Science and Technology, Avgda. Països Catalans, 16, 43007 Tarragona, Spain.
| | - Jose A Mata
- Institute of Advanced Materials (INAM), Net of organometallic chemistry for sustainable solutions (OASIS), Universitat Jaume I, Avda. Sos Baynat s/n, 12071, Castellón, Spain.
| | - Feliu Maseras
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), The Barcelona Institute of Science and Technology, Avgda. Països Catalans, 16, 43007 Tarragona, Spain.
| | - Cristian Vicent
- Serveis Centrals d'Instrumentació Científica (SCIC). Universitat Jaume I, Avda. Sos Baynat s/n, 12071, Castellón, Spain.
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35
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Vallejo DD, Corstvet JL, Fernández FM. Triboelectric Nanogenerators: Low-Cost Power Supplies for Improved Electrospray Ionization. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2024; 495:117167. [PMID: 38053979 PMCID: PMC10695355 DOI: 10.1016/j.ijms.2023.117167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Electrospray ionization (ESI) is one of the most popular methods to generate ions for mass spectrometry (MS). When compared with other ionization techniques, it can generate ions from liquid-phase samples without additives, retaining covalent and non-covalent interactions of the molecules of interest. When hyphenated to liquid chromatography, it greatly expands the versatility of MS analysis of complex mixtures. However, despite the extensive growth in the application of ESI, the technique still suffers from some drawbacks when powered by direct current (DC) power supplies. Triboelectric nanogenerators promise to be a new power source for the generation of ions by ESI, improving on the analytical capabilities of traditional DC ESI. In this review we highlight the fundamentals of ESI driven by DC power supplies, its contrasting qualities to triboelectric nanogenerator power supplies, and its applications to three distinct fields of research: forensics, metabolomics, and protein structure analysis.
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Affiliation(s)
- Daniel D. Vallejo
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Joseph L. Corstvet
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Facundo M. Fernández
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
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36
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Chapman EA, Roberts DS, Tiambeng TN, Andrews J, Wang MD, Reasoner EA, Melby JA, Li BH, Kim D, Alpert AJ, Jin S, Ge Y. Structure and dynamics of endogenous cardiac troponin complex in human heart tissue captured by native nanoproteomics. Nat Commun 2023; 14:8400. [PMID: 38110393 PMCID: PMC10728164 DOI: 10.1038/s41467-023-43321-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 11/07/2023] [Indexed: 12/20/2023] Open
Abstract
Protein complexes are highly dynamic entities that display substantial diversity in their assembly, post-translational modifications, and non-covalent interactions, allowing them to play critical roles in various biological processes. The heterogeneity, dynamic nature, and low abundance of protein complexes in their native states present challenges to study using conventional structural biology techniques. Here we develop a native nanoproteomics strategy for the enrichment and subsequent native top-down mass spectrometry (nTDMS) analysis of endogenous cardiac troponin (cTn) complex directly from human heart tissue. The cTn complex is enriched and purified using peptide-functionalized superparamagnetic nanoparticles under non-denaturing conditions to enable the isotopic resolution of cTn complex, revealing their complex structure and assembly. Moreover, nTDMS elucidates the stoichiometry and composition of the cTn complex, localizes Ca2+ binding domains, defines cTn-Ca2+ binding dynamics, and provides high-resolution mapping of the proteoform landscape. This native nanoproteomics strategy opens a paradigm for structural characterization of endogenous native protein complexes.
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Affiliation(s)
- Emily A Chapman
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - David S Roberts
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Timothy N Tiambeng
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jãán Andrews
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Man-Di Wang
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Emily A Reasoner
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jake A Melby
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Brad H Li
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Donguk Kim
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | | | - Song Jin
- 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, 53705, USA.
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA.
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37
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Fisher NP, McGee JP, Bowen KP, Goodwin M, Senko MW, Kelleher NL, Kafader JO. Determining Collisional Cross Sections from Ion Decay with Individual Ion Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2625-2629. [PMID: 38011219 PMCID: PMC10840072 DOI: 10.1021/jasms.3c00340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Collision cross section (CCS) measurements determined by ion mobility spectrometry (IMS) provide useful information about gas-phase protein structure that is complementary to mass analysis. Methods for determining CCS without a dedicated IMS system have been developed for Fourier transform mass spectrometry (FT-MS) platforms by measuring the signal decay during detection. Individual ion mass spectrometry (I2MS) provides charge detection and measures ion lifetimes across the length of an FT-MS detection event. By tracking lifetimes for entire ion populations, we demonstrate simultaneous determination of charge, mass, and CCS for proteins and complexes ranging from ∼8 to ∼232 kDa.
