1
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Huang CF, Kline JT, Negrão F, Robey MT, Toby TK, Durbin KR, Fellers RT, Friedewald JJ, Levitsky J, Abecassis MMI, Melani RD, Kelleher NL, Fornelli L. Targeted Quantification of Proteoforms in Complex Samples by Proteoform Reaction Monitoring. Anal Chem 2024; 96:3578-3586. [PMID: 38354049 PMCID: PMC11008684 DOI: 10.1021/acs.analchem.3c05578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Existing mass spectrometric assays used for sensitive and specific measurements of target proteins across multiple samples, such as selected/multiple reaction monitoring (SRM/MRM) or parallel reaction monitoring (PRM), are peptide-based methods for bottom-up proteomics. Here, we describe an approach based on the principle of PRM for the measurement of intact proteoforms by targeted top-down proteomics, termed proteoform reaction monitoring (PfRM). We explore the ability of our method to circumvent traditional limitations of top-down proteomics, such as sensitivity and reproducibility. We also introduce a new software program, Proteoform Finder (part of ProSight Native), specifically designed for the easy analysis of PfRM data. PfRM was initially benchmarked by quantifying three standard proteins. The linearity of the assay was shown over almost 3 orders of magnitude in the femtomole range, with limits of detection and quantification in the low femtomolar range. We later applied our multiplexed PfRM assay to complex samples to quantify biomarker candidates in peripheral blood mononuclear cells (PBMCs) from liver-transplanted patients, suggesting their possible translational applications. These results demonstrate that PfRM has the potential to contribute to the accurate quantification of protein biomarkers for diagnostic purposes and to improve our understanding of disease etiology at the proteoform level.
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Affiliation(s)
- Che-Fan Huang
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
| | - Jake T Kline
- School of Biological Sciences, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Fernanda Negrão
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
| | - Matthew T Robey
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
- Proteinaceous, Inc., Evanston, Illinois 60201, United States
| | - Timothy K Toby
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
| | - Kenneth R Durbin
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
- Proteinaceous, Inc., Evanston, Illinois 60201, United States
| | - Ryan T Fellers
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
- Proteinaceous, Inc., Evanston, Illinois 60201, United States
| | - John J Friedewald
- Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Josh Levitsky
- Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Michael M I Abecassis
- Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Rafael D Melani
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
| | - Neil L Kelleher
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
| | - Luca Fornelli
- School of Biological Sciences, 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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2
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Weerawarna PM, Schiefer IT, Soares P, Fox S, Morimoto RI, Melani RD, Kelleher NL, Luan CH, Silverman RB. Target Identification of a Class of Pyrazolone Protein Aggregation Inhibitor Therapeutics for Amyotrophic Lateral Sclerosis. ACS Cent Sci 2024; 10:87-103. [PMID: 38292603 PMCID: PMC10823514 DOI: 10.1021/acscentsci.3c00213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 11/01/2023] [Accepted: 11/27/2023] [Indexed: 02/01/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with no cure, and current treatment options are very limited. Previously, we performed a high-throughput screen to identify small molecules that inhibit protein aggregation caused by a mutation in the gene that encodes superoxide dismutase 1 (SOD1), which is responsible for about 25% of familial ALS. This resulted in three hit series of compounds that were optimized over several years to give three compounds that were highly active in a mutant SOD1 ALS model. Here we identify the target of two of the active compounds (6 and 7) with the use of photoaffinity labeling, chemical biology reporters, affinity purification, proteomic analysis, and fluorescent/cellular thermal shift assays. Evidence is provided to demonstrate that these two pyrazolone compounds directly interact with 14-3-3-E and 14-3-3-Q isoforms, which have chaperone activity and are known to interact with mutant SOD1G93A aggregates and become insoluble in the subcellular JUNQ compartment, leading to apoptosis. Because protein aggregation is the hallmark of all neurodegenerative diseases, knowledge of the target compounds that inhibit protein aggregation allows for the design of more effective molecules for the treatment of ALS and possibly other neurodegenerative diseases.
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Affiliation(s)
- Pathum M. Weerawarna
- Department
of Chemistry, Chemistry of Life Processes Institute, Center for Developmental
Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
| | - Isaac T. Schiefer
- Department
of Chemistry, Chemistry of Life Processes Institute, Center for Developmental
Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
| | - Pedro Soares
- Department
of Chemistry, Chemistry of Life Processes Institute, Center for Developmental
Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
| | - Susan Fox
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Richard I. Morimoto
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Rafael D. Melani
- Department
of Chemistry and Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Neil L. Kelleher
- Department
of Chemistry, Chemistry of Life Processes Institute, Center for Developmental
Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
- Proteomics
Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Chi-Hao Luan
- High
Throughput
Analysis Laboratory, Chemistry of Life Processes Institute, and Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Richard B. Silverman
- Department
of Chemistry, Chemistry of Life Processes Institute, Center for Developmental
Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
- Department
of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, United States
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3
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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. Author Correction: Automated imaging and identification of proteoforms directly from ovarian cancer tissue. Nat Commun 2023; 14:7946. [PMID: 38040721 PMCID: PMC10692193 DOI: 10.1038/s41467-023-43898-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2023] Open
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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4
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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5
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McGee JP, Melani RD, Des Soye B, Croote D, Winton V, Quake SR, Kafader JO, Kelleher NL. Immunocomplexed Antigen Capture and Identification by Native Top-Down Mass Spectrometry. J Am Soc Mass Spectrom 2023; 34:2093-2097. [PMID: 37683262 PMCID: PMC10557138 DOI: 10.1021/jasms.3c00235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/26/2023] [Accepted: 09/01/2023] [Indexed: 09/10/2023]
Abstract
Antibody-antigen interactions are central to the immune response. Variation of protein antigens such as isoforms and post-translational modifications can alter their antibody binding sites. To directly connect the recognition of protein antigens with their molecular composition, we probed antibody-antigen complexes by using native tandem mass spectrometry. Specifically, we characterized the prominent peanut allergen Ara h 2 and a convergent IgE variable region discovered in patients who are allergic to peanuts. In addition to measuring the antigen-induced dimerization of IgE antibodies, we demonstrated how immunocomplexes can be isolated in the gas phase and activated to eject, identify, and characterize proteoforms of their bound antigens. Using tandem experiments, we isolated the ejected antigens and then fragmented them to identify their chemical composition. These results establish native top-down mass spectrometry as a viable platform for precise and thorough characterization of immunocomplexes to relate structure to function and enable the discovery of antigen proteoforms and their binding sites.
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Affiliation(s)
- John P. McGee
- Departments
of Chemistry and Molecular Biosciences and the Proteomics Center of
Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Rafael D. Melani
- Departments
of Chemistry and Molecular Biosciences and the Proteomics Center of
Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Ben Des Soye
- Departments
of Chemistry and Molecular Biosciences and the Proteomics Center of
Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Derek Croote
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
| | - Valerie Winton
- Departments
of Chemistry and Molecular Biosciences and the Proteomics Center of
Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Stephen R. Quake
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
- Department
of Applied Physics, Stanford University, Stanford, California 94305, United States
| | - Jared O. Kafader
- Departments
of Chemistry and Molecular Biosciences and the Proteomics Center of
Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Neil L. Kelleher
- Departments
of Chemistry and Molecular Biosciences and the Proteomics Center of
Excellence, Northwestern University, Evanston, Illinois 60208, United States
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6
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McGann CD, Barshop WD, Canterbury JD, Lin C, Gabriel W, Huang J, Bergen D, Zabrouskov V, Melani RD, Wilhelm M, McAlister GC, Schweppe DK. Real-Time Spectral Library Matching for Sample Multiplexed Quantitative Proteomics. J Proteome Res 2023; 22:2836-2846. [PMID: 37557900 DOI: 10.1021/acs.jproteome.3c00085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
Sample multiplexed quantitative proteomics assays have proved to be a highly versatile means to assay molecular phenotypes. Yet, stochastic precursor selection and precursor coisolation can dramatically reduce the efficiency of data acquisition and quantitative accuracy. To address this, intelligent data acquisition (IDA) strategies have recently been developed to improve instrument efficiency and quantitative accuracy for both discovery and targeted methods. Toward this end, we sought to develop and implement a new real-time spectral library searching (RTLS) workflow that could enable intelligent scan triggering and peak selection within milliseconds of scan acquisition. To ensure ease of use and general applicability, we built an application to read in diverse spectral libraries and file types from both empirical and predicted spectral libraries. We demonstrate that RTLS methods enable improved quantitation of multiplexed samples, particularly with consideration for quantitation from chimeric fragment spectra. We used RTLS to profile proteome responses to small molecule perturbations and were able to quantify up to 15% more significantly regulated proteins in half the gradient time compared to traditional methods. Taken together, the development of RTLS expands the IDA toolbox to improve instrument efficiency and quantitative accuracy for sample multiplexed analyses.
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Affiliation(s)
- Chris D McGann
- University of Washington, Seattle, Washington 98105, United States
| | | | | | - Chuwei Lin
- University of Washington, Seattle, Washington 98105, United States
| | | | - Jingjing Huang
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - David Bergen
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Vlad Zabrouskov
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Rafael D Melani
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | | | | | - Devin K Schweppe
- University of Washington, Seattle, Washington 98105, United States
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7
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Zhu W, Butrin A, Melani RD, Doubleday PF, Ferreira GM, Tavares MT, Habeeb Mohammad TS, Beaupre BA, Kelleher NL, Moran GR, Liu D, Silverman RB. Correction to "Rational Design, Synthesis, and Mechanism of (3 S,4 R)-3-Amino-4-(difluoromethyl)cyclopent-1-ene-1-carboxylic Acid: Employing a Second-Deprotonation Strategy for Selectivity of Human Ornithine Aminotransferase over GABA Aminotransferase". J Am Chem Soc 2023; 145:9895-9896. [PMID: 37075548 DOI: 10.1021/jacs.3c03364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
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8
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Ives A, Dunn HA, Afsari HS, Seckler HDS, Foroutan MJ, Chavez E, Melani RD, Fellers RT, LeDuc RD, Thomas PM, Martemyanov KA, Kelleher NL, Vafabakhsh R. Middle-Down Mass Spectrometry Reveals Activity-Modifying Phosphorylation Barcode in a Class C G Protein-Coupled Receptor. J Am Chem Soc 2022; 144:23104-23114. [PMID: 36475650 PMCID: PMC9785046 DOI: 10.1021/jacs.2c10697] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
G protein-coupled receptors (GPCRs) are the largest family of membrane receptors in humans. They mediate nearly all aspects of human physiology and thus are of high therapeutic interest. GPCR signaling is regulated in space and time by receptor phosphorylation. It is believed that different phosphorylation states are possible for a single receptor, and each encodes for unique signaling outcomes. Methods to determine the phosphorylation status of GPCRs are critical for understanding receptor physiology and signaling properties of GPCR ligands and therapeutics. However, common proteomic techniques have provided limited quantitative information regarding total receptor phosphorylation stoichiometry, relative abundances of isomeric modification states, and temporal dynamics of these parameters. Here, we report a novel middle-down proteomic strategy and parallel reaction monitoring (PRM) to quantify the phosphorylation states of the C-terminal tail of metabotropic glutamate receptor 2 (mGluR2). By this approach, we found that mGluR2 is subject to both basal and agonist-induced phosphorylation at up to four simultaneous sites with varying probability. Using a PRM tandem mass spectrometry methodology, we localized the positions and quantified the relative abundance of phosphorylations following treatment with an agonist. Our analysis showed that phosphorylation within specific regions of the C-terminal tail of mGluR2 is sensitive to receptor activation, and subsequent site-directed mutagenesis of these sites identified key regions which tune receptor sensitivity. This study demonstrates that middle-down purification followed by label-free quantification is a powerful, quantitative, and accessible tool for characterizing phosphorylation states of GPCRs and other challenging proteins.
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Affiliation(s)
- Ashley
N. Ives
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208 United States
| | - Henry A. Dunn
- Department
of Neuroscience, The Scripps Research Institute, Jupiter, Florida 33458, United States,Department
of Pharmacology and Therapeutics, University
of Manitoba, Winnipeg, Manitoba R3E 0T6, Canada,Division
of Neurodegenerative Disorders, St. Boniface Hospital Albrechtsen
Research Centre, Winnipeg, Manitoba R2H 2A6, Canada
| | - Hamid Samareh Afsari
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | | | - Max J. Foroutan
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Erica Chavez
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Rafael D. Melani
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States,National
Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois 60208, United States
| | - Ryan T. Fellers
- National
Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois 60208, United States
| | - Richard D. LeDuc
- National
Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois 60208, United States
| | - Paul M. Thomas
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States,National
Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois 60208, United States
| | - Kirill A. Martemyanov
- Department
of Neuroscience, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Neil L. Kelleher
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208 United States,Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States,National
Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois 60208, United States
| | - Reza Vafabakhsh
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States,
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9
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Forte E, Des Soye BJ, Melani RD, Hollas MAR, Kafader JO, Sha BE, Schneider JR, Kelleher NL. Divergent Antibody Repertoires Found for Omicron versus Wuhan SARS-CoV-2 Strains Using Ig-MS. J Proteome Res 2022; 21:2987-2997. [PMID: 36343328 PMCID: PMC9668041 DOI: 10.1021/acs.jproteome.2c00514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Indexed: 11/09/2022]
Abstract
SARS-CoV-2 Omicron (B.1.1.529) and its subvariants are currently the most common variants of concern worldwide, featuring numerous mutations in the spike protein and elsewhere that collectively make Omicron variants more transmissible and more resistant to antibody-mediated neutralization provided by vaccination, previous infections, and monoclonal antibody therapies than their predecessors. We recently reported the creation and characterization of Ig-MS, a new mass spectrometry-based serology platform that can define the repertoire of antibodies against an antigen of interest at single proteoform resolution. Here, we applied Ig-MS to investigate the evolution of plasma antibody repertoires against the receptor-binding domain (RBD) of SARS-CoV-2 in response to the booster shot and natural viral infection. We also assessed the capacity for antibody repertoires generated in response to vaccination and/or infection with the Omicron variant to bind to both Wuhan- and Omicron-RBDs. Our results show that (1) the booster increases antibody titers against both Wuhan- and Omicron- RBDs and elicits an Omicron-specific response and (2) vaccination and infection act synergistically in generating anti-RBD antibody repertoires able to bind both Wuhan- and Omicron-RBDs with variant-specific antibodies.
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Affiliation(s)
- Eleonora Forte
- Proteomics Center of Excellence, Evanston, IL, 60208, USA
- Department of Surgery, Comprehensive Transplant Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | | | - Rafael D. Melani
- Proteomics Center of Excellence, Evanston, IL, 60208, USA
- Department of Molecular Biosciences, Chemistry, Northwestern University, Evanston, IL, 60208, 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
- Proteomics Center of Excellence, Evanston, IL, 60208, USA
- Department of Surgery, Comprehensive Transplant Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
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10
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Rangel DL, Melani RD, Carvalho EL, Boldo JT, Gomes Dos Santos T, Kelleher NL, Pinto PM. Venom characterization of the Brazilian Pampa snake Bothrops pubescens by top-down and bottom-up proteomics. Toxicon 2022; 220:106937. [PMID: 36228757 PMCID: PMC9901210 DOI: 10.1016/j.toxicon.2022.106937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/29/2022] [Accepted: 09/29/2022] [Indexed: 11/07/2022]
Abstract
The envenomation from the Bothrops genus is characterized by systemic and local effects caused by the main toxin families in the venom. In Bothrops pubescens venom we were able to identify 89 protein groups belonging to 13 toxin families with the bottom-up proteomics approach and 40 unique proteoforms belonging to 6 toxin families with the top-down proteomics approach. We also identified multi-proteoform complexes of dimeric L-amino acid oxidase using native top-down mass spectrometry.
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Affiliation(s)
- Darlene Lopes Rangel
- Applied Proteomics Laboratory, Federal University of Pampa, São Gabriel, Brazil; Pos Graduation in Biological Sciences, Federal University of Pampa, São Gabriel, Brazil
| | - Rafael D Melani
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, 60208, United States
| | - Evelise Leis Carvalho
- Applied Proteomics Laboratory, Federal University of Pampa, São Gabriel, Brazil; Pos Graduation in Biological Sciences, Federal University of Pampa, São Gabriel, Brazil
| | | | - Tiago Gomes Dos Santos
- Pampa Biodiversity Studies Laboratory (LEBIP), Federal University of Pampa, São Gabriel, Brazil
| | - Neil L Kelleher
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, 60208, United States
| | - Paulo Marcos Pinto
- Applied Proteomics Laboratory, Federal University of Pampa, São Gabriel, Brazil; Pos Graduation in Biological Sciences, Federal University of Pampa, São Gabriel, Brazil.
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11
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Abstract
A functional understanding of the human body requires structure-function studies of proteins at scale. The chemical structure of proteins is controlled at the transcriptional, translational, and post-translational levels, creating a variety of products with modulated functions within the cell. The term "proteoform" encapsulates this complexity at the level of chemical composition. Comprehensive mapping of the proteoform landscape in human tissues necessitates analytical techniques with increased sensitivity and depth of coverage. Here, we took a top-down proteomics approach, combining data generated using capillary zone electrophoresis (CZE) and nanoflow reversed-phase liquid chromatography (RPLC) hyphenated to mass spectrometry to identify and characterize proteoforms from the human lungs, heart, spleen, small intestine, and kidneys. CZE and RPLC provided complementary post-translational modification and proteoform selectivity, thereby enhancing the overall proteome coverage when used in combination. Of the 11,466 proteoforms identified in this study, 7373 (64%) were not reported previously. Large differences in the protein and proteoform level were readily quantified, with initial inferences about proteoform biology operative in the analyzed organs. Differential proteoform regulation of defensins, glutathione transferases, and sarcomeric proteins across tissues generate hypotheses about how they function and are regulated in human health and disease.
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Affiliation(s)
- Bryon S Drown
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
| | - Kevin Jooß
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
| | - Rafael D Melani
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
| | - Cameron Lloyd-Jones
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
| | - Jeannie M Camarillo
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
| | - Neil L Kelleher
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
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12
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Zhu W, Butrin A, Melani RD, Doubleday PF, Ferreira GM, Tavares MT, Habeeb Mohammad TS, Beaupre BA, Kelleher NL, Moran GR, Liu D, Silverman RB. Rational Design, Synthesis, and Mechanism of (3 S,4 R)-3-Amino-4-(difluoromethyl)cyclopent-1-ene-1-carboxylic Acid: Employing a Second-Deprotonation Strategy for Selectivity of Human Ornithine Aminotransferase over GABA Aminotransferase. J Am Chem Soc 2022; 144:5629-5642. [PMID: 35293728 PMCID: PMC9181902 DOI: 10.1021/jacs.2c00924] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human ornithine aminotransferase (hOAT) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that contains a similar active site to that of γ-aminobutyric acid aminotransferase (GABA-AT). Recently, pharmacological inhibition of hOAT was recognized as a potential therapeutic approach for hepatocellular carcinoma. In this work, we first studied the inactivation mechanisms of hOAT by two well-known GABA-AT inactivators (CPP-115 and OV329). Inspired by the inactivation mechanistic difference between these two aminotransferases, a series of analogues were designed and synthesized, leading to the discovery of analogue 10b as a highly selective and potent hOAT inhibitor. Intact protein mass spectrometry, protein crystallography, and dialysis experiments indicated that 10b was converted to an irreversible tight-binding adduct (34) in the active site of hOAT, as was the unsaturated analogue (11). The comparison of kinetic studies between 10b and 11 suggested that the active intermediate (17b) was only generated in hOAT and not in GABA-AT. Molecular docking studies and pKa computational calculations highlighted the importance of chirality and the endocyclic double bond for inhibitory activity. The turnover mechanism of 10b was supported by mass spectrometric analysis of dissociable products and fluoride ion release experiments. Notably, the stopped-flow experiments were highly consistent with the proposed mechanism, suggesting a relatively slow hydrolysis rate for hOAT. The novel second-deprotonation mechanism of 10b contributes to its high potency and significantly enhanced selectivity for hOAT inhibition.
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Affiliation(s)
- Wei Zhu
- Department of Chemistry, Chemistry of Life Processes Institute, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
| | - Arseniy Butrin
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Rafael D Melani
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Peter F Doubleday
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Glaucio Monteiro Ferreira
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil
| | - Mauricio T Tavares
- Department of Molecular Medicine, Scripps Research, Jupiter, Florida 33458, United States
| | - Thahani S Habeeb Mohammad
- Department of Chemistry, Chemistry of Life Processes Institute, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
| | - Brett A Beaupre
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Neil L Kelleher
- Department of Chemistry, Chemistry of Life Processes Institute, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States.,Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Graham R Moran
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Richard B Silverman
- Department of Chemistry, Chemistry of Life Processes Institute, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States.,Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States.,Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, United States
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13
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Melani RD, Gerbasi VR, Anderson LC, Sikora JW, Toby TK, Hutton JE, Butcher DS, Negrão F, Seckler HS, Srzentić K, Fornelli L, Camarillo JM, LeDuc RD, Cesnik AJ, Lundberg E, Greer JB, Fellers RT, Robey MT, DeHart CJ, Forte E, Hendrickson CL, Abbatiello SE, Thomas PM, Kokaji AI, Levitsky J, Kelleher NL. The Blood Proteoform Atlas: A reference map of proteoforms in human hematopoietic cells. Science 2022; 375:411-418. [PMID: 35084980 PMCID: PMC9097315 DOI: 10.1126/science.aaz5284] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Human biology is tightly linked to proteins, yet most measurements do not precisely determine alternatively spliced sequences or posttranslational modifications. Here, we present the primary structures of ~30,000 unique proteoforms, nearly 10 times more than in previous studies, expressed from 1690 human genes across 21 cell types and plasma from human blood and bone marrow. The results, compiled in the Blood Proteoform Atlas (BPA), indicate that proteoforms better describe protein-level biology and are more specific indicators of differentiation than their corresponding proteins, which are more broadly expressed across cell types. We demonstrate the potential for clinical application, by interrogating the BPA in the context of liver transplantation and identifying cell and proteoform signatures that distinguish normal graft function from acute rejection and other causes of graft dysfunction.
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Affiliation(s)
- Rafael D. Melani
- Department of Molecular Biosciences, Department of Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Vincent R. Gerbasi
- Department of Molecular Biosciences, Department of Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Lissa C. Anderson
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL, USA
| | - Jacek W. Sikora
- Department of Molecular Biosciences, Department of Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Timothy K. Toby
- Department of Molecular Biosciences, Department of Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Josiah E. Hutton
- Department of Molecular Biosciences, Department of Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - David S. Butcher
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL, USA
| | - Fernanda Negrão
- Department of Molecular Biosciences, Department of Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Henrique S. Seckler
- Department of Molecular Biosciences, Department of Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Kristina Srzentić
- Department of Molecular Biosciences, Department of Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Luca Fornelli
- Department of Molecular Biosciences, Department of Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Jeannie M. Camarillo
- Department of Molecular Biosciences, Department of Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Richard D. LeDuc
- Department of Molecular Biosciences, Department of Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Anthony J. Cesnik
- Department of Genetics, Stanford University, Stanford, CA, USA
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Emma Lundberg
- Department of Genetics, Stanford University, Stanford, CA, USA
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Joseph B. Greer
- Department of Molecular Biosciences, Department of Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Ryan T. Fellers
- Department of Molecular Biosciences, Department of Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Matthew T. Robey
- Department of Molecular Biosciences, Department of Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Caroline J. DeHart
- Department of Molecular Biosciences, Department of Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Eleonora Forte
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
- Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | | | | | - Paul M. Thomas
- Department of Molecular Biosciences, Department of Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | | | - Josh Levitsky
- Comprehensive Transplant Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Neil L. Kelleher
- Department of Molecular Biosciences, Department of 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
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14
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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: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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15
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de Oliveira NB, Magalhães ACM, Bloch C, Beirão PSL, Silva ADO, Melani RD, Barbosa EA, Pires OR, Schwartz CA. Characterization of the first two toxins isolated from the venom of the ancient scorpion Tityus (Archaeotityus) mattogrossensis (Borelli, 1901). J Venom Anim Toxins Incl Trop Dis 2021; 27:e20210035. [PMID: 34925481 PMCID: PMC8670738 DOI: 10.1590/1678-9199-jvatitd-2021-0035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/12/2021] [Indexed: 11/22/2022] Open
Abstract
Background: Almost all Tityus characterized toxins are from subgenera Atreus and Tityus, there are only a few data about toxins produced by Archaeotityus, an ancient group in Tityus genus. Methods: Tityus (Archaeotityus) mattogrossensis crude venom was fractionated by high performance liquid chromatography, the major fractions were tested in a frog sciatic nerve single sucrose-gap technique. Two fractions (Tm1 and Tm2) were isolated, partially sequenced by MALDI-TOF/MS and electrophysiological assayed on HEK293 Nav 1.3, HEK293 Nav 1.6, DUM and DRG cells. Results: The sucrose-gap technique showed neurotoxicity in four fractions. One fraction caused a delay of action potential repolarization and other three caused a reduction in amplitude. An electrophysiological assay showed that Tm1 is active on HEK293 Nav 1.3, HEK293 Nav 1.6, DUM and DRG cells, and Tm2 on HEK293 Nav 1.3 and DRG cells, but not in HEK293 Nav 1.6. In addition, Tm1 and Tm2 did promote a shift to more negative potentials strongly suggesting that both are α-NaScTx. Conclusion: Although Tityus (Archaeotityus) mattogrossensis is considered an ancient group in Tityus genus, the primary structure of Tm1 and Tm2 is more related to Tityus subgenus. The patch clamp electrophysiological tests suggest that Tm1 and Tm2 are NaScTx, and also promoted no shift to more negative potentials, strongly suggesting that both are α-NaScTx. This paper aimed to explore and characterize for the first time toxins from the ancient scorpion Tityus (Archaeotityus) mattogrossensis.
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Affiliation(s)
- Natiela Beatriz de Oliveira
- Laboratory of Toxinology, Department of Physiological Sciences, Institute of Biology, University of Brasilia (UnB), Brasília, DF, Brazil
| | - Ana Carolina Martins Magalhães
- Laboratory of Toxinology, Department of Physiological Sciences, Institute of Biology, University of Brasilia (UnB), Brasília, DF, Brazil
| | - Carlos Bloch
- EMPRABA Center of Genetic Resources and Biotechnology, Brazilian Agricultural Research Corporation, Brasília, DF, Brazil
| | - Paulo Sérgio Lacerda Beirão
- Department of Biochemistry and Immunology, Institute of Exact Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Anita de Oliveira Silva
- Department of Biochemistry and Immunology, Institute of Exact Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Rafael D Melani
- Laboratory of Toxinology, Department of Physiological Sciences, Institute of Biology, University of Brasilia (UnB), Brasília, DF, Brazil
| | - Eder Alves Barbosa
- EMPRABA Center of Genetic Resources and Biotechnology, Brazilian Agricultural Research Corporation, Brasília, DF, Brazil.,Laboratory of Biomolecule Synthesis and Analy sis, Institute of Chemistry, University of Brasilia (UnB), Brasília, DF, Brazil
| | - Osmindo Rodrigues Pires
- Laboratory of Toxinology, Department of Physiological Sciences, Institute of Biology, University of Brasilia (UnB), Brasília, DF, Brazil
| | - Carlos Alberto Schwartz
- Laboratory of Toxinology, Department of Physiological Sciences, Institute of Biology, University of Brasilia (UnB), Brasília, DF, Brazil
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16
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Sosa-Acosta P, Melani RD, Quiñones-Vega M, Melo A, Garcez PP, Nogueira FCS, Domont GB. Proteomics of ZIKV infected amniotic fluids of microcephalic fetuses reveals extracellular matrix and immune system dysregulation. Proteomics Clin Appl 2021; 16:e2100041. [PMID: 34676661 DOI: 10.1002/prca.202100041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/17/2021] [Accepted: 10/13/2021] [Indexed: 11/10/2022]
Abstract
During pregnancy, the vertical transmission of the Zika virus (ZIKV) can cause some disorders in the fetus, called Congenital Zika Syndrome (CZS). Several efforts have been made to understand the molecular mechanism of the CZS. However, the study of CZS pathogenesis through infected human samples is scarce. Therefore, the main goal of this study is to identify and understand the biological processes affected by CZS development. We analyzed by a shotgun proteomic approach the amniotic fluid of pregnant women infected with Zika carrying microcephalic (MC+ ) or non-microcephalic (Z+ ) fetuses compared to Zika negative controls (CTR). Several groups of extracellular matrix (ECM) proteins were dysregulated in the Z+ and MC+ patients, triggering an opposite dysregulation. The down-regulation of the ECM proteins in the MC+ groups can be another factor that contributes to CZS. On the contrary, the Z+ group could be developing a neuroprotective response through ECM proteins up-regulation. The neutrophil degranulation process was disrupted in the Z+ and MC+ groups, where the MC+ groups showed a complex dysregulation. These results suggest that the microcephalic phenotypes are modulated by a down-regulation of the ECM and the impairment of the innate immune system processes.
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Affiliation(s)
- Patricia Sosa-Acosta
- Proteomics Unit, Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-909, Brazil
| | - Rafael D Melani
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA
| | - Mauricio Quiñones-Vega
- Proteomics Unit, Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-909, Brazil
| | - Adriana Melo
- Instituto Pesquisa Professor Joaquim Amorim Neto (IPESQ), Campina Grande, Paraíba, Brazil
| | - Patrícia P Garcez
- Institute of Biomedical Science, Federal University of Rio de Janeiro, RJ, Brazil
| | - Fábio C S Nogueira
- Proteomics Unit, Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-909, Brazil.,Laboratory of Proteomics (LabProt), LADETEC, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-598, Brazil
| | - Gilberto B Domont
- Proteomics Unit, Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-909, Brazil
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17
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Santos Seckler HD, Park HM, Lloyd-Jones CM, Melani RD, Camarillo JM, Wilkins JT, Compton PD, Kelleher NL. New Interface for Faster Proteoform Analysis: Immunoprecipitation Coupled with SampleStream-Mass Spectrometry. J Am Soc Mass Spectrom 2021; 32:1659-1670. [PMID: 34043341 PMCID: PMC8530194 DOI: 10.1021/jasms.1c00026] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Different proteoform products of the same gene can exhibit differing associations with health and disease, and their patterns of modifications may offer more precise markers of phenotypic differences between individuals. However, currently employed protein-biomarker discovery and quantification tools, such as bottom-up proteomics and ELISAs, are mostly proteoform-unaware. Moreover, the current throughput for proteoform-level analyses by liquid chromatography mass spectrometry (LCMS) for quantitative top-down proteomics is incompatible with population-level biomarker surveys requiring robust, faster proteoform analysis. To this end, we developed immunoprecipitation coupled to SampleStream mass spectrometry (IP-SampleStream-MS) as a high-throughput, automated technique for the targeted quantification of proteoforms. We applied IP-SampleStream-MS to serum samples of 25 individuals to assess the proteoform abundances of apolipoproteins A-I (ApoA-I) and C-III (ApoC-III). The results for ApoA-I were compared to those of LCMS for these individuals, with IP-SampleStream-MS showing a >7-fold higher throughput with >50% better analytical variation. Proteoform abundances measured by IP-SampleStream-MS correlated strongly to LCMS-based values (R2 = 0.6-0.9) and produced convergent proteoform-to-phenotype associations, namely, the abundance of canonical ApoA-I was associated with lower HDL-C (R = 0.5) and glycated ApoA-I with higher fasting glucose (R = 0.6). We also observed proteoform-to-phenotype associations for ApoC-III, 22 glycoproteoforms of which were characterized in this study. The abundance of ApoC-III modified by a single N-acetyl hexosamine (HexNAc) was associated with indices of obesity, such as BMI, weight, and waist circumference (R ∼ 0.7). These data show IP-SampleStream-MS to be a robust, scalable workflow for high-throughput associations of proteoforms to phenotypes.
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Affiliation(s)
- Henrique Dos Santos Seckler
- Department of Chemistry, Chemistry of Life Processes Institute and Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Hae-Min Park
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon 34134, South Korea
| | - Cameron M Lloyd-Jones
- Department of Chemistry, Chemistry of Life Processes Institute and Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Rafael D Melani
- Department of Chemistry, Chemistry of Life Processes Institute and Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Jeannie M Camarillo
- Department of Chemistry, Chemistry of Life Processes Institute and Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - John T Wilkins
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, United States
| | - Philip D Compton
- Department of Chemistry, Chemistry of Life Processes Institute and Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
- Integrated Protein Technologies, Inc., Evanston, Illinois 60646, United States
| | - Neil L Kelleher
- Department of Chemistry, Chemistry of Life Processes Institute and Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
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18
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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 2021. [PMID: 34268518 DOI: 10.1101/2021.07.06.21259226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [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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19
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Shen S, Butrin A, Doubleday PF, Melani RD, Beaupre BA, Tavares MT, Ferreira GM, Kelleher NL, Moran GR, Liu D, Silverman RB. Turnover and Inactivation Mechanisms for ( S)-3-Amino-4,4-difluorocyclopent-1-enecarboxylic Acid, a Selective Mechanism-Based Inactivator of Human Ornithine Aminotransferase. J Am Chem Soc 2021; 143:8689-8703. [PMID: 34097381 PMCID: PMC8367020 DOI: 10.1021/jacs.1c02456] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The inhibition of human ornithine δ-aminotransferase (hOAT) is a potential therapeutic approach to treat hepatocellular carcinoma. In this work, (S)-3-amino-4,4-difluorocyclopent-1-enecarboxylic acid (SS-1-148, 6) was identified as a potent mechanism-based inactivator of hOAT while showing excellent selectivity over other related aminotransferases (e.g., GABA-AT). An integrated mechanistic study was performed to investigate the turnover and inactivation mechanisms of 6. A monofluorinated ketone (M10) was identified as the primary metabolite of 6 in hOAT. By soaking hOAT holoenzyme crystals with 6, a precursor to M10 was successfully captured. This gem-diamine intermediate, covalently bound to Lys292, observed for the first time in hOAT/ligand crystals, validates the turnover mechanism proposed for 6. Co-crystallization yielded hOAT in complex with 6 and revealed a novel noncovalent inactivation mechanism in hOAT. Native protein mass spectrometry was utilized for the first time in a study of an aminotransferase inactivator to validate the noncovalent interactions between the ligand and the enzyme; a covalently bonded complex was also identified as a minor form observed in the denaturing intact protein mass spectrum. Spectral and stopped-flow kinetic experiments supported a lysine-assisted E2 fluoride ion elimination, which has never been observed experimentally in other studies of related aminotransferase inactivators. This elimination generated the second external aldimine directly from the initial external aldimine, rather than the typical E1cB elimination mechanism, forming a quinonoid transient state between the two external aldimines. The use of native protein mass spectrometry, X-ray crystallography employing both soaking and co-crystallization methods, and stopped-flow kinetics allowed for the detailed elucidation of unusual turnover and inactivation pathways.
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Affiliation(s)
- Sida Shen
- Department of Chemistry, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
| | - Arseniy Butrin
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Peter F. Doubleday
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Rafael D. Melani
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Brett A. Beaupre
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Mauricio T. Tavares
- Department of Molecular Medicine, Scripps Research, Jupiter, Florida 33458, United States
| | - Glaucio M. Ferreira
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, 05508-000, Brazil
| | - Neil L. Kelleher
- Department of Chemistry, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States,Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Graham R. Moran
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States,Corresponding authors: (R.B.S.) . Phone: +1-847-491-5653; (D.L.) . Phone: +1-773-508-3093
| | - Richard B. Silverman
- Department of Chemistry, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States,Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States,Department of Pharmacology, Northwestern University, Chicago, Illinois, 60611, United States,Corresponding authors: (R.B.S.) . Phone: +1-847-491-5653; (D.L.) . Phone: +1-773-508-3093
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20
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Jooß K, McGee JP, Melani RD, Kelleher NL. Standard procedures for native CZE-MS of proteins and protein complexes up to 800 kDa. Electrophoresis 2021; 42:1050-1059. [PMID: 33502026 PMCID: PMC8122066 DOI: 10.1002/elps.202000317] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 01/02/2021] [Accepted: 01/04/2021] [Indexed: 12/17/2022]
Abstract
Native mass spectrometry (nMS) is a rapidly growing method for the characterization of large proteins and protein complexes, preserving "native" non-covalent inter- and intramolecular interactions. Direct infusion of purified analytes into a mass spectrometer represents the standard approach for conducting nMS experiments. Alternatively, CZE can be performed under native conditions, providing high separation performance while consuming trace amounts of sample material. Here, we provide standard operating procedures for acquiring high-quality data using CZE in native mode coupled online to various Orbitrap mass spectrometers via a commercial sheathless interface, covering a wide range of analytes from 30-800 kDa. Using a standard protein mix, the influence of various CZE method parameters were evaluated, such as BGE/conductive liquid composition and separation voltage. Additionally, a universal approach for the optimization of fragmentation settings in the context of protein subunit and metalloenzyme characterization is discussed in detail for model analytes. A short section is dedicated to troubleshooting of the nCZE-MS setup. This study is aimed to help normalize nCZE-MS practices to enhance the CE community and provide a resource for the production of reproducible and high-quality data.
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Affiliation(s)
- Kevin Jooß
- Department of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA
| | - John P McGee
- Department of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
| | - Rafael D Melani
- Department of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA
| | - Neil L Kelleher
- Department of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA
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21
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Gerbasi VR, Melani RD, Abbatiello SE, Belford MW, Huguet R, McGee JP, Dayhoff D, Thomas PM, Kelleher NL. Deeper Protein Identification Using Field Asymmetric Ion Mobility Spectrometry in Top-Down Proteomics. Anal Chem 2021; 93:6323-6328. [PMID: 33844503 DOI: 10.1021/acs.analchem.1c00402] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Field asymmetric ion mobility spectrometry (FAIMS), when used in proteomics studies, provides superior selectivity and enables more proteins to be identified by providing additional gas-phase separation. Here, we tested the performance of cylindrical FAIMS for the identification and characterization of proteoforms by top-down mass spectrometry of heterogeneous protein mixtures. Combining FAIMS with chromatographic separation resulted in a 62% increase in protein identifications, an 8% increase in proteoform identifications, and an improvement in proteoform identification compared to samples analyzed without FAIMS. In addition, utilization of FAIMS resulted in the identification of proteins encoded by lower-abundance mRNA transcripts. These improvements were attributable, in part, to improved signal-to-noise for proteoforms with similar retention times. Additionally, our results show that the optimal compensation voltage of any given proteoform was correlated with the molecular weight of the analyte. Collectively these results suggest that the addition of FAIMS can enhance top-down proteomics in both discovery and targeted applications.
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Affiliation(s)
- Vincent R Gerbasi
- Northwestern University, National Resource for Translational and Developmental Proteomics, Evanston, Illinois 60208, United States.,Pacific Northwest National Laboratories, Richland, Washington 99352, United States
| | - Rafael D Melani
- Northwestern University, National Resource for Translational and Developmental Proteomics, Evanston, Illinois 60208, United States
| | - Susan E Abbatiello
- Northeastern University, Boston, Massachusetts 02115, United States.,Thermo Fisher Scientific, San Jose, California 98665, United States
| | | | - Romain Huguet
- Thermo Fisher Scientific, San Jose, California 98665, United States
| | - John P McGee
- Northwestern University, National Resource for Translational and Developmental Proteomics, Evanston, Illinois 60208, United States
| | - Dawson Dayhoff
- Northwestern University, National Resource for Translational and Developmental Proteomics, Evanston, Illinois 60208, United States
| | - Paul M Thomas
- Northwestern University, National Resource for Translational and Developmental Proteomics, Evanston, Illinois 60208, United States
| | - Neil L Kelleher
- Northwestern University, National Resource for Translational and Developmental Proteomics, Evanston, Illinois 60208, United States
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22
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Magalhães ACM, de Santana CJC, Melani RD, Domont GB, Castro MS, Fontes W, Roepstorff P, Júnior ORP. Exploring the biological activities and proteome of Brazilian scorpion Rhopalurus agamemnon venom. J Proteomics 2021; 237:104119. [PMID: 33540062 DOI: 10.1016/j.jprot.2021.104119] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/19/2020] [Accepted: 01/19/2021] [Indexed: 12/11/2022]
Abstract
Scorpion venoms are formed by toxins harmful to various organisms, including humans. Several techniques have been developed to understand the role of proteins in animal venoms, including proteomics approach. Rhopalurus agamemnon (Koch, 1839) is the largest scorpion in the Buthidae family in the Brazilian Cerrado, measuring up to 110 mm in total length. The accident with R. agamemnon is painful and causes some systemic reactions, but the specie's venom remains uninvestigated. We explore the venom protein composition using a proteomic and a biological-directed approach identifying 230 protein compounds including enzymes like Hyaluronidase, metalloproteinase, L-amino acid oxidase and amylase, the last two are first reported for scorpion venoms. Some of those new reports are important to demonstrate how distant we are from a total comprehension of the diversity about venoms in general, due to their diversity in composition and function. BIOLOGICAL SIGNIFICANCE: In this study, we explored the composition of venom proteins from the scorpion Rhopalurus agamemnon. We identified 230 proteins from the venom including new enzyme reports. These data highlight the unique diversity of the venom proteins from the scorpion R. agamemnon, provide insights into new mechanisms of envenomation and enlarge the protein database of scorpion venoms. The discovery of new proteins provides a new scenario for the development of new drugs and suggests molecular targets to venom components.
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Affiliation(s)
- Ana Carolina Martins Magalhães
- Toxinology Laboratory, Department of Physiological Sciences, Institute of Biology, University of Brasilia, Brasilia-DF 70910-900, Brazil.
| | - Carlos José Correia de Santana
- Toxinology Laboratory, Department of Physiological Sciences, Institute of Biology, University of Brasilia, Brasilia-DF 70910-900, Brazil; Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology/IB, University of Brasilia, Brasilia-DF 70910-900, Brazil
| | - Rafael D Melani
- Proteomic Laboratory, Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gilberto B Domont
- Proteomic Laboratory, Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mariana S Castro
- Toxinology Laboratory, Department of Physiological Sciences, Institute of Biology, University of Brasilia, Brasilia-DF 70910-900, Brazil; Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology/IB, University of Brasilia, Brasilia-DF 70910-900, Brazil
| | - Wagner Fontes
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology/IB, University of Brasilia, Brasilia-DF 70910-900, Brazil
| | - Peter Roepstorff
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M 5230, Denmark
| | - Osmindo Rodrigues Pires Júnior
- Toxinology Laboratory, Department of Physiological Sciences, Institute of Biology, University of Brasilia, Brasilia-DF 70910-900, Brazil
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23
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McGee JP, Melani RD, Yip PF, Senko MW, Compton PD, Kafader JO, Kelleher NL. Isotopic Resolution of Protein Complexes up to 466 kDa Using Individual Ion Mass Spectrometry. Anal Chem 2020; 93:2723-2727. [PMID: 33322893 DOI: 10.1021/acs.analchem.0c03282] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Native mass spectrometry involves transferring large biomolecular complexes into the gas phase, enabling the characterization of their composition and stoichiometry. However, the overlap in distributions created by residual solvation, ionic adducts, and post-translational modifications creates a high degree of complexity that typically goes unresolved at masses above ∼150 kDa. Therefore, native mass spectrometry would greatly benefit from higher resolution approaches for intact proteins and their complexes. By recording mass spectra of individual ions via charge detection mass spectrometry, we report isotopic resolution for pyruvate kinase (232 kDa) and β-galactosidase (466 kDa), extending the limits of isotopic resolution for high mass and high m/z by >2.5-fold and >1.6-fold, respectively.
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Affiliation(s)
- John P McGee
- Departments of Chemical and Biological Engineering, Chemistry, and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Rafael D Melani
- Departments of Chemical and Biological Engineering, Chemistry, and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Ping F Yip
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Michael W Senko
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Philip D Compton
- Departments of Chemical and Biological Engineering, Chemistry, and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Jared O Kafader
- Departments of Chemical and Biological Engineering, Chemistry, and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Neil L Kelleher
- Departments of Chemical and Biological Engineering, Chemistry, and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
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24
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Deighan WI, Winton VJ, Melani RD, Anderson LC, McGee JP, Schachner LF, Barnidge D, Murray D, Alexander HD, Gibson DS, Deery MJ, McNicholl FP, McLaughlin J, Kelleher NL, Thomas PM. Development of novel methods for non-canonical myeloma protein analysis with an innovative adaptation of immunofixation electrophoresis, native top-down mass spectrometry, and middle-down de novo sequencing. Clin Chem Lab Med 2020; 59:653-661. [PMID: 33079696 DOI: 10.1515/cclm-2020-1072] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 10/07/2020] [Indexed: 12/18/2022]
Abstract
Objectives Multiple myeloma (MM) is a malignant plasma cell neoplasm, requiring the integration of clinical examination, laboratory and radiological investigations for diagnosis. Detection and isotypic identification of the monoclonal protein(s) and measurement of other relevant biomarkers in serum and urine are pivotal analyses. However, occasionally this approach fails to characterize complex protein signatures. Here we describe the development and application of next generation mass spectrometry (MS) techniques, and a novel adaptation of immunofixation, to interrogate non-canonical monoclonal immunoproteins. Methods Immunoprecipitation immunofixation (IP-IFE) was performed on a Sebia Hydrasys Scan2. Middle-down de novo sequencing and native MS were performed with multiple instruments (21T FT-ICR, Q Exactive HF, Orbitrap Fusion Lumos, and Orbitrap Eclipse). Post-acquisition data analysis was performed using Xcalibur Qual Browser, ProSight Lite, and TDValidator. Results We adapted a novel variation of immunofixation electrophoresis (IFE) with an antibody-specific immunosubtraction step, providing insight into the clonal signature of gamma-zone monoclonal immunoglobulin (M-protein) species. We developed and applied advanced mass spectrometric techniques such as middle-down de novo sequencing to attain in-depth characterization of the primary sequence of an M-protein. Quaternary structures of M-proteins were elucidated by native MS, revealing a previously unprecedented non-covalently associated hetero-tetrameric immunoglobulin. Conclusions Next generation proteomic solutions offer great potential for characterizing complex protein structures and may eventually replace current electrophoretic approaches for the identification and quantification of M-proteins. They can also contribute to greater understanding of MM pathogenesis, enabling classification of patients into new subtypes, improved risk stratification and the potential to inform decisions on future personalized treatment modalities.
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Affiliation(s)
- W Ian Deighan
- Department of Clinical Chemistry, Altnagelvin Area Hospital, Londonderry, UK
| | - Valerie J Winton
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
| | - Rafael D Melani
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
| | - Lissa C Anderson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Tallahassee, FL, USA
| | - John P McGee
- Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | - Luis F Schachner
- Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - David Barnidge
- Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - David Murray
- Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - H Denis Alexander
- Northern Ireland Centre for Stratified Medicine, Biomedical Sciences Research Institute, Ulster University, Londonderry, UK
| | - David S Gibson
- Northern Ireland Centre for Stratified Medicine, Biomedical Sciences Research Institute, Ulster University, Londonderry, UK
| | - Michael J Deery
- Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK
| | | | - Joseph McLaughlin
- Northern Ireland Centre for Stratified Medicine, Biomedical Sciences Research Institute, Ulster University, Londonderry, UK
| | - Neil L Kelleher
- Proteomics Center of Excellence & Departments of Chemistry and Molecular Biology,Northwestern University, Evanston, IL, USA
| | - Paul M Thomas
- Proteomics Center of Excellence & Departments of Chemistry and Molecular Biology,Northwestern University, Evanston, IL, USA
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25
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Aguiar RS, Pohl F, Morais GL, Nogueira FCS, Carvalho JB, Guida L, Arge LWP, Melo A, Moreira MEL, Cunha DP, Gomes L, Portari EA, Velasquez E, Melani RD, Pezzuto P, de Castro FL, Geddes VEV, Gerber AL, Azevedo GS, Schamber-Reis BL, Gonçalves AL, Junqueira-de-Azevedo I, Nishiyama MY, Ho PL, Schanoski AS, Schuch V, Tanuri A, Chimelli L, Vasconcelos ZFM, Domont GB, Vasconcelos ATR, Nakaya HI. Molecular alterations in the extracellular matrix in the brains of newborns with congenital Zika syndrome. Sci Signal 2020; 13:eaay6736. [PMID: 32518143 DOI: 10.1126/scisignal.aay6736] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Zika virus (ZIKV) infection during pregnancy can cause a set of severe abnormalities in the fetus known as congenital Zika syndrome (CZS). Experiments with animal models and in vitro systems have substantially contributed to our understanding of the pathophysiology of ZIKV infection. Here, to investigate the molecular basis of CZS in humans, we used a systems biology approach to integrate transcriptomic, proteomic, and genomic data from the postmortem brains of neonates with CZS. We observed that collagens were greatly reduced in expression in CZS brains at both the RNA and protein levels and that neonates with CZS had several single-nucleotide polymorphisms in collagen-encoding genes that are associated with osteogenesis imperfecta and arthrogryposis. These findings were validated by immunohistochemistry and comparative analysis of collagen abundance in ZIKV-infected and uninfected samples. In addition, we showed a ZIKV-dependent increase in the expression of cell adhesion factors that are essential for neurite outgrowth and axon guidance, findings that are consistent with the neuronal migration defects observed in CZS. Together, these findings provide insights into the underlying molecular alterations in the ZIKV-infected brain and reveal host genes associated with CZS susceptibility.
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Affiliation(s)
- Renato S Aguiar
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Fabio Pohl
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Guilherme L Morais
- National Laboratory of Scientific Computation, LNCC/MCTI, Petrópolis, Brazil
| | - Fabio C S Nogueira
- Proteomics Unit, Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratory of Proteomics, LADETEC, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Joseane B Carvalho
- National Laboratory of Scientific Computation, LNCC/MCTI, Petrópolis, Brazil
| | - Letícia Guida
- Fernandes Figueira Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Luis W P Arge
- National Laboratory of Scientific Computation, LNCC/MCTI, Petrópolis, Brazil
| | - Adriana Melo
- Instituto de Pesquisa Professor Amorim Neto, Campina Grande, Paraíba, Brazil
| | | | - Daniela P Cunha
- Fernandes Figueira Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Leonardo Gomes
- Fernandes Figueira Institute, Fiocruz, Rio de Janeiro, Brazil
| | | | - Erika Velasquez
- Proteomics Unit, Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rafael D Melani
- Proteomics Unit, Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paula Pezzuto
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fernanda L de Castro
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Victor E V Geddes
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alexandra L Gerber
- National Laboratory of Scientific Computation, LNCC/MCTI, Petrópolis, Brazil
| | - Girlene S Azevedo
- Instituto de Pesquisa Professor Amorim Neto, Campina Grande, Paraíba, Brazil
| | - Bruno L Schamber-Reis
- Faculdade de Ciências Médicas de Campina Grande, Núcleo de Genética Médica, Centro Universitário UniFacisa, Campina Grande, Paraíba, Brazil
| | - Alessandro L Gonçalves
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Milton Y Nishiyama
- Special Laboratory for Applied Toxinology, Butantan Institute, São Paulo, Brazil
| | - Paulo L Ho
- Bacteriology Laboratory, Butantan Institute, São Paulo, Brazil
| | | | - Viviane Schuch
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Amilcar Tanuri
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Leila Chimelli
- Laboratório de Neuropatologia, Instituto Estadual do Cérebro, Rio de Janeiro, Brazil.
| | | | - Gilberto B Domont
- Proteomics Unit, Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Ana T R Vasconcelos
- National Laboratory of Scientific Computation, LNCC/MCTI, Petrópolis, Brazil.
| | - Helder I Nakaya
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil.
- Scientific Platform Pasteur-USP, São Paulo, Brazil
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26
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Kafader JO, Durbin KR, Melani RD, Des Soye BJ, Schachner LF, Senko MW, Compton PD, Kelleher NL. Individual Ion Mass Spectrometry Enhances the Sensitivity and Sequence Coverage of Top-Down Mass Spectrometry. J Proteome Res 2020; 19:1346-1350. [PMID: 32032494 PMCID: PMC7060802 DOI: 10.1021/acs.jproteome.9b00797] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Charge detection mass spectrometry (CDMS) is mainly utilized to determine the mass of intact molecules. Previous applications of CDMS have determined the mass-to-charge ratio and the charge of large polymers, DNA molecules, and native protein complexes, from which corresponding mass values could be assigned. Recent advances have demonstrated that CDMS using an Orbitrap mass analyzer yields the reliable assignment of integer charge states that enables individual ion mass spectrometry (I2MS) and spectral output directly into the mass domain. Here I2MS analysis was extended to isotopically resolved fragment ions from intact proteoforms for the first time. With a radically different bias for ion readout, I2MS identified low-abundance fragment ions containing many hundreds of residues that were undetectable by standard Orbitrap measurements, leading to a doubling in the sequence coverage of triosephosphate isomerase. Thus MS/MS with the detection of individual ions (MS/I2MS) provides a far greater ability to detect high mass fragment ions and exhibits strong complementarity to traditional spectral readout in this, its first application to top-down mass spectrometry.
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Affiliation(s)
- Jared O. Kafader
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Kenneth R. Durbin
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Rafael D. Melani
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Benjamin J. Des Soye
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Luis F. Schachner
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Michael W. Senko
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Philip D. Compton
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Neil L. Kelleher
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
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27
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McGee JP, Melani RD, Goodwin M, McAlister G, Huguet R, Senko MW, Compton PD, Kelleher NL. Voltage Rollercoaster Filtering of Low-Mass Contaminants During Native Protein Analysis. J Am Soc Mass Spectrom 2020; 31:763-767. [PMID: 32126774 PMCID: PMC7274025 DOI: 10.1021/jasms.9b00037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Intact protein mass spectrometry (MS) via electrospray-based methods is often degraded by low-mass contaminants, which can suppress the spectral quality of the analyte of interest via space-charge effects. Consequently, selective removal of contaminants by their mobilities would benefit native MS if achieved without additional hardware and before the mass analyzer regions used for selection, analyte readout, or tandem MS. Here, we use the high-pressure multipole within the source of an Orbitrap Tribrid as the foundation for a coarse ion filter. Using this method, we show complete filtration of 2 mM polyethylene glycol (PEG-1000) during native MS of SILu mAb antibody present at a 200× lower concentration. We also show the generality of the process by rescuing 10 μM tetrameric pyruvate kinase from 2 mM PEG-1000, asserting this voltage rollercoaster filtering (VRF) method for use in native MS as an efficient alternative to conventional purification methods.
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Affiliation(s)
- John P McGee
- Departments of Chemical and Biological Engineering, Chemistry, and Molecular Biosciences, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Rafael D Melani
- Departments of Chemical and Biological Engineering, Chemistry, and Molecular Biosciences, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Michael Goodwin
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Graeme McAlister
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Romain Huguet
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Michael W Senko
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Philip D Compton
- Departments of Chemical and Biological Engineering, Chemistry, and Molecular Biosciences, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Neil L Kelleher
- Departments of Chemical and Biological Engineering, Chemistry, and Molecular Biosciences, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
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Kafader JO, Melani RD, Schachner LF, Ives AN, Patrie SM, Kelleher NL, Compton PD. Native vs Denatured: An in Depth Investigation of Charge State and Isotope Distributions. J Am Soc Mass Spectrom 2020; 31:574-581. [PMID: 31971796 PMCID: PMC7539638 DOI: 10.1021/jasms.9b00040] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
New tools and techniques have dramatically accelerated the field of structural biology over the past several decades. One potