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Wang CR, McFarlane LO, Pukala TL. Exploring snake venoms beyond the primary sequence: From proteoforms to protein-protein interactions. Toxicon 2024; 247:107841. [PMID: 38950738 DOI: 10.1016/j.toxicon.2024.107841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/26/2024] [Accepted: 06/28/2024] [Indexed: 07/03/2024]
Abstract
Snakebite envenomation has been a long-standing global issue that is difficult to treat, largely owing to the flawed nature of current immunoglobulin-based antivenom therapy and the complexity of snake venoms as sophisticated mixtures of bioactive proteins and peptides. Comprehensive characterisation of venom compositions is essential to better understanding snake venom toxicity and inform effective and rationally designed antivenoms. Additionally, a greater understanding of snake venom composition will likely unearth novel biologically active proteins and peptides that have promising therapeutic or biotechnological applications. While a bottom-up proteomic workflow has been the main approach for cataloguing snake venom compositions at the toxin family level, it is unable to capture snake venom heterogeneity in the form of protein isoforms and higher-order protein interactions that are important in driving venom toxicity but remain underexplored. This review aims to highlight the importance of understanding snake venom heterogeneity beyond the primary sequence, in the form of post-translational modifications that give rise to different proteoforms and the myriad of higher-order protein complexes in snake venoms. We focus on current top-down proteomic workflows to identify snake venom proteoforms and further discuss alternative or novel separation, instrumentation, and data processing strategies that may improve proteoform identification. The current higher-order structural characterisation techniques implemented for snake venom proteins are also discussed; we emphasise the need for complementary and higher resolution structural bioanalytical techniques such as mass spectrometry-based approaches, X-ray crystallography and cryogenic electron microscopy, to elucidate poorly characterised tertiary and quaternary protein structures. We envisage that the expansion of the snake venom characterisation "toolbox" with top-down proteomics and high-resolution protein structure determination techniques will be pivotal in advancing structural understanding of snake venoms towards the development of improved therapeutic and biotechnology applications.
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Affiliation(s)
- C Ruth Wang
- Discipline of Chemistry, School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide, 5005, Australia
| | - Lewis O McFarlane
- Discipline of Chemistry, School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide, 5005, Australia
| | - Tara L Pukala
- Discipline of Chemistry, School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide, 5005, Australia.
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2
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Faizi M, Fellers RT, Lu D, Drown BS, Jambhekar A, Lahav G, Kelleher NL, Gunawardena J. MSModDetector: a tool for detecting mass shifts and post-translational modifications in individual ion mass spectrometry data. Bioinformatics 2024; 40:btae335. [PMID: 38796681 PMCID: PMC11157153 DOI: 10.1093/bioinformatics/btae335] [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] [Revised: 02/28/2024] [Accepted: 05/24/2024] [Indexed: 05/28/2024] Open
Abstract
MOTIVATION Post-translational modifications (PTMs) on proteins regulate protein structures and functions. A single protein molecule can possess multiple modification sites that can accommodate various PTM types, leading to a variety of different patterns, or combinations of PTMs, on that protein. Different PTM patterns can give rise to distinct biological functions. To facilitate the study of multiple PTMs on the same protein molecule, top-down mass spectrometry (MS) has proven to be a useful tool to measure the mass of intact proteins, thereby enabling even PTMs at distant sites to be assigned to the same protein molecule and allowing determination of how many PTMs are attached to a single protein. RESULTS We developed a Python module called MSModDetector that studies PTM patterns from individual ion mass spectrometry (I2MS) data. I2MS is an intact protein mass spectrometry approach that generates true mass spectra without the need to infer charge states. The algorithm first detects and quantifies mass shifts for a protein of interest and subsequently infers potential PTM patterns using linear programming. The algorithm is evaluated on simulated I2MS data and experimental I2MS data for the tumor suppressor protein p53. We show that MSModDetector is a useful tool for comparing a protein's PTM pattern landscape across different conditions. An improved analysis of PTM patterns will enable a deeper understanding of PTM-regulated cellular processes. AVAILABILITY AND IMPLEMENTATION The source code is available at https://github.com/marjanfaizi/MSModDetector.
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Affiliation(s)
- Marjan Faizi
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, United States
| | - Ryan T Fellers
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL 60208, United States
| | - Dan Lu
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, United States
| | - Bryon S Drown
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL 60208, United States
| | - Ashwini Jambhekar
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, United States
| | - Galit Lahav
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, United States
| | - Neil L Kelleher
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL 60208, United States
| | - Jeremy Gunawardena
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, United States
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3
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Peters-Clarke TM, Coon JJ, Riley NM. Instrumentation at the Leading Edge of Proteomics. Anal Chem 2024; 96:7976-8010. [PMID: 38738990 DOI: 10.1021/acs.analchem.3c04497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Affiliation(s)
- Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - Nicholas M Riley
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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4
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Habeck T, Brown KA, Des Soye B, Lantz C, Zhou M, Alam N, Hossain MA, Jung W, Keener JE, Volny M, Wilson JW, Ying Y, Agar JN, Danis PO, Ge Y, Kelleher NL, Li H, Loo JA, Marty MT, Paša-Tolić L, Sandoval W, Lermyte F. Top-down mass spectrometry of native proteoforms and their complexes: a community study. Nat Methods 2024:10.1038/s41592-024-02279-6. [PMID: 38744918 DOI: 10.1038/s41592-024-02279-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 04/10/2024] [Indexed: 05/16/2024]
Abstract
The combination of native electrospray ionization with top-down fragmentation in mass spectrometry (MS) allows simultaneous determination of the stoichiometry of noncovalent complexes and identification of their component proteoforms and cofactors. Although this approach is powerful, both native MS and top-down MS are not yet well standardized, and only a limited number of laboratories regularly carry out this type of research. To address this challenge, the Consortium for Top-Down Proteomics initiated a study to develop and test protocols for native MS combined with top-down fragmentation of proteins and protein complexes across 11 instruments in nine laboratories. Here we report the summary of the outcomes to provide robust benchmarks and a valuable entry point for the scientific community.
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Affiliation(s)
- Tanja Habeck
- Technische Universität Darmstadt, Darmstadt, Germany
| | - Kyle A Brown
- University of Wisconsin-Madison, Madison, WI, USA
| | | | | | - Mowei Zhou
- Pacific Northwest National Laboratory, Richland, WA, USA
- Zhejiang University, Zhejiang, China
| | | | | | | | | | | | - Jesse W Wilson
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Yujia Ying
- Sun Yat-sen University, Guangzhou, China
| | - Jeffrey N Agar
- Northeastern University, Boston, MA, USA
- Consortium for Top-Down Proteomics, Cambridge, MA, USA
| | - Paul O Danis
- Consortium for Top-Down Proteomics, Cambridge, MA, USA
| | - Ying Ge
- University of Wisconsin-Madison, Madison, WI, USA
- Consortium for Top-Down Proteomics, Cambridge, MA, USA
| | - Neil L Kelleher
- Northwestern University, Evanston, IL, USA
- Consortium for Top-Down Proteomics, Cambridge, MA, USA
| | - Huilin Li
- Sun Yat-sen University, Guangzhou, China
| | - Joseph A Loo
- University of California, Los Angeles, CA, USA
- Consortium for Top-Down Proteomics, Cambridge, MA, USA
| | | | - Ljiljana Paša-Tolić
- Pacific Northwest National Laboratory, Richland, WA, USA
- Consortium for Top-Down Proteomics, Cambridge, MA, USA
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5
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Coorssen JR, Padula MP. Proteomics-The State of the Field: The Definition and Analysis of Proteomes Should Be Based in Reality, Not Convenience. Proteomes 2024; 12:14. [PMID: 38651373 PMCID: PMC11036260 DOI: 10.3390/proteomes12020014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 04/17/2024] [Accepted: 04/17/2024] [Indexed: 04/25/2024] Open
Abstract
With growing recognition and acknowledgement of the genuine complexity of proteomes, we are finally entering the post-proteogenomic era. Routine assessment of proteomes as inferred correlates of gene sequences (i.e., canonical 'proteins') cannot provide the necessary critical analysis of systems-level biology that is needed to understand underlying molecular mechanisms and pathways or identify the most selective biomarkers and therapeutic targets. These critical requirements demand the analysis of proteomes at the level of proteoforms/protein species, the actual active molecular players. Currently, only highly refined integrated or integrative top-down proteomics (iTDP) enables the analytical depth necessary to provide routine, comprehensive, and quantitative proteome assessments across the widest range of proteoforms inherent to native systems. Here we provide a broad perspective of the field, taking in historical and current realities, to establish a more balanced understanding of where the field has come from (in particular during the ten years since Proteomes was launched), current issues, and how things likely need to proceed if necessary deep proteome analyses are to succeed. We base this in our firm belief that the best proteomic analyses reflect, as closely as possible, the native sample at the moment of sampling. We also seek to emphasise that this and future analytical approaches are likely best based on the broad recognition and exploitation of the complementarity of currently successful approaches. This also emphasises the need to continuously evaluate and further optimize established approaches, to avoid complacency in thinking and expectations but also to promote the critical and careful development and introduction of new approaches, most notably those that address proteoforms. Above all, we wish to emphasise that a rigorous focus on analytical quality must override current thinking that largely values analytical speed; the latter would certainly be nice, if only proteoforms could thus be effectively, routinely, and quantitatively assessed. Alas, proteomes are composed of proteoforms, not molecular species that can be amplified or that directly mirror genes (i.e., 'canonical'). The problem is hard, and we must accept and address it as such, but the payoff in playing this longer game of rigorous deep proteome analyses is the promise of far more selective biomarkers, drug targets, and truly personalised or even individualised medicine.
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Affiliation(s)
- Jens R. Coorssen
- Department of Biological Sciences, Faculty of Mathematics and Science, Brock University, St. Catharines, ON L2S 3A1, Canada
- Institute for Globally Distributed Open Research and Education (IGDORE), St. Catharines, ON L2N 4X2, Canada
| | - Matthew P. Padula
- School of Life Sciences and Proteomics, Lipidomics and Metabolomics Core Facility, Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia
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6
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Drown BS, Gupta R, McGee JP, Hollas MAR, Hergenrother PJ, Kafader JO, Kelleher NL. Precise Readout of MEK1 Proteoforms upon MAPK Pathway Modulation by Individual Ion Mass Spectrometry. Anal Chem 2024; 96:4455-4462. [PMID: 38458998 PMCID: PMC11008683 DOI: 10.1021/acs.analchem.3c04758] [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: 03/10/2024]
Abstract
The functions of proteins bearing multiple post-translational modifications (PTMs) are modulated by their modification patterns, yet precise characterization of them is difficult. MEK1 (also known as MAP2K1) is one such example that acts as a gatekeeper of the mitogen-activating protein kinase (MAPK) pathway and propagates signals via phosphorylation by upstream kinases. In principle, top-down mass spectrometry can precisely characterize whole MEK1 proteoforms, but fragmentation methods that would enable the site-specific characterization of labile modifications on 43 kDa protein ions result in overly dense tandem mass spectra. By using the charge-detection method called individual ion mass spectrometry, we demonstrate how complex mixtures of phosphoproteoforms and their fragment ions can be reproducibly handled to provide a "bird's eye" view of signaling activity through mapping proteoform landscapes in a pathway. Using this approach, the overall stoichiometry and distribution of 0-4 phosphorylations on MEK1 was determined in a cellular model of drug-resistant metastatic melanoma. This approach can be generalized to other multiply modified proteoforms, for which PTM combinations are key to their function and drug action.
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Affiliation(s)
- Bryon S Drown
- Proteomics Center of Excellence, Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60202, United States
| | - Raveena Gupta
- Proteomics Center of Excellence, Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60202, United States
| | - John P McGee
- Proteomics Center of Excellence, Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60202, United States
| | - Michael A R Hollas
- Proteomics Center of Excellence, Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60202, United States
| | - Paul J Hergenrother
- Department of Chemistry, Carl R. Woese Institute for Genomic Biology, Cancer Center at Illinois, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
| | - Jared O Kafader
- Proteomics Center of Excellence, Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60202, United States
| | - Neil L Kelleher
- Proteomics Center of Excellence, Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60202, United States
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7
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Kaltashov IA, Ivanov DG, Yang Y. Mass spectrometry-based methods to characterize highly heterogeneous biopharmaceuticals, vaccines, and nonbiological complex drugs at the intact-mass level. MASS SPECTROMETRY REVIEWS 2024; 43:139-165. [PMID: 36582075 PMCID: PMC10307928 DOI: 10.1002/mas.21829] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 11/21/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
The intact-mass MS measurements are becoming increasingly popular in characterization of a range of biopolymers, especially those of interest to biopharmaceutical industry. However, as the complexity of protein therapeutics and other macromolecular medicines increases, the new challenges arise, one of which is the high levels of structural heterogeneity that are frequently exhibited by such products. The very notion of the molecular mass measurement loses its clear and intuitive meaning when applied to an extremely heterogenous system that cannot be characterized by a unique mass, but instead requires that a mass distribution be considered. Furthermore, convoluted mass distributions frequently give rise to unresolved ionic signal in mass spectra, from which little-to-none meaningful information can be extracted using standard approaches that work well for homogeneous systems. However, a range of technological advances made in the last decade, such as the hyphenation of intact-mass MS measurements with front-end separations, better integration of ion mobility in MS workflows, development of an impressive arsenal of gas-phase ion chemistry tools to supplement MS methods, as well as the revival of the charge detection MS and its triumphant entry into the field of bioanalysis already made impressive contributions towards addressing the structural heterogeneity challenge. An overview of these techniques is accompanied by critical analysis of the strengths and weaknesses of different approaches, and a brief overview of their applications to specific classes of biopharmaceutical products, vaccines, and nonbiological complex drugs.
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Affiliation(s)
- Igor A. Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst MA 01003
| | - Daniil G. Ivanov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst MA 01003
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8
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Ryan JP, Kostelic MM, Hsieh CC, Powers J, Aspinwall C, Dodds JN, Schiel JE, Marty MT, Baker ES. Characterizing Adeno-Associated Virus Capsids with Both Denaturing and Intact Analysis Methods. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2811-2821. [PMID: 38010134 DOI: 10.1021/jasms.3c00321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Adeno-associated virus (AAV) capsids are among the leading gene delivery platforms used to treat a vast array of human diseases and conditions. AAVs exist in a variety of serotypes due to differences in viral protein (VP) sequences with distinct serotypes targeting specific cells and tissues. As the utility of AAVs in gene therapy increases, ensuring their specific composition is imperative for the correct targeting and gene delivery. From a quality control perspective, current analytical tools are limited in their selectivity for viral protein (VP) subunits due to their sequence similarities, instrumental difficulties in assessing the large molecular weights of intact capsids, and the uncertainty in distinguishing empty and filled capsids. To address these challenges, we combined two distinct analytical workflows that assess the intact capsids and VP subunits separately. First, a selective temporal overview of resonant ion (STORI)-based charge detection-mass spectrometry (CD-MS) was applied for characterization of the intact capsids. Liquid chromatography, ion mobility spectrometry, and mass spectrometry (LC-IMS-MS) separations were then used for the capsid denaturing measurements. This multimethod combination was applied to three AAV serotypes (AAV2, AAV6, and AAV8) to evaluate their intact empty and filled capsid ratios and then examine the distinct VP sequences and modifications present.
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Affiliation(s)
- Jack P Ryan
- University of North Carolina, Department of Chemistry, Chapel Hill, North Carolina 27599, United States
| | - Marius M Kostelic
- University of Arizona, Department of Chemistry and Biochemistry, Tucson, Arizona 85721, United States
| | - Chih-Chieh Hsieh
- University of Arizona, Department of Chemistry and Biochemistry, Tucson, Arizona 85721, United States
| | - Joshua Powers
- Institute for Bioscience and Biotechnology Research (NIST), Gaithersburg Maryland 20899, United States
- North Carolina State University, Biomanufacturing Training and Education Center (BTEC), Raleigh, North Carolina 27695, United States
| | - Craig Aspinwall
- University of Arizona, Department of Chemistry and Biochemistry, Tucson, Arizona 85721, United States
| | - James N Dodds
- University of North Carolina, Department of Chemistry, Chapel Hill, North Carolina 27599, United States
| | - John E Schiel
- Institute for Bioscience and Biotechnology Research (NIST), Gaithersburg Maryland 20899, United States
| | - Michael T Marty
- University of Arizona, Department of Chemistry and Biochemistry, Tucson, Arizona 85721, United States
| | - Erin S Baker
- University of North Carolina, Department of Chemistry, Chapel Hill, North Carolina 27599, United States
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9
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McGee JP, Su P, Durbin KR, Hollas MAR, Bateman NW, Maxwell GL, Conrads TP, Fellers RT, Melani RD, Camarillo JM, Kafader JO, Kelleher NL. Automated imaging and identification of proteoforms directly from ovarian cancer tissue. Nat Commun 2023; 14:6478. [PMID: 37838706 PMCID: PMC10576781 DOI: 10.1038/s41467-023-42208-3] [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: 02/21/2023] [Accepted: 09/28/2023] [Indexed: 10/16/2023] Open
Abstract
The molecular identification of tissue proteoforms by top-down mass spectrometry (TDMS) is significantly limited by throughput and dynamic range. We introduce AutoPiMS, a single-ion MS based multiplexed workflow for top-down tandem MS (MS2) directly from tissue microenvironments in a semi-automated manner. AutoPiMS directly off human ovarian cancer sections allowed for MS2 identification of 73 proteoforms up to 54 kDa at a rate of <1 min per proteoform. AutoPiMS is directly interfaced with multifaceted proteoform imaging MS data modalities for the identification of proteoform signatures in tumor and stromal regions in ovarian cancer biopsies. From a total of ~1000 proteoforms detected by region-of-interest label-free quantitation, we discover 303 differential proteoforms in stroma versus tumor from the same patient. 14 of the top proteoform signatures are corroborated by MSI at 20 micron resolution including the differential localization of methylated forms of CRIP1, indicating the importance of proteoform-enabled spatial biology in ovarian cancer.
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Affiliation(s)
- John P McGee
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Pei Su
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | | | | | - Nicholas W Bateman
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
- Department of Gynecologic Surgery and Obstetrics and the Gynecologic Cancer Center of Excellence, John P. Murtha Cancer Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - G Larry Maxwell
- Department of Gynecologic Surgery and Obstetrics and the Gynecologic Cancer Center of Excellence, John P. Murtha Cancer Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Women's Health Integrated Research Center, Inova Women's Service Line, Inova Health System, Falls Church, VA, USA
| | - Thomas P Conrads
- Department of Gynecologic Surgery and Obstetrics and the Gynecologic Cancer Center of Excellence, John P. Murtha Cancer Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Women's Health Integrated Research Center, Inova Women's Service Line, Inova Health System, Falls Church, VA, USA
| | | | - Rafael D Melani
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Jeannie M Camarillo
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Jared O Kafader
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Neil L Kelleher
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA.
- Proteomics Center of Excellence, Evanston, IL, USA.
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
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10
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Liu FC, Ridgeway ME, Wootton CA, Theisen A, Panczyk EM, Meier F, Park MA, Bleiholder C. Top-Down Protein Analysis by Tandem-Trapped Ion Mobility Spectrometry/Mass Spectrometry (Tandem-TIMS/MS) Coupled with Ultraviolet Photodissociation (UVPD) and Parallel Accumulation/Serial Fragmentation (PASEF) MS/MS Analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2232-2246. [PMID: 37638640 PMCID: PMC11162218 DOI: 10.1021/jasms.3c00187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Abstract
"Top-down" proteomics analyzes intact proteins and identifies proteoforms by their intact mass as well as the observed fragmentation pattern in tandem mass spectrometry (MS/MS) experiments. Recently, hybrid ion mobility spectrometry-mass spectrometry (IM/MS) methods have gained traction for top-down experiments, either by allowing top-down analysis of individual isomers or alternatively by improving signal/noise and dynamic range for fragment ion assignment. We recently described the construction of a tandem-trapped ion mobility spectrometer/mass spectrometer (tandem-TIMS/MS) coupled with an ultraviolet (UV) laser and demonstrated a proof-of-principle for top-down analysis by UV photodissociation (UVPD) at 2-3 mbar. The present work builds on this with an exploration of a top-down method that couples tandem-TIMS/MS with UVPD and parallel-accumulation serial fragmentation (PASEF) MS/MS analysis. We first survey types and structures of UVPD-specific fragment ions generated in the 2-3 mbar pressure regime of our instrument. Notably, we observe UVPD-induced fragment ions with multiple conformations that differ from those produced in the absence of UV irradiation. Subsequently, we discuss how MS/MS spectra of top-down fragment ions lend themselves ideally for probability-based scoring methods developed in the bottom-up proteomics field and how the ability to record automated PASEF-MS/MS spectra resolves ambiguities in the assignment of top-down fragment ions. Finally, we describe the coupling of tandem-TIMS/MS workflows with UVPD and PASEF-MS/MS analysis for native top-down protein analysis.
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Affiliation(s)
- Fanny C. Liu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32304, USA
| | | | | | | | | | - Florian Meier
- Functional Proteomics, Jena University Hospital, 07747 Jena, Germany
| | | | - Christian Bleiholder
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32304, USA
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11
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Kline JT, Melani RD, Fornelli L. Mass spectrometry characterization of antibodies at the intact and subunit levels: from targeted to large-scale analysis. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2023; 492:117117. [PMID: 38855125 PMCID: PMC11160972 DOI: 10.1016/j.ijms.2023.117117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Antibodies are one of the most formidable molecular weapons available to our immune system. Their high specificity against a target (antigen) and capability of triggering different immune responses (e.g., complement system activation and antibody-dependent cell-mediated cytotoxicity) make them ideal drugs to fight many different human diseases. Currently, both monoclonal antibodies and more complex molecules based on the antibody scaffold are used as biologics. Naturally, such highly heterogeneous molecules require dedicated analytical methodologies for their accurate characterization. Mass spectrometry (MS) can define the presence and relative abundance of multiple features of antibodies, including critical quality attributes. The combination of small and large variations within a single molecule can only be determined by analyzing intact antibodies or their large (25 to 100 kDa) subunits. Hence, top-down (TD) and middle-down (MD) MS approaches have gained popularity over the last decade. In this Young Scientist Feature we discuss the evolution of TD and MD MS analysis of antibodies, including the new frontiers that go beyond biopharma applications. We will show how this field is now moving from the "quality control" analysis of a known, single antibody to the high-throughput investigation of complex antibody repertoires isolated from clinical samples, where the ultimate goal is represented by the complete gas-phase sequencing of antibody molecules without the need of any a priori knowledge.
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Affiliation(s)
- Jake T. Kline
- Department of Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Rafael D. Melani
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Luca Fornelli
- Department of Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
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12
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Lermyte F, Habeck T, Brown K, Des Soye B, Lantz C, Zhou M, Alam N, Hossain MA, Jung W, Keener J, Volny M, Wilson J, Ying Y, Agar J, Danis P, Ge Y, Kelleher N, Li H, Loo J, Marty M, Pasa-Tolic L, Sandoval W. Top-down mass spectrometry of native proteoforms and their complexes: A community study. RESEARCH SQUARE 2023:rs.3.rs-3228472. [PMID: 37674709 PMCID: PMC10479449 DOI: 10.21203/rs.3.rs-3228472/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
The combination of native electrospray ionisation with top-down fragmentation in mass spectrometry allows simultaneous determination of the stoichiometry of noncovalent complexes and identification of their component proteoforms and co-factors. While this approach is powerful, both native mass spectrometry and top-down mass spectrometry are not yet well standardised, and only a limited number of laboratories regularly carry out this type of research. To address this challenge, the Consortium for Top-Down Proteomics (CTDP) initiated a study to develop and test protocols for native mass spectrometry combined with top-down fragmentation of proteins and protein complexes across eleven instruments in nine laboratories. The outcomes are summarised in this report to provide robust benchmarks and a valuable entry point for the scientific community.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Jeffrey Agar
- Department of Chemistry and Chemical Biology, Northeastern University
| | | | - Ying Ge
- University of Wisconsin-Madison
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13
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Faizi M, Fellers RT, Lu D, Drown BS, Jambhekar A, Lahav G, Kelleher NL, Gunawardena J. MSModDetector: A Tool for Detecting Mass Shifts and Post-Translational Modifications in Individual Ion Mass Spectrometry Data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.06.543961. [PMID: 37333327 PMCID: PMC10274720 DOI: 10.1101/2023.06.06.543961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Motivation Post-translational modifications (PTMs) on proteins regulate protein structures and functions. A single protein molecule can possess multiple modification sites that can accommodate various PTM types, leading to a variety of different patterns, or combinations of PTMs, on that protein. Different PTM patterns can give rise to distinct biological functions. To facilitate the study of multiple PTMs, top-down mass spectrometry (MS) has proven to be a useful tool to measure the mass of intact proteins, thereby enabling even widely separated PTMs to be assigned to the same protein molecule and allowing determination of how many PTMs are attached to a single protein. Results We developed a Python module called MSModDetector that studies PTM patterns from individual ion mass spectrometry (I MS) data. I MS is an intact protein mass spectrometry approach that generates true mass spectra without the need to infer charge states. The algorithm first detects and quantifies mass shifts for a protein of interest and subsequently infers potential PTM patterns using linear programming. The algorithm is evaluated on simulated I MS data and experimental I MS data for the tumor suppressor protein p53. We show that MSModDetector is a useful tool for comparing a protein's PTM pattern landscape across different conditions. An improved analysis of PTM patterns will enable a deeper understanding of PTM-regulated cellular processes. Availability The source code is available at https://github.com/marjanfaizi/MSModDetector together with the scripts used for analyses and to generate the figures presented in this study.
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14
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Dafun AS, Živković D, Leon-Icaza SA, Möller S, Froment C, Bonnet D, de Jesus AA, Alric L, Quaranta-Nicaise M, Ferrand A, Cougoule C, Meunier E, Burlet-Schiltz O, Ebstein F, Goldbach-Mansky R, Krüger E, Bousquet MP, Marcoux J. Establishing 20S Proteasome Genetic, Translational and Post-Translational Status from Precious Biological and Patient Samples with Top-Down MS. Cells 2023; 12:cells12060844. [PMID: 36980185 PMCID: PMC10047880 DOI: 10.3390/cells12060844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/23/2023] [Accepted: 02/27/2023] [Indexed: 03/11/2023] Open
Abstract
The mammalian 20S catalytic core of the proteasome is made of 14 different subunits (α1-7 and β1-7) but exists as different subtypes depending on the cell type. In immune cells, for instance, constitutive catalytic proteasome subunits can be replaced by the so-called immuno-catalytic subunits, giving rise to the immunoproteasome. Proteasome activity is also altered by post-translational modifications (PTMs) and by genetic variants. Immunochemical methods are commonly used to investigate these PTMs whereby protein-tagging is necessary to monitor their effect on 20S assembly. Here, we present a new miniaturized workflow combining top-down and bottom-up mass spectrometry of immunopurified 20S proteasomes that analyze the proteasome assembly status as well as the full proteoform footprint, revealing PTMs, mutations, single nucleotide polymorphisms (SNPs) and induction of immune-subunits in different biological samples, including organoids, biopsies and B-lymphoblastoid cell lines derived from patients with proteasome-associated autoinflammatory syndromes (PRAAS). We emphasize the benefits of using top-down mass spectrometry in preserving the endogenous conformation of protein modifications, while enabling a rapid turnaround (1 h run) and ensuring high sensitivity (1–2 pmol) and demonstrate its capacity to semi-quantify constitutive and immune proteasome subunits.
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Affiliation(s)
- Angelique Sanchez Dafun
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III—Paul Sabatier (UPS), 31077 Toulouse, France
| | - Dušan Živković
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III—Paul Sabatier (UPS), 31077 Toulouse, France
| | - Stephen Adonai Leon-Icaza
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III—Paul Sabatier (UPS), 31077 Toulouse, France
| | - Sophie Möller
- Institute of Medical Biochemistry and Molecular Biology, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Carine Froment
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III—Paul Sabatier (UPS), 31077 Toulouse, France
| | - Delphine Bonnet
- IRSD, Université de Toulouse, INSERM, INRAE, ENVT, Université de Toulouse III—Paul Sabatier (UPS), 31300 Toulouse, France
- Internal Medicine Department of Digestive Disease, Rangueil Hospital, Université de Toulouse III—Paul Sabatier (UPS), 31400 Toulouse, France
| | - Adriana Almeida de Jesus
- Translational Autoinflammatory Diseases Section, LCIM, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Laurent Alric
- Internal Medicine Department of Digestive Disease, Rangueil Hospital, Université de Toulouse III—Paul Sabatier (UPS), 31400 Toulouse, France
| | - Muriel Quaranta-Nicaise
- IRSD, Université de Toulouse, INSERM, INRAE, ENVT, Université de Toulouse III—Paul Sabatier (UPS), 31300 Toulouse, France
| | - Audrey Ferrand
- IRSD, Université de Toulouse, INSERM, INRAE, ENVT, Université de Toulouse III—Paul Sabatier (UPS), 31300 Toulouse, France
| | - Céline Cougoule
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III—Paul Sabatier (UPS), 31077 Toulouse, France
| | - Etienne Meunier
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III—Paul Sabatier (UPS), 31077 Toulouse, France
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III—Paul Sabatier (UPS), 31077 Toulouse, France
| | - Frédéric Ebstein
- Institute of Medical Biochemistry and Molecular Biology, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Raphaela Goldbach-Mansky
- Translational Autoinflammatory Diseases Section, LCIM, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Elke Krüger
- Institute of Medical Biochemistry and Molecular Biology, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Marie-Pierre Bousquet
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III—Paul Sabatier (UPS), 31077 Toulouse, France
- Correspondence: (M.-P.B.); (J.M.)
| | - Julien Marcoux
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III—Paul Sabatier (UPS), 31077 Toulouse, France
- Correspondence: (M.-P.B.); (J.M.)
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15
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Eberwine J, Kim J, Anafi RC, Brem S, Bucan M, Fisher SA, Grady MS, Herr AE, Issadore D, Jeong H, Kim H, Lee D, Rubakhin S, Sul JY, Sweedler JV, Wolf JA, Zaret KS, Zou J. Subcellular omics: a new frontier pushing the limits of resolution, complexity and throughput. Nat Methods 2023; 20:331-335. [PMID: 36899160 PMCID: PMC10049458 DOI: 10.1038/s41592-023-01788-0] [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: 03/12/2023]
Abstract
We argue that the study of single-cell subcellular organelle omics is needed to understand and regulate cell function. This requires and is being enabled by new technology development.
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Affiliation(s)
- James Eberwine
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Junhyong Kim
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA.
| | - Ron C Anafi
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Steven Brem
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Maja Bucan
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Stephen A Fisher
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - M Sean Grady
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Amy E Herr
- Department of Bioengineering, University of California at Berkeley, Berkeley, CA, USA
| | - David Issadore
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Hyejoong Jeong
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
- Department of Chemical and Biomolecular Engineering, , University of Pennsylvania, Philadelphia, PA, USA
| | - HyunBum Kim
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Daeyeon Lee
- Department of Chemical and Biomolecular Engineering, , University of Pennsylvania, Philadelphia, PA, USA
| | - Stanislav Rubakhin
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jai-Yoon Sul
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jonathan V Sweedler
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - John A Wolf
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kenneth S Zaret
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - James Zou
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
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16
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Nickerson JL, Baghalabadi V, Rajendran SRCK, Jakubec PJ, Said H, McMillen TS, Dang Z, Doucette AA. Recent advances in top-down proteome sample processing ahead of MS analysis. MASS SPECTROMETRY REVIEWS 2023; 42:457-495. [PMID: 34047392 DOI: 10.1002/mas.21706] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/21/2021] [Accepted: 05/06/2021] [Indexed: 06/12/2023]
Abstract
Top-down proteomics is emerging as a preferred approach to investigate biological systems, with objectives ranging from the detailed assessment of a single protein therapeutic, to the complete characterization of every possible protein including their modifications, which define the human proteoform. Given the controlling influence of protein modifications on their biological function, understanding how gene products manifest or respond to disease is most precisely achieved by characterization at the intact protein level. Top-down mass spectrometry (MS) analysis of proteins entails unique challenges associated with processing whole proteins while maintaining their integrity throughout the processes of extraction, enrichment, purification, and fractionation. Recent advances in each of these critical front-end preparation processes, including minimalistic workflows, have greatly expanded the capacity of MS for top-down proteome analysis. Acknowledging the many contributions in MS technology and sample processing, the present review aims to highlight the diverse strategies that have forged a pathway for top-down proteomics. We comprehensively discuss the evolution of front-end workflows that today facilitate optimal characterization of proteoform-driven biology, including a brief description of the clinical applications that have motivated these impactful contributions.
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Affiliation(s)
| | - Venus Baghalabadi
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Subin R C K Rajendran
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
- Verschuren Centre for Sustainability in Energy and the Environment, Sydney, Nova Scotia, Canada
| | - Philip J Jakubec
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Hammam Said
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Teresa S McMillen
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Ziheng Dang
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Alan A Doucette
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
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17
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McGee JP, Senko MW, Jooß K, Des Soye BJ, Compton PD, Kelleher NL, Kafader JO. Automated Control of Injection Times for Unattended Acquisition of Multiplexed Individual Ion Mass Spectra. Anal Chem 2022; 94:16543-16548. [PMID: 36416365 PMCID: PMC9969899 DOI: 10.1021/acs.analchem.2c03495] [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: 11/24/2022]
Abstract
Charge detection mass spectrometry (CDMS) provides mass domain spectra of large and highly heterogeneous analytes. Over the past few years, we have multiplexed CDMS on Orbitrap instruments, an approach termed Individual Ion Mass Spectrometry (I2MS). Until now, I2MS required manual adjustment of injection times to collect spectra in the individual ion regime. To increase sample adaptability, enable online separations, and reduce the barrier for entry, we report an automated method for adjusting ion injection times in I2MS for image current detectors like the Orbitrap. Automatic Ion Control (AIC) utilizes the density of signals in the m/z domain to adjust an ensemble of ions down to the individual ion regime in real-time. The AIC technique was applied to both denatured and native proteins yielding high quality data without human intervention directly in the mass domain.
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Affiliation(s)
- 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, Illinois60208, United States
| | - Michael W Senko
- Thermo Fisher Scientific, San Jose, California95134, United States
| | - Kevin Jooß
- 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, Illinois60208, United States
| | - Benjamin J Des Soye
- 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, Illinois60208, United States
| | - Philip D Compton
- Integrated Protein Technologies, Inc., Evanston, Illinois60201, 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, Illinois60208, 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, Illinois60208, United States
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18
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Brodbelt JS. Deciphering combinatorial post-translational modifications by top-down mass spectrometry. Curr Opin Chem Biol 2022; 70:102180. [PMID: 35779351 PMCID: PMC9489649 DOI: 10.1016/j.cbpa.2022.102180] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/30/2022] [Accepted: 05/31/2022] [Indexed: 12/15/2022]
Abstract
Post-translational modifications (PTMs) create vast structural and functional diversity of proteins, ultimately modulating protein function and degradation, influencing cellular signaling, and regulating transcription. The combinatorial patterns of PTMs increase the heterogeneity of proteins and further mediates their interactions. Advances in mass spectrometry-based proteomics have resulted in identification of thousands of proteins and allowed characterization of numerous types and sites of PTMs. Examination of intact proteins, termed the top-down approach, offers the potential to map protein sequences and localize multiple PTMs on each protein, providing the most comprehensive cataloging of proteoforms. This review describes some of the dividends of using mass spectrometry to analyze intact proteins and showcases innovative strategies that have enhanced the promise of top-down proteomics for exploring the impact of combinatorial PTMs in unsurpassed detail.
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Affiliation(s)
- Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
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19
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Su P, McGee JP, Durbin KR, Hollas MAR, Yang M, Neumann EK, Allen JL, Drown BS, Butun FA, Greer JB, Early BP, Fellers RT, Spraggins JM, Laskin J, Camarillo JM, Kafader JO, Kelleher NL. Highly multiplexed, label-free proteoform imaging of tissues by individual ion mass spectrometry. SCIENCE ADVANCES 2022; 8:eabp9929. [PMID: 35947651 PMCID: PMC9365283 DOI: 10.1126/sciadv.abp9929] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 06/24/2022] [Indexed: 05/25/2023]
Abstract
Imaging of proteoforms in human tissues is hindered by low molecular specificity and limited proteome coverage. Here, we introduce proteoform imaging mass spectrometry (PiMS), which increases the size limit for proteoform detection and identification by fourfold compared to reported methods and reveals tissue localization of proteoforms at <80-μm spatial resolution. PiMS advances proteoform imaging by combining ambient nanospray desorption electrospray ionization with ion detection using individual ion mass spectrometry. We demonstrate highly multiplexed proteoform imaging of human kidney, annotating 169 of 400 proteoforms of <70 kDa using top-down MS and a database lookup of ~1000 kidney candidate proteoforms, including dozens of key enzymes in primary metabolism. PiMS images reveal distinct spatial localizations of proteoforms to both anatomical structures and cellular neighborhoods in the vasculature, medulla, and cortex regions of the human kidney. The benefits of PiMS are poised to increase proteome coverage for label-free protein imaging of tissues.
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Affiliation(s)
- Pei Su
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - John P. McGee
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Kenneth R. Durbin
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Michael A. R. Hollas
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Manxi Yang
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Elizabeth K. Neumann
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
| | - Jamie L. Allen
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
| | - Bryon S. Drown
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | | | - Joseph B. Greer
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Bryan P. Early
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Ryan T. Fellers
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Jeffrey M. Spraggins
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
- Departments of Chemistry and Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Julia Laskin
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Jeannie M. Camarillo
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
| | - Jared O. Kafader
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
| | - Neil L. Kelleher
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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20
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Yang M, Hu H, Su P, Thomas PM, Camarillo JM, Greer JB, Early BP, Fellers RT, Kelleher NL, Laskin J. Proteoform-Selective Imaging of Tissues Using Mass Spectrometry. Angew Chem Int Ed Engl 2022; 61:e202200721. [PMID: 35446460 PMCID: PMC9276647 DOI: 10.1002/anie.202200721] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Indexed: 01/28/2023]
Abstract
Unraveling the complexity of biological systems relies on the development of new approaches for spatially resolved proteoform‐specific analysis of the proteome. Herein, we employ nanospray desorption electrospray ionization mass spectrometry imaging (nano‐DESI MSI) for the proteoform‐selective imaging of biological tissues. Nano‐DESI generates multiply charged protein ions, which is advantageous for their structural characterization using tandem mass spectrometry (MS/MS) directly on the tissue. Proof‐of‐concept experiments demonstrate that nano‐DESI MSI combined with on‐tissue top‐down proteomics is ideally suited for the proteoform‐selective imaging of tissue sections. Using rat brain tissue as a model system, we provide the first evidence of differential proteoform expression in different regions of the brain.
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Affiliation(s)
- Manxi Yang
- Department of ChemistryPurdue University560 Oval DriveWest LafayetteIN 47907USA
| | - Hang Hu
- Department of ChemistryPurdue University560 Oval DriveWest LafayetteIN 47907USA
| | - Pei Su
- Department of ChemistryPurdue University560 Oval DriveWest LafayetteIN 47907USA
- Departments of Chemistry and Molecular BiosciencesNorthwestern University2145 Sheridan RoadEvanstonIL 60208USA
| | - Paul M. Thomas
- Departments of Chemistry and Molecular BiosciencesNorthwestern University2145 Sheridan RoadEvanstonIL 60208USA
| | - Jeannie M. Camarillo
- Departments of Chemistry and Molecular BiosciencesNorthwestern University2145 Sheridan RoadEvanstonIL 60208USA
| | - Joseph B. Greer
- Departments of Chemistry and Molecular BiosciencesNorthwestern University2145 Sheridan RoadEvanstonIL 60208USA
| | - Bryan P. Early
- Departments of Chemistry and Molecular BiosciencesNorthwestern University2145 Sheridan RoadEvanstonIL 60208USA
| | - Ryan T. Fellers
- Departments of Chemistry and Molecular BiosciencesNorthwestern University2145 Sheridan RoadEvanstonIL 60208USA
| | - Neil L. Kelleher
- Departments of Chemistry and Molecular BiosciencesNorthwestern University2145 Sheridan RoadEvanstonIL 60208USA
| | - Julia Laskin
- Department of ChemistryPurdue University560 Oval DriveWest LafayetteIN 47907USA
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21
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Liu R, Xia S, Li H. Native top-down mass spectrometry for higher-order structural characterization of proteins and complexes. MASS SPECTROMETRY REVIEWS 2022:e21793. [PMID: 35757976 DOI: 10.1002/mas.21793] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Progress in structural biology research has led to a high demand for powerful and yet complementary analytical tools for structural characterization of proteins and protein complexes. This demand has significantly increased interest in native mass spectrometry (nMS), particularly native top-down mass spectrometry (nTDMS) in the past decade. This review highlights recent advances in nTDMS for structural research of biological assemblies, with a particular focus on the extra multi-layers of information enabled by TDMS. We include a short introduction of sample preparation and ionization to nMS, tandem fragmentation techniques as well as mass analyzers and software/analysis pipelines used for nTDMS. We highlight unique structural information offered by nTDMS and examples of its broad range of applications in proteins, protein-ligand interactions (metal, cofactor/drug, DNA/RNA, and protein), therapeutic antibodies and antigen-antibody complexes, membrane proteins, macromolecular machineries (ribosome, nucleosome, proteosome, and viruses), to endogenous protein complexes. The challenges, potential, along with perspectives of nTDMS methods for the analysis of proteins and protein assemblies in recombinant and biological samples are discussed.
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Affiliation(s)
- Ruijie Liu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shujun Xia
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Huilin Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
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22
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Liu FC, Kirk SR, Caldwell KA, Pedrete T, Meier F, Bleiholder C. Tandem Trapped Ion Mobility Spectrometry/Mass Spectrometry (tTIMS/MS) Reveals Sequence-Specific Determinants of Top-Down Protein Fragment Ion Cross Sections. Anal Chem 2022; 94:8146-8155. [PMID: 35621336 PMCID: PMC10032035 DOI: 10.1021/acs.analchem.1c05171] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Top-down proteomics provides a straightforward approach to the level of proteoforms but remains technologically challenging. Using ion mobility spectrometry/mass spectrometry (IMS/MS) to separate top-down fragment ions improves signal/noise and dynamic range. Such applications, however, do not yet leverage the primary information obtained from IMS/MS, which is the characterization of the fragment ion structure by the measured momentum transfer cross sections. Here, we perform top-down analysis of intact proteins and assemblies using our tandem trapped ion mobility spectrometer/mass spectrometer (tTIMS/MS) and compile over 1400 cross section values of fragment ions. Our analysis reveals that most fragment ions exhibit multiple, stable conformations similar to those of intact polypeptides and proteins. The data further indicate that the conformational heterogeneity is strongly influenced by the amino acid sequences of the fragment ions. Moreover, time-resolved tTIMS/MS experiments reveal that conformations of top-down fragment ions can be metastable on the timescale of ion mobility measurements. Taken together, our analysis indicates that top-down fragment ions undergo a folding process in the gas phase and that this folding process can lead to kinetic trapping of intermediate states in ion mobility measurements. Hence, because the folding free energy surface of a polypeptide ion is encoded by its amino acid sequence and charge state, our analysis suggests that cross sections can be exploited as sequence-specific determinants of top-down fragment ions.
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Affiliation(s)
- Fanny C. Liu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4390, USA
| | - Samuel R. Kirk
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4390, USA
| | - Kirsten A. Caldwell
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4390, USA
| | - Thais Pedrete
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4390, USA
| | - Florian Meier
- Functional Proteomics, Jena University Hospital, 07747 Jena, Germany
| | - Christian Bleiholder
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4390, USA
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4390, USA
- Corresponding Author
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23
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Eller MJ, Sandoval JM, Verkhoturov SV, Schweikert EA. Nanoprojectile Secondary Ion Mass Spectrometry for Nanometrology of Nanoparticles and Their Interfaces. Anal Chem 2022; 94:7868-7876. [PMID: 35594187 DOI: 10.1021/acs.analchem.2c00303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nanoscale molecular characterization plays a crucial role in enhancing our insights into fundamental and materials processes occurring at the nanoscale. However, for many traditional techniques, measurements on different ensembles are mixed and the analytical result reflects the average surface composition or arrangement. Advances in nanometrologies that allow for measurements to be differentiated based on the chemical environment examined are critical for accurate analysis. Here, we present a variant of secondary ion mass spectrometry, SIMS, termed nanoprojectile SIMS, NP-SIMS, capable of nanoscale molecular analysis. The technique examines the sample with a suite, 106-107, of individual gold nanoprojectiles (e.g., Au4004+) which stochastically probe the surface. Analysis of coemitted ions from each impact allows for the inspection of colocalized moieties within the ejected volume of a single projectile impact (10-15 nm in diameter). If some of these 106-107 measurements arise from nanodomains of similar composition, data can be grouped based on the detected secondary ions. We applied the method to examine a mixture of three different-sized nanoparticles with identical metal cores (3-5 nm in diameter), differing in the length of the attached ligand (decanetiol, tetradecanethiol, and hexadecanethiol). Using NP-SIMS, we determined the relative abundance of the three particles on the surface and isolated measurements based on the impact parameter between the impacting nanoprojectile and the surface particle, demonstrating that measurements occurring near the center of the particle can be differentiated from those at the particle-particle and particle-substrate interfaces. The results suggest that the described methodology is well-suited for molecular analysis of nanoassemblies and may be applied for tracking defects. Here we demonstrate that, using NP-SIMS, ensemble averaging can be avoided and molecular analysis can be undertaken at a scale below 5 nm, allowing for nanoscale molecular analysis of nano-objects and their interfaces.
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Affiliation(s)
- Michael J Eller
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Jesse M Sandoval
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | | | - Emile A Schweikert
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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24
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Snyder DT, Harvey SR, Wysocki VH. Surface-induced Dissociation Mass Spectrometry as a Structural Biology Tool. Chem Rev 2022; 122:7442-7487. [PMID: 34726898 PMCID: PMC9282826 DOI: 10.1021/acs.chemrev.1c00309] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Native mass spectrometry (nMS) is evolving into a workhorse for structural biology. The plethora of online and offline preparation, separation, and purification methods as well as numerous ionization techniques combined with powerful new hybrid ion mobility and mass spectrometry systems has illustrated the great potential of nMS for structural biology. Fundamental to the progression of nMS has been the development of novel activation methods for dissociating proteins and protein complexes to deduce primary, secondary, tertiary, and quaternary structure through the combined use of multiple MS/MS technologies. This review highlights the key features and advantages of surface collisions (surface-induced dissociation, SID) for probing the connectivity of subunits within protein and nucleoprotein complexes and, in particular, for solving protein structure in conjunction with complementary techniques such as cryo-EM and computational modeling. Several case studies highlight the significant role SID, and more generally nMS, will play in structural elucidation of biological assemblies in the future as the technology becomes more widely adopted. Cases are presented where SID agrees with solved crystal or cryoEM structures or provides connectivity maps that are otherwise inaccessible by "gold standard" structural biology techniques.
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Affiliation(s)
- Dalton T. Snyder
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
| | - Sophie R. Harvey
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
| | - Vicki H. Wysocki
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210,Corresponding author:
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25
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Yang M, Hu H, Su P, Thomas PM, Camarillo JM, Greer JB, Early BP, Fellers RT, Kelleher NL, Laskin J. Proteoform‐Selective Imaging of Tissues Using Mass Spectrometry. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202200721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Manxi Yang
- Purdue University Department of Chemistry chemistry 560 Oval Dr. 47906 West Lafayette UNITED STATES
| | - Hang Hu
- Purdue University Chemistry UNITED STATES
| | - Pei Su
- Northwestern University Chemistry and Molecular Biosciences UNITED STATES
| | - Paul M. Thomas
- Northwestern University Chemistry and Molecular Biosciences UNITED STATES
| | | | - Joseph B. Greer
- Northwestern University Chemistry and Molecular Biosciences UNITED STATES
| | - Bryan P. Early
- Northwestern University Chemistry and Molecular Biosciences UNITED STATES
| | - Ryan T. Fellers
- Northwestern University Chemistry and Molecular Biosciences UNITED STATES
| | - Neil L. Kelleher
- Northwestern University Chemistry and Molecular Biosciences UNITED STATES
| | - Julia Laskin
- Purdue University Department of Chemistry 560 Oval Dr. 47907 West Lafayette UNITED STATES
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26
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Melani RD, Des Soye BJ, Kafader JO, Forte E, Hollas M, Blagojevic V, Negrão F, McGee JP, Drown B, Lloyd-Jones C, Seckler HS, Camarillo JM, Compton PD, LeDuc RD, Early B, Fellers RT, Cho BK, Mattamana BB, Goo YA, Thomas PM, Ash MK, Bhimalli PP, Al-Harthi L, Sha BE, Schneider JR, Kelleher NL. Next-Generation Serology by Mass Spectrometry: Readout of the SARS-CoV-2 Antibody Repertoire. J Proteome Res 2022; 21:274-288. [PMID: 34878788 PMCID: PMC8673472 DOI: 10.1021/acs.jproteome.1c00882] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Indexed: 01/03/2023]
Abstract
Methods of antibody detection are used to assess exposure or immunity to a pathogen. Here, we present Ig-MS, a novel serological readout that captures the immunoglobulin (Ig) repertoire at molecular resolution, including entire variable regions in Ig light and heavy chains. Ig-MS uses recent advances in protein mass spectrometry (MS) for multiparametric readout of antibodies, with new metrics like Ion Titer (IT) and Degree of Clonality (DoC) capturing the heterogeneity and relative abundance of individual clones without sequencing of B cells. We applied Ig-MS to plasma from subjects with severe and mild COVID-19 and immunized subjects after two vaccine doses, using the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2 as the bait for antibody capture. Importantly, we report a new data type for human serology, that could use other antigens of interest to gauge immune responses to vaccination, pathogens, or autoimmune disorders.
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Affiliation(s)
- Rafael D. Melani
- Departments of Molecular Biosciences, Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - Benjamin J. Des Soye
- Departments of Molecular Biosciences, Chemistry, Northwestern University, Evanston, IL, 60208, USA
- Proteomics Center of Excellence, Evanston, IL, 60208, USA
| | - Jared O. Kafader
- Departments of Molecular Biosciences, Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - Eleonora Forte
- Proteomics Center of Excellence, Evanston, IL, 60208, USA
- Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Michael Hollas
- Departments of Molecular Biosciences, Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - Voislav Blagojevic
- Departments of Molecular Biosciences, Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - Fernanda Negrão
- Departments of Molecular Biosciences, Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - John P. McGee
- Departments of Molecular Biosciences, Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - Bryon Drown
- Departments of Molecular Biosciences, Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - Cameron Lloyd-Jones
- Departments of Molecular Biosciences, Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - Henrique S. Seckler
- Departments of Molecular Biosciences, Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - Jeannie M. Camarillo
- Departments of Molecular Biosciences, Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - Philip D. Compton
- Departments of Molecular Biosciences, Chemistry, Northwestern University, Evanston, IL, 60208, USA
- Integrated Protein Technologies, Evanston, IL, 60201, USA
| | - Richard D. LeDuc
- Departments of Molecular Biosciences, Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - Bryan Early
- Departments of Molecular Biosciences, Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - Ryan T. Fellers
- Departments of Molecular Biosciences, Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - Byoung-Kyu Cho
- Proteomics Center of Excellence, Evanston, IL, 60208, USA
| | | | - Young Ah Goo
- Departments of Molecular Biosciences, Chemistry, Northwestern University, Evanston, IL, 60208, USA
- Proteomics Center of Excellence, Evanston, IL, 60208, USA
| | - Paul M. Thomas
- Departments of Molecular Biosciences, Chemistry, Northwestern University, Evanston, IL, 60208, USA
- Proteomics Center of Excellence, Evanston, IL, 60208, USA
| | - Michelle K. Ash
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Pavan P. Bhimalli
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Lena Al-Harthi
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Beverly E. Sha
- Division of Infectious Diseases, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Jeffrey R. Schneider
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Neil L. Kelleher
- Departments of Molecular Biosciences, Chemistry, Northwestern University, Evanston, IL, 60208, USA
- Proteomics Center of Excellence, Evanston, IL, 60208, USA
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611 USA
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27
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Macias LA, Sipe SN, Santos IC, Bashyal A, Mehaffey MR, Brodbelt JS. Influence of Primary Structure on Fragmentation of Native-Like Proteins by Ultraviolet Photodissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2860-2873. [PMID: 34714071 PMCID: PMC8639798 DOI: 10.1021/jasms.1c00269] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Analysis of native-like protein structures in the gas phase via native mass spectrometry and auxiliary techniques has become a powerful tool for structural biology applications. In combination with ultraviolet photodissociation (UVPD), native top-down mass spectrometry informs backbone flexibility, topology, hydrogen bonding networks, and conformational changes in protein structure. Although it is known that the primary structure affects dissociation of peptides and proteins in the gas phase, its effect on the types and locations of backbone cleavages promoted by UVPD and concomitant influence on structural characterization of native-like proteins is not well understood. Here, trends in the fragmentation of native-like proteins were evaluated by tracking the propensity of 10 fragment types (a, a+1, b, c, x, x+1, y, y-1, Y, and z) in relation to primary structure in a native-top down UVPD data set encompassing >9600 fragment ions. Differing fragmentation trends are reported for the production of distinct fragment types, attributed to a combination of both direct dissociation pathways from excited electronic states and those surmised to involve intramolecular vibrational energy redistribution after internal conversion. The latter pathways were systematically evaluated to evince the role of proton mobility in the generation of "CID-like" fragments through UVPD, providing pertinent insight into the characterization of native-like proteins. Fragmentation trends presented here are envisioned to enhance analysis of the protein higher-order structure or augment scoring algorithms in the high-throughput analysis of intact proteins.
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Affiliation(s)
- Luis A Macias
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Sarah N Sipe
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Inês C Santos
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Aarti Bashyal
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - M Rachel Mehaffey
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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28
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Lai SH, Tamara S, Heck AJ. Single-particle mass analysis of intact ribosomes by mass photometry and Orbitrap-based charge detection mass spectrometry. iScience 2021; 24:103211. [PMID: 34712917 PMCID: PMC8529500 DOI: 10.1016/j.isci.2021.103211] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 09/04/2021] [Accepted: 09/29/2021] [Indexed: 12/28/2022] Open
Abstract
Standard methods for mass analysis measure ensembles of thousand to millions of molecules. This approach enables analysis of monodisperse recombinant proteins, whereas some heterogeneous protein assemblies pose a significant challenge, whereby co-occurring stoichiometries, sub-complexes, and modifications hamper analysis using native mass spectrometry. To tackle the challenges posed by mass heterogeneity, single-particle methods may come to the rescue. Recently, two such approaches have been introduced, namely, mass photometry (MP) and Orbitrap-based charge detection mass spectrometry (CDMS). Both methods assess masses of individual molecules, albeit adhering to distinct physical principles. To evaluate these methods side by side, we analyzed a set of ribosomal particles, representing polydisperse ribonucleoprotein assemblies in the MDa range. MP and CDMS provide accurate masses for intact ribosomes and enable quantitative analysis of concomitant distinct particles within each ribosome sample. Here, we discuss pros and cons of these single-molecule techniques, also in the context of other techniques used for mass analysis.
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Affiliation(s)
- Szu-Hsueh Lai
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Sem Tamara
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Albert J.R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
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29
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Koudelka T, Winkels K, Kaleja P, Tholey A. Shedding light on both ends: An update on analytical approaches for N- and C-terminomics. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1869:119137. [PMID: 34626679 DOI: 10.1016/j.bbamcr.2021.119137] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/27/2021] [Accepted: 09/06/2021] [Indexed: 02/04/2023]
Abstract
Though proteases were long regarded as nonspecific degradative enzymes, over time, it was recognized that they also hydrolyze peptide bonds very specifically with a limited substrate pool. This irreversible posttranslational modification modulates the fate and activity of many proteins, making proteolytic processing a master switch in the regulation of e.g., the immune system, apoptosis and cancer progression. N- and C-terminomics, the identification of protein termini, has become indispensable in elucidating protease substrates and therefore protease function. Further, terminomics has the potential to identify yet unknown proteoforms, e.g. formed by alternative splicing or the recently discovered alternative ORFs. Different strategies and workflows have been developed that achieve higher sensitivity, a greater depth of coverage or higher throughput. In this review, we summarize recent developments in both N- and C-terminomics and include the potential of top-down proteomics which inherently delivers information on both ends of analytes in a single analysis.
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Affiliation(s)
- Tomas Koudelka
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Konrad Winkels
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Patrick Kaleja
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Andreas Tholey
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.
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30
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Abstract
Native mass spectrometry (MS) is aimed at preserving and determining the native structure, composition, and stoichiometry of biomolecules and their complexes from solution after they are transferred into the gas phase. Major improvements in native MS instrumentation and experimental methods over the past few decades have led to a concomitant increase in the complexity and heterogeneity of samples that can be analyzed, including protein-ligand complexes, protein complexes with multiple coexisting stoichiometries, and membrane protein-lipid assemblies. Heterogeneous features of these biomolecular samples can be important for understanding structure and function. However, sample heterogeneity can make assignment of ion mass, charge, composition, and structure very challenging due to the overlap of tens or even hundreds of peaks in the mass spectrum. In this review, we cover data analysis, experimental, and instrumental advances and strategies aimed at solving this problem, with an in-depth discussion of theoretical and practical aspects of the use of available deconvolution algorithms and tools. We also reflect upon current challenges and provide a view of the future of this exciting field.
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Affiliation(s)
- Amber D Rolland
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
| | - James S Prell
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States.,Materials Science Institute, University of Oregon, Eugene, Oregon 97403-1252, United States
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31
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Carbonara K, Andonovski M, Coorssen JR. Proteomes Are of Proteoforms: Embracing the Complexity. Proteomes 2021; 9:38. [PMID: 34564541 PMCID: PMC8482110 DOI: 10.3390/proteomes9030038] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 08/24/2021] [Accepted: 08/29/2021] [Indexed: 12/17/2022] Open
Abstract
Proteomes are complex-much more so than genomes or transcriptomes. Thus, simplifying their analysis does not simplify the issue. Proteomes are of proteoforms, not canonical proteins. While having a catalogue of amino acid sequences provides invaluable information, this is the Proteome-lite. To dissect biological mechanisms and identify critical biomarkers/drug targets, we must assess the myriad of proteoforms that arise at any point before, after, and between translation and transcription (e.g., isoforms, splice variants, and post-translational modifications [PTM]), as well as newly defined species. There are numerous analytical methods currently used to address proteome depth and here we critically evaluate these in terms of the current 'state-of-the-field'. We thus discuss both pros and cons of available approaches and where improvements or refinements are needed to quantitatively characterize proteomes. To enable a next-generation approach, we suggest that advances lie in transdisciplinarity via integration of current proteomic methods to yield a unified discipline that capitalizes on the strongest qualities of each. Such a necessary (if not revolutionary) shift cannot be accomplished by a continued primary focus on proteo-genomics/-transcriptomics. We must embrace the complexity. Yes, these are the hard questions, and this will not be easy…but where is the fun in easy?
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Affiliation(s)
| | | | - Jens R. Coorssen
- Faculties of Applied Health Sciences and Mathematics & Science, Departments of Health Sciences and Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON L2S 3A1, Canada; (K.C.); (M.A.)
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32
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Melani RD, Soye BJD, Kafader JO, Forte E, Hollas M, Blagojevic V, Negrão F, McGee JP, Drown B, Lloyd-Jones C, Seckler HS, Camarillo JM, Compton PD, LeDuc RD, Early B, Fellers RT, Cho BK, Mattamana BB, Goo YA, Thomas PM, Ash MK, Bhimalli PP, Al-Harthi L, Sha BE, Schneider JR, Kelleher NL. Next-generation Serology by Mass Spectrometry: Readout of the SARS-CoV-2 Antibody Repertoire. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021. [PMID: 34268518 DOI: 10.1101/2021.07.06.21259226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Methods of antibody detection are used to assess exposure or immunity to a pathogen. Here, we present Ig-MS , a novel serological readout that captures the immunoglobulin (Ig) repertoire at molecular resolution, including entire variable regions in Ig light and heavy chains. Ig-MS uses recent advances in protein mass spectrometry (MS) for multi-parametric readout of antibodies, with new metrics like Ion Titer (IT) and Degree of Clonality (DoC) capturing the heterogeneity and relative abundance of individual clones without sequencing of B cells. We apply Ig-MS to plasma from subjects with severe & mild COVID-19, using the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2 as the bait for antibody capture. Importantly, we report a new data type for human serology, with compatibility to any recombinant antigen to gauge our immune responses to vaccination, pathogens, or autoimmune disorders.
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33
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Alfaro JA, Bohländer P, Dai M, Filius M, Howard CJ, van Kooten XF, Ohayon S, Pomorski A, Schmid S, Aksimentiev A, Anslyn EV, Bedran G, Cao C, Chinappi M, Coyaud E, Dekker C, Dittmar G, Drachman N, Eelkema R, Goodlett D, Hentz S, Kalathiya U, Kelleher NL, Kelly RT, Kelman Z, Kim SH, Kuster B, Rodriguez-Larrea D, Lindsay S, Maglia G, Marcotte EM, Marino JP, Masselon C, Mayer M, Samaras P, Sarthak K, Sepiashvili L, Stein D, Wanunu M, Wilhelm M, Yin P, Meller A, Joo C. The emerging landscape of single-molecule protein sequencing technologies. Nat Methods 2021; 18:604-617. [PMID: 34099939 PMCID: PMC8223677 DOI: 10.1038/s41592-021-01143-1] [Citation(s) in RCA: 158] [Impact Index Per Article: 52.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 04/02/2021] [Indexed: 02/04/2023]
Abstract
Single-cell profiling methods have had a profound impact on the understanding of cellular heterogeneity. While genomes and transcriptomes can be explored at the single-cell level, single-cell profiling of proteomes is not yet established. Here we describe new single-molecule protein sequencing and identification technologies alongside innovations in mass spectrometry that will eventually enable broad sequence coverage in single-cell profiling. These technologies will in turn facilitate biological discovery and open new avenues for ultrasensitive disease diagnostics.
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Affiliation(s)
- Javier Antonio Alfaro
- International Centre for Cancer Vaccine Science, University of Gdańsk, Gdańsk, Poland.
| | - Peggy Bohländer
- Faculty of Applied Sciences, Delft University of Technology, Delft, the Netherlands
| | - Mingjie Dai
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Mike Filius
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Cecil J Howard
- Department of Chemistry, University of Texas at Austin, Austin, TX, USA
| | - Xander F van Kooten
- Department of Biomedical Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Shilo Ohayon
- Department of Biomedical Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Adam Pomorski
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Sonja Schmid
- NanoDynamicsLab, Laboratory of Biophysics, Wageningen University, Wageningen, the Netherlands
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Eric V Anslyn
- Department of Chemistry, University of Texas at Austin, Austin, TX, USA
| | - Georges Bedran
- International Centre for Cancer Vaccine Science, University of Gdańsk, Gdańsk, Poland
| | - Chan Cao
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Mauro Chinappi
- Dipartimento di Ingegneria Industriale, Università di Roma Tor Vergata, Rome, Italy
| | - Etienne Coyaud
- Univ. Lille, Inserm, CHU Lille, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Lille, France
| | - Cees Dekker
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Gunnar Dittmar
- Department of Infection and Immunity, Luxembourg Institute of Health, Strassen, Luxembourg
- Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | | | - Rienk Eelkema
- Faculty of Applied Sciences, Delft University of Technology, Delft, the Netherlands
| | - David Goodlett
- International Centre for Cancer Vaccine Science, University of Gdańsk, Gdańsk, Poland
- Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia, Canada
| | | | - Umesh Kalathiya
- International Centre for Cancer Vaccine Science, University of Gdańsk, Gdańsk, Poland
| | - Neil L Kelleher
- Departments of Chemistry and Molecular Biosciences, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Ryan T Kelly
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Zvi Kelman
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, University of Maryland, Rockville, MD, USA
- Biomolecular Labeling Laboratory, Institute for Bioscience and Biotechnology Research, Rockville, MD, USA
| | - Sung Hyun Kim
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany
- Bavarian Center for Biomolecular Mass Spectrometry, Freising, Germany
| | - David Rodriguez-Larrea
- Department of Biochemistry and Molecular Biology, Biofisika Institute (CSIC, UPV/EHU), Leioa, Spain
| | - Stuart Lindsay
- Biodesign Institute, School of Molecular Sciences, Department of Physics, Arizona State University, Tempe, AZ, USA
| | - Giovanni Maglia
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Edward M Marcotte
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA
| | - John P Marino
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, University of Maryland, Rockville, MD, USA
| | | | - Michael Mayer
- Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland
| | - Patroklos Samaras
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany
| | - Kumar Sarthak
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Lusia Sepiashvili
- University of Toronto, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Derek Stein
- Department of Physics, Brown University, Providence, RI, USA
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, MA, USA
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Mathias Wilhelm
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Amit Meller
- Department of Biomedical Engineering, Technion-Israel Institute of Technology, Haifa, Israel.
- Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa, Israel.
| | - Chirlmin Joo
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands.
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Verkhoturov DS, Crulhas BP, Eller MJ, Han YD, Verkhoturov SV, Bisrat Y, Revzin A, Schweikert EA. Nanoprojectile Secondary Ion Mass Spectrometry for Analysis of Extracellular Vesicles. Anal Chem 2021; 93:7481-7490. [PMID: 33988360 DOI: 10.1021/acs.analchem.1c00689] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We describe a technique based on secondary ion mass spectrometry with nanoprojectiles (NP-SIMS) for determining the protein content of extracellular vesicles, EVs, via tagged antibodies. The technique uses individual gold nanoprojectiles (e.g., Au4004+ and Au28008+), separated in time and space, to bombard a surface. For each projectile impact (10-20 nm in diameter), the co-emitted molecules are mass analyzed and recorded as an individual mass spectrum. Examining these individual mass spectra for co-localized species allows for nanoscale mass spectrometry to be performed. The high lateral resolution of this technique is well suited for analyzing nano-objects. SIMS is generally limited to analyzing small molecules (below ∼1500 Da); therefore, we evaluated three molecules (eosin, erythrosine, and BHHTEGST) as prospective mass spectrometry tags. We tested these on a model surface comprising a mixture of all three tags conjugated to antibodies and found that NP-SIMS could detect all three tags from a single projectile impact. Applying the method, we tagged two surface proteins common in urinary EVs, CD63 and CD81, with anti-CD63-erythrosine and anti-CD81-BHHTEGST. We found that NP-SIMS could determine the relative abundance of the two proteins and required only a few hundred or thousand EVs in the analysis region to detect the presence of the tagged antibodies.
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Affiliation(s)
- Dmitriy S Verkhoturov
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Bruno P Crulhas
- Department of Physiology and Biomedical Engineering, Mayo Clinic, 200 1st Street SW St-11-14, Rochester, Minnesota 55905, United States
| | - Michael J Eller
- Department of Chemistry and Biochemistry, California State University Northridge, Northridge, California 91330, United States
| | - Yong D Han
- Department of Physiology and Biomedical Engineering, Mayo Clinic, 200 1st Street SW St-11-14, Rochester, Minnesota 55905, United States
| | | | - Yordanos Bisrat
- Materials Characterization Facility, Texas A&M University, College Station, Texas 77843, United States
| | - Alexander Revzin
- Department of Physiology and Biomedical Engineering, Mayo Clinic, 200 1st Street SW St-11-14, Rochester, Minnesota 55905, United States
| | - Emile A Schweikert
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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35
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Thomas SL, Thacker JB, Schug KA, Maráková K. Sample preparation and fractionation techniques for intact proteins for mass spectrometric analysis. J Sep Sci 2020; 44:211-246. [DOI: 10.1002/jssc.202000936] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Shannon L. Thomas
- Department of Chemistry & Biochemistry The University of Texas Arlington Arlington Texas USA
| | - Jonathan B. Thacker
- Department of Chemistry & Biochemistry The University of Texas Arlington Arlington Texas USA
| | - Kevin A. Schug
- Department of Chemistry & Biochemistry The University of Texas Arlington Arlington Texas USA
| | - Katarína Maráková
- Department of Pharmaceutical Analysis and Nuclear Pharmacy Faculty of Pharmacy Comenius University in Bratislava Bratislava Slovakia
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36
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Brown KA, Melby JA, Roberts DS, Ge Y. Top-down proteomics: challenges, innovations, and applications in basic and clinical research. Expert Rev Proteomics 2020; 17:719-733. [PMID: 33232185 PMCID: PMC7864889 DOI: 10.1080/14789450.2020.1855982] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 11/23/2020] [Indexed: 12/14/2022]
Abstract
Introduction- A better understanding of the underlying molecular mechanism of diseases is critical for developing more effective diagnostic tools and therapeutics toward precision medicine. However, many challenges remain to unravel the complex nature of diseases. Areas covered- Changes in protein isoform expression and post-translation modifications (PTMs) have gained recognition for their role in underlying disease mechanisms. Top-down mass spectrometry (MS)-based proteomics is increasingly recognized as an important method for the comprehensive characterization of proteoforms that arise from alternative splicing events and/or PTMs for basic and clinical research. Here, we review the challenges, technological innovations, and recent studies that utilize top-down proteomics to elucidate changes in the proteome with an emphasis on its use to study heart diseases. Expert opinion- Proteoform-resolved information can substantially contribute to the understanding of the molecular mechanisms underlying various diseases and for the identification of novel proteoform targets for better therapeutic development . Despite the challenges of sequencing intact proteins, top-down proteomics has enabled a wealth of information regarding protein isoform switching and changes in PTMs. Continuous developments in sample preparation, intact protein separation, and instrumentation for top-down MS have broadened its capabilities to characterize proteoforms from a range of samples on an increasingly global scale.
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Affiliation(s)
- Kyle A. Brown
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - Jake A. Melby
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - David S. Roberts
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, United States
- Human Proteomics Program, University of Wisconsin-Madison, Madison, Wisconsin, United States
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