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Affiliation(s)
- Nickolas P Fisher
- Departments of Chemistry and Molecular Biosciences, Department of Chemical and Biological Engineering, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - John P McGee
- Departments of Chemistry and Molecular Biosciences, Department of Chemical and Biological Engineering, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Kyle P Bowen
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Michael Goodwin
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Michael W Senko
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Neil L Kelleher
- Departments of Chemistry and Molecular Biosciences, Department of Chemical and Biological Engineering, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Jared O Kafader
- Departments of Chemistry and Molecular Biosciences, Department of Chemical and Biological Engineering, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
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38
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Castel J, Delaux S, Hernandez-Alba O, Cianférani S. Recent advances in structural mass spectrometry methods in the context of biosimilarity assessment: from sequence heterogeneities to higher order structures. J Pharm Biomed Anal 2023; 236:115696. [PMID: 37713983 DOI: 10.1016/j.jpba.2023.115696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 09/17/2023]
Abstract
Biotherapeutics and their biosimilar versions have been flourishing in the biopharmaceutical market for several years. Structural and functional characterization is needed to achieve analytical biosimilarity through the assessment of critical quality attributes as required by regulatory authorities. The role of analytical strategies, particularly mass spectrometry-based methods, is pivotal to gathering valuable information for the in-depth characterization of biotherapeutics and biosimilarity assessment. Structural mass spectrometry methods (native MS, HDX-MS, top-down MS, etc.) provide information ranging from primary sequence assessment to higher order structure evaluation. This review focuses on recent developments and applications in structural mass spectrometry for biotherapeutic and biosimilar characterization.
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Affiliation(s)
- Jérôme Castel
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France
| | - Sarah Delaux
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France
| | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France.
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39
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Hua Y, Strauss M, Fisher S, Mauser MFX, Manchet P, Smacchia M, Geyer P, Shayeghi A, Pfeffer M, Eggenweiler TH, Daly S, Commandeur J, Mayor M, Arndt M, Šolomek T, Köhler V. Giving the Green Light to Photochemical Uncaging of Large Biomolecules in High Vacuum. JACS AU 2023; 3:2790-2799. [PMID: 37885583 PMCID: PMC10598566 DOI: 10.1021/jacsau.3c00351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/02/2023] [Accepted: 10/02/2023] [Indexed: 10/28/2023]
Abstract
The isolation of biomolecules in a high vacuum enables experiments on fragile species in the absence of a perturbing environment. Since many molecular properties are influenced by local electric fields, here we seek to gain control over the number of charges on a biopolymer by photochemical uncaging. We present the design, modeling, and synthesis of photoactive molecular tags, their labeling to peptides and proteins as well as their photochemical validation in solution and in the gas phase. The tailored tags can be selectively cleaved off at a well-defined time and without the need for any external charge-transferring agents. The energy of a single or two green photons can already trigger the process, and it is soft enough to ensure the integrity of the released biomolecular cargo. We exploit differences in the cleavage pathways in solution and in vacuum and observe a surprising robustness in upscaling the approach from a model system to genuine proteins. The interaction wavelength of 532 nm is compatible with various biomolecular entities, such as oligonucleotides or oligosaccharides.
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Affiliation(s)
- Yong Hua
- Department
of Chemistry, University of Basel, St. Johannsring 19, CH-4056 Basel, Switzerland
| | - Marcel Strauss
- Vienna
Faculty of Physics, University of Vienna,
VDSP & VCQ, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Sergey Fisher
- Van’t
Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, PO Box 94157, 1090 GD Amsterdam, The Netherlands
| | - Martin F. X. Mauser
- Vienna
Faculty of Physics, University of Vienna,
VDSP & VCQ, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Pierre Manchet
- Vienna
Faculty of Physics, University of Vienna,
VDSP & VCQ, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Martina Smacchia
- Vienna
Faculty of Physics, University of Vienna,
VDSP & VCQ, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Philipp Geyer
- Vienna
Faculty of Physics, University of Vienna,
VDSP & VCQ, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Armin Shayeghi
- Vienna
Faculty of Physics, University of Vienna,
VDSP & VCQ, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Michael Pfeffer
- Department
of Chemistry, University of Basel, St. Johannsring 19, CH-4056 Basel, Switzerland
| | - Tim Henri Eggenweiler
- Department
of Chemistry, University of Basel, St. Johannsring 19, CH-4056 Basel, Switzerland
| | - Steven Daly
- MS
Vision, Televisieweg
40, 1322 AM Almere, The Netherlands
| | - Jan Commandeur
- MS
Vision, Televisieweg
40, 1322 AM Almere, The Netherlands
| | - Marcel Mayor
- Department
of Chemistry, University of Basel, St. Johannsring 19, CH-4056 Basel, Switzerland
- Institute
for Nanotechnology (INT), Karlsruhe Institute
of Technology (KIT), P.O. Box 3640, DE-76021 Karlsruhe Eggenstein-Leopoldshafen, Germany
- Lehn Institute
of Functional Materials, School of Chemistry, Sun Yat-Sen University, Guangzhou 510274, P. R. China
| | - Markus Arndt
- Vienna
Faculty of Physics, University of Vienna,
VDSP & VCQ, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Tomáš Šolomek
- Van’t
Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, PO Box 94157, 1090 GD Amsterdam, The Netherlands
| | - Valentin Köhler
- Department
of Chemistry, University of Basel, St. Johannsring 19, CH-4056 Basel, Switzerland
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40
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Wan J, Nytka M, Qian H, Lemr K, Tureček F. Do d(GCGAAGC) Cations Retain the Hairpin Structure in the Gas Phase? A Cyclic Ion Mobility Mass Spectrometry and Density Functional Theory Computational Study. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2323-2340. [PMID: 37696624 DOI: 10.1021/jasms.3c00228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
d(GCGAAGC) is the smallest oligonucleotide with a well-defined hairpin structure in solution. We report a study of multiply protonated d(GCGAAGC) and its sequence-scrambled isomers, d(CGAAGCG), d(GCGAACG), and d(CGGAAGC), that were produced by electrospray ionization with the goal of investigating their gas-phase structures and dissociations. Cyclic ion mobility measurements revealed that dications of d(GCGAAGC) as well as the scrambled-sequence ions were mixtures of protomers and/or conformers that had collision cross sections (CCS) within a 439-481 Å2 range. Multiple ion conformers were obtained by electrospray under native conditions as well as from aqueous methanol. Arrival time distribution profiles were characteristic of individual isomeric heptanucleotides. Extensive Born-Oppenheimer molecular dynamics (BOMD) and density functional theory (DFT) calculations of d(GCGAAGC)2+ isomers indicated that hairpin structures were high-energy isomers of more compact distorted conformers. Protonation caused a break up of the C2···G6 pair that was associated with the formation of strong hydrogen bonds in zwitterionic phosphate anion-nucleobase cation motifs that predominated in low energy ions. Multiple components were also obtained for d(GCGAAGC)3+ trications under native and denaturing electrospray conditions. The calculated trication structures showed disruption of the G···C pairs in low energy zwitterions. A hairpin trication was calculated to be a high energy isomer. d(GCGAAGC)4+ tetracations were produced and separated by c-IMS as two major isomers. All low energy d(GCGAAGC)4+ ions obtained by DFT geometry optimizations were zwitterions in which all five purine bases were protonated, and the ion charge was balanced by a phosphate anion. Tetracations of the scrambled sequences were each formed as one dominant isomer. The CCS calculated with the MobCal-MPI method were found to closely match experimental values. Collision-induced dissociation (CID) spectra of multiply charged heptanucleotides showed nucleobase loss and backbone cleavages occurring chiefly at the terminal nucleosides. Electron-transfer-CID tandem mass spectra were used to investigate dissociations of different charge and spin states of charge-reduced heptanucleotide cation radicals.
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Affiliation(s)
- Jiahao Wan
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - Marianna Nytka
- Department of Analytical Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, 779 00 Olomouc, Czech Republic
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Haocheng Qian
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - Karel Lemr
- Department of Analytical Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, 779 00 Olomouc, Czech Republic
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - František Tureček
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
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41
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Zhao R, Liu N, Zheng Z, Li G. Enhanced Stability Differentiation of Therapeutic Polyclonal Antibodies with All Ion Unfolding-Ion Mobility-Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2289-2295. [PMID: 37682774 DOI: 10.1021/jasms.3c00215] [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: 09/10/2023]
Abstract
Compared with monoclonal antibodies, polyclonal antibodies (pAbs) have rather significant characteristics, including lower cost, shorter production cycle, and higher affinity. Therefore, to facilitate their applications in clinic, it is equally critical to comprehensively characterize the conformational stabilities of pAb at the molecular weight-resolved scale, which is technically challenging due to the lack of an effective analytical tool capable of simultaneously providing both stability and molecular weight information within an acceptable error range. Ion mobility-mass spectrometry (IM-MS) has grown as an alternative to rapidly assess protein conformational stability with accurate molecular weight information maintained, especially when equipped with a collision-induced unfolding (CIU) regime. Dynamic and transient conformational intermediates can be captured with the CIU-IM-MS technique, adding to traditional static structural measurements with collisional cross section. Most CIU-IM-MS-centered protocols are focusing on the application to isolated, targeted protein ions, namely, analyzing one single charge state at one time, limiting its analytical throughput and speed. In this study, we employed an enhanced unfolding regime, all ion unfolding (AIU), capable of the simultaneous operation of numerous ions at a time during stepped unfolding processes to analyze pAb. Results show that AIU can quantitatively characterize the subtle differences in conformational stability among four structurally similar pAbs with improved resolving capability by around a 2-4-fold increment in both stability and structure differentiating parameters. Besides, AIU also benefits from considerably saved time cost and improved spectrum quality with an elevated signal-to-noise ratio.
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Affiliation(s)
- Rui Zhao
- State Key Laboratory of Medicinal 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
| | - Ning Liu
- State Key Laboratory of Medicinal 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
| | - Zhen Zheng
- School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Gongyu Li
- State Key Laboratory of Medicinal 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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42
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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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Edwards AN, Blue AJ, Conforti JM, Cordes MS, Trakselis MA, Gallagher ES. Gas-phase stability and thermodynamics of ligand-bound, binary complexes of chloramphenicol acetyltransferase reveal negative cooperativity. Anal Bioanal Chem 2023; 415:6201-6212. [PMID: 37542535 DOI: 10.1007/s00216-023-04891-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/17/2023] [Accepted: 07/24/2023] [Indexed: 08/07/2023]
Abstract
The biological role of the bacterial chloramphenicol (Chl)-resistance enzyme, chloramphenicol acetyltransferase (CAT), has seen renewed interest due to the resurgent use of Chl against multi-drug-resistant microbes. This looming threat calls for more rationally designed antibiotic derivatives that have improved antimicrobial properties and reduced toxicity in humans. Herein, we utilize native ion mobility spectrometry-mass spectrometry (IMS-MS) to investigate the gas-phase structure and thermodynamic stability of the type I variant of CAT from Escherichia coli (EcCATI) and several EcCATI:ligand-bound complexes. EcCATI readily binds multiple Chl without incurring significant changes to its gas-phase structure or stability. A non-hydrolyzable acetyl-CoA derivative (S-ethyl-CoA, S-Et-CoA) was used to kinetically trap EcCATI and Chl in a ternary, ligand-bound state (EcCATI:S-Et-CoA:Chl). Using collision-induced unfolding (CIU)-IMS-MS, we find that Chl dissociates from EcCATI:S-Et-CoA:Chl complexes at low collision energies, while S-Et-CoA remains bound to EcCATI even as protein unfolding occurs. Gas-phase binding constants further suggest that EcCATI binds S-Et-CoA more tightly than Chl. Both ligands exhibit negative cooperativity of subsequent ligand binding in their respective binary complexes. While we observe no significant change in structure or stability to EcCATI when bound to either or both ligands, we have elucidated novel gas-phase unfolding and dissociation behavior and provided a foundation for further characterization of alternative substrates and/or inhibitors of EcCATI.
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Affiliation(s)
- Alexis N Edwards
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA
| | - Anthony J Blue
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA
| | - Jessica M Conforti
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA
| | - Michael S Cordes
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA
| | - Michael A Trakselis
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA
| | - Elyssia S Gallagher
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA.
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Le LTHL, Lee J, Im D, Park S, Hwang K, Lee JH, Jiang Y, Lee Y, Suh YH, Kim HI, Lee MJ. Self-Aggregating Tau Fragments Recapitulate Pathologic Phenotypes and Neurotoxicity of Alzheimer's Disease in Mice. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2302035. [PMID: 37594721 PMCID: PMC10582461 DOI: 10.1002/advs.202302035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/10/2023] [Indexed: 08/19/2023]
Abstract
In tauopathy conditions, such as Alzheimer's disease (AD), highly soluble and natively unfolded tau polymerizes into an insoluble filament; however, the mechanistic details of this process remain unclear. In the brains of AD patients, only a minor segment of tau forms β-helix-stacked protofilaments, while its flanking regions form disordered fuzzy coats. Here, it is demonstrated that the tau AD nucleation core (tau-AC) sufficiently induced self-aggregation and recruited full-length tau to filaments. Unexpectedly, phospho-mimetic forms of tau-AC (at Ser324 or Ser356) show markedly reduced oligomerization and seeding propensities. Biophysical analysis reveal that the N-terminus of tau-AC facilitates the fibrillization kinetics as a nucleation motif, which becomes sterically shielded through phosphorylation-induced conformational changes in tau-AC. Tau-AC oligomers are efficiently internalized into cells via endocytosis and induced endogenous tau aggregation. In primary hippocampal neurons, tau-AC impaired axon initial segment plasticity upon chronic depolarization and is mislocalized to the somatodendritic compartments. Furthermore, it is observed significantly impaired memory retrieval in mice intrahippocampally injected with tau-AC fibrils, which corresponds to the neuropathological staining and neuronal loss in the brain. These findings identify tau-AC species as a key neuropathological driver in AD, suggesting novel strategies for therapeutic intervention.
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Affiliation(s)
- Ly Thi Huong Luu Le
- Department of Biochemistry and Molecular BiologySeoul National University College of MedicineSeoul03080South Korea
- Department of Biomedical SciencesSeoul National University Graduate SchoolSeoul03080South Korea
| | - Jeeyoung Lee
- Department of Biochemistry and Molecular BiologySeoul National University College of MedicineSeoul03080South Korea
- Brain Science InstituteKorea Institute of Science and TechnologySeoul02792South Korea
| | - Dongjoon Im
- Department of ChemistryKorea UniversitySeoul02841South Korea
| | - Sunha Park
- Department of Biomedical SciencesSeoul National University Graduate SchoolSeoul03080South Korea
| | - Kyoung‐Doo Hwang
- Department of Biomedical SciencesSeoul National University Graduate SchoolSeoul03080South Korea
- Department of PhysiologySeoul National University College of MedicineSeoul03080South Korea
| | - Jung Hoon Lee
- Department of Biochemistry and Molecular BiologySeoul National University College of MedicineSeoul03080South Korea
| | - Yanxialei Jiang
- Department of Biochemistry and Molecular BiologySeoul National University College of MedicineSeoul03080South Korea
- School of MedicineLinyi UniversityLinyi276000China
| | - Yong‐Seok Lee
- Department of Biomedical SciencesSeoul National University Graduate SchoolSeoul03080South Korea
- Department of PhysiologySeoul National University College of MedicineSeoul03080South Korea
- Neuroscience Research InstituteSeoul National University College of MedicineSeoul03080South Korea
| | - Young Ho Suh
- Department of Biomedical SciencesSeoul National University Graduate SchoolSeoul03080South Korea
- Neuroscience Research InstituteSeoul National University College of MedicineSeoul03080South Korea
| | - Hugh I. Kim
- Department of ChemistryKorea UniversitySeoul02841South Korea
| | - Min Jae Lee
- Department of Biochemistry and Molecular BiologySeoul National University College of MedicineSeoul03080South Korea
- Department of Biomedical SciencesSeoul National University Graduate SchoolSeoul03080South Korea
- Ischemic/Hypoxic Disease Institute, Convergence Research Center for DementiaSeoul National University College of MedicineSeoul03080South Korea
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45
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Daly LA, Clarke CJ, Po A, Oswald SO, Eyers CE. Considerations for defining +80 Da mass shifts in mass spectrometry-based proteomics: phosphorylation and beyond. Chem Commun (Camb) 2023; 59:11484-11499. [PMID: 37681662 PMCID: PMC10521633 DOI: 10.1039/d3cc02909c] [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] [Received: 06/16/2023] [Accepted: 08/21/2023] [Indexed: 09/09/2023]
Abstract
Post-translational modifications (PTMs) are ubiquitous and key to regulating protein function. Understanding the dynamics of individual PTMs and their biological roles requires robust characterisation. Mass spectrometry (MS) is the method of choice for the identification and quantification of protein modifications. This article focusses on the MS-based analysis of those covalent modifications that induce a mass shift of +80 Da, notably phosphorylation and sulfation, given the challenges associated with their discrimination and pinpointing the sites of modification on a polypeptide chain. Phosphorylation in particular is highly abundant, dynamic and can occur on numerous residues to invoke specific functions, hence robust characterisation is crucial to understanding biological relevance. Showcasing our work in the context of other developments in the field, we highlight approaches for enrichment and site localisation of phosphorylated (canonical and non-canonical) and sulfated peptides, as well as modification analysis in the context of intact proteins (top down proteomics) to explore combinatorial roles. Finally, we discuss the application of native ion-mobility MS to explore the effect of these PTMs on protein structure and ligand binding.
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Affiliation(s)
- Leonard A Daly
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Christopher J Clarke
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Allen Po
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Sally O Oswald
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Claire E Eyers
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
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46
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Purder P, Meyners C, Sugiarto WO, Kolos J, Löhr F, Gebel J, Nehls T, Dötsch V, Lermyte F, Hausch F. Deconstructing Protein Binding of Sulfonamides and Sulfonamide Analogues. JACS AU 2023; 3:2478-2486. [PMID: 37772190 PMCID: PMC10523370 DOI: 10.1021/jacsau.3c00241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/20/2023] [Accepted: 07/21/2023] [Indexed: 09/30/2023]
Abstract
Sulfonamides are one of the most important pharmacophores in medicinal chemistry, and sulfonamide analogues have gained substantial interest in recent years. However, the protein interactions of sulfonamides and especially of their analogues are underexplored. Using FKBP12 as a model system, we describe the synthesis of optically pure sulfenamide, sulfinamide, and sulfonimidamide analogues of a well characterized sulfonamide ligand. This allowed us to precisely determine the binding contributions of each sulfonamide oxygen atom and the consequences of nitrogen replacements. We also present high-resolution cocrystal structures of sulfonamide analogues buried in the pocket of a protein target. This revealed intimate contacts with the protein including an unprecedented hydrogen bond acceptor of sulfonimidamides. The use of sulfonamide analogues enabled new exit vectors that allowed remodeling of a subpocket in FKBP12. Our results illuminate the protein interaction potential of sulfonamides/sulfonamide analogues and will aid in their rational design.
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Affiliation(s)
- Patrick
L. Purder
- Department
of Organic Chemistry and Biochemistry, Clemens-Schöpf-Institute, Technical University Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
| | - Christian Meyners
- Department
of Organic Chemistry and Biochemistry, Clemens-Schöpf-Institute, Technical University Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
| | - Wisely Oki Sugiarto
- Department
of Organic Chemistry and Biochemistry, Clemens-Schöpf-Institute, Technical University Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
| | - Jürgen Kolos
- Department
of Organic Chemistry and Biochemistry, Clemens-Schöpf-Institute, Technical University Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
| | - Frank Löhr
- Institute
of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
| | - Jakob Gebel
- Institute
of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
| | - Thomas Nehls
- Department
of Organic Chemistry and Biochemistry, Clemens-Schöpf-Institute, Technical University Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
| | - Volker Dötsch
- Institute
of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
| | - Frederik Lermyte
- Department
of Organic Chemistry and Biochemistry, Clemens-Schöpf-Institute, Technical University Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
| | - Felix Hausch
- Department
of Organic Chemistry and Biochemistry, Clemens-Schöpf-Institute, Technical University Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
- Centre
for Synthetic Biology, Technical University
of Darmstadt, 64287 Darmstadt, Germany
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47
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Turzo SMBA, Seffernick JT, Lyskov S, Lindert S. Predicting ion mobility collision cross sections using projection approximation with ROSIE-PARCS webserver. Brief Bioinform 2023; 24:bbad308. [PMID: 37609950 PMCID: PMC10516336 DOI: 10.1093/bib/bbad308] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 07/03/2023] [Accepted: 08/08/2023] [Indexed: 08/24/2023] Open
Abstract
Ion mobility coupled to mass spectrometry informs on the shape and size of protein structures in the form of a collision cross section (CCSIM). Although there are several computational methods for predicting CCSIM based on protein structures, including our previously developed projection approximation using rough circular shapes (PARCS), the process usually requires prior experience with the command-line interface. To overcome this challenge, here we present a web application on the Rosetta Online Server that Includes Everyone (ROSIE) webserver to predict CCSIM from protein structure using projection approximation with PARCS. In this web interface, the user is only required to provide one or more PDB files as input. Results from our case studies suggest that CCSIM predictions (with ROSIE-PARCS) are highly accurate with an average error of 6.12%. Furthermore, the absolute difference between CCSIM and CCSPARCS can help in distinguishing accurate from inaccurate AlphaFold2 protein structure predictions. ROSIE-PARCS is designed with a user-friendly interface, is available publicly and is free to use. The ROSIE-PARCS web interface is supported by all major web browsers and can be accessed via this link (https://rosie.graylab.jhu.edu).
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Affiliation(s)
- S M Bargeen Alam Turzo
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, Ohio State University, Columbus, OH 43210, USA
| | - Justin T Seffernick
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, Ohio State University, Columbus, OH 43210, USA
| | - Sergey Lyskov
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Steffen Lindert
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, Ohio State University, Columbus, OH 43210, USA
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48
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Zhang H, Jia H, Hong J, Zhang M, Jiang T, Xu W. Development of a High-Field "Brick" Mass Spectrometer with Extended Mass Range and Capable of Characterizing Native Proteins. Anal Chem 2023; 95:13503-13508. [PMID: 37650728 DOI: 10.1021/acs.analchem.3c01769] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
One of the main challenges of analyzing intact proteins on an ion trap mass spectrometer is the mass range limitation, especially for miniature mass spectrometers. In this study, a high-field frequency scanning ion trap miniature mass spectrometer, namely the high-field "Brick" mass spectrometer, was developed to analyze intact proteins. A high-voltage broadband radio frequency (rf) amplifier was designed with a maximum output of 900 Vp-p over a frequency range of 130-700 kHz. Compared to the 600 Vp-p rf amplifier equipped in the conventional "Brick" mass spectrometer, the mass range of the instrument could be extended from 2000 to over 8000 Th. Sensitivity and mass resolution for native protein analyses were also evaluated and compared. Various proteins as well as their mixtures were analyzed on the high-field "Brick" mass spectrometer. The noncovalent interaction between protein-ligand complexes, lysozyme with triN-acetylchitotriose, was also analyzed. In addition, a hybrid ion scan mode was explored to further expand the mass range of the instrument at both low- and high-mass ends. In the hybrid ion scan mode, both rf frequency and amplitude were tuned, and a mass range from 100 to 12,000 Th was realized. As a result, both small drugs and proteins could be analyzed in a single mass scan. As proof-of-concept demonstrations, a mixture of atenolol and bovine serum albuminand oligomers of transferrin were analyzed.
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Affiliation(s)
- Hongjia Zhang
- School of Medical Technology, Beijing Institute of Technology, Beijing 100081, China
| | - Heyuan Jia
- Kunshan Nier Precision Instrumentation Inc., Kunshan, Suzhou 215316, China
| | - Jie Hong
- School of Medical Technology, Beijing Institute of Technology, Beijing 100081, China
| | - Mei Zhang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Ting Jiang
- School of Medical Technology, Beijing Institute of Technology, Beijing 100081, China
| | - Wei Xu
- School of Medical Technology, Beijing Institute of Technology, Beijing 100081, China
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49
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Nagy K, Gellén G, Papp D, Schlosser G, Révész Á. Optimum collision energies for proteomics: The impact of ion mobility separation. JOURNAL OF MASS SPECTROMETRY : JMS 2023; 58:e4957. [PMID: 37415399 DOI: 10.1002/jms.4957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 05/28/2023] [Accepted: 06/19/2023] [Indexed: 07/08/2023]
Abstract
Ion mobility spectrometry (IMS) is a widespread separation technique used in various research fields. It can be coupled to liquid chromatography-mass spectrometry (LC-MS/MS) methods providing an additional separation dimension. During IMS, ions are subjected to multiple collisions with buffer gas, which may cause significant ion heating. The present project addresses this phenomenon from the bottom-up proteomics point of view. We performed LC-MS/MS measurements on a cyclic ion mobility mass spectrometer with varied collision energy (CE) settings both with and without IMS. We investigated the CE dependence of identification score, using Byonic search engine, for more than 1000 tryptic peptides from HeLa digest standard. We determined the optimal CE values-giving the highest identification score-for both setups (i.e., with and without IMS). Results show that lower CE is advantageous when IMS separation is applied, by 6.3 V on average. This value belongs to the one-cycle separation configuration, and multiple cycles may supposedly have even larger impact. The effect of IMS is also reflected in the trends of optimal CE values versus m/z functions. The parameters suggested by the manufacturer were found to be almost optimal for the setup without IMS; on the other hand, they are obviously too high with IMS. Practical consideration on setting up a mass spectrometric platform hyphenated to IMS is also presented. Furthermore, the two CID (collision induced dissociation) fragmentation cells of the instrument-located before and after the IMS cell-were also compared, and we found that CE adjustment is needed when the trap cell is used for activation instead of the transfer cell. Data have been deposited in the MassIVE repository (MSV000090944).
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Affiliation(s)
- Kinga Nagy
- MS Proteomics Research Group, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
- Hevesy György PhD School of Chemistry, Faculty of Science, Institute of Chemistry, Eötvös Loránd University, Budapest, H-1117, Hungary
| | - Gabriella Gellén
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Faculty of Science, Institute of Chemistry, Eötvös Loránd University, Budapest, H-1117, Hungary
| | - Dávid Papp
- Hevesy György PhD School of Chemistry, Faculty of Science, Institute of Chemistry, Eötvös Loránd University, Budapest, H-1117, Hungary
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Faculty of Science, Institute of Chemistry, Eötvös Loránd University, Budapest, H-1117, Hungary
| | - Gitta Schlosser
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Faculty of Science, Institute of Chemistry, Eötvös Loránd University, Budapest, H-1117, Hungary
| | - Ágnes Révész
- MS Proteomics Research Group, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
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50
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Kartowikromo KY, Olajide OE, Hamid AM. Collision cross section measurement and prediction methods in omics. JOURNAL OF MASS SPECTROMETRY : JMS 2023; 58:e4973. [PMID: 37620034 PMCID: PMC10530098 DOI: 10.1002/jms.4973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/26/2023] [Accepted: 07/20/2023] [Indexed: 08/26/2023]
Abstract
Omics studies such as metabolomics, lipidomics, and proteomics have become important for understanding the mechanisms in living organisms. However, the compounds detected are structurally different and contain isomers, with each structure or isomer leading to a different result in terms of the role they play in the cell or tissue in the organism. Therefore, it is important to detect, characterize, and elucidate the structures of these compounds. Liquid chromatography and mass spectrometry have been utilized for decades in the structure elucidation of key compounds. While prediction models of parameters (such as retention time and fragmentation pattern) have also been developed for these separation techniques, they have some limitations. Moreover, ion mobility has become one of the most promising techniques to give a fingerprint to these compounds by determining their collision cross section (CCS) values, which reflect their shape and size. Obtaining accurate CCS enables its use as a filter for potential analyte structures. These CCS values can be measured experimentally using calibrant-independent and calibrant-dependent approaches. Identification of compounds based on experimental CCS values in untargeted analysis typically requires CCS references from standards, which are currently limited and, if available, would require a large amount of time for experimental measurements. Therefore, researchers use theoretical tools to predict CCS values for untargeted and targeted analysis. In this review, an overview of the different methods for the experimental and theoretical estimation of CCS values is given where theoretical prediction tools include computational and machine modeling type approaches. Moreover, the limitations of the current experimental and theoretical approaches and their potential mitigation methods were discussed.
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Affiliation(s)
| | - Orobola E Olajide
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama, USA
| | - Ahmed M Hamid
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama, USA
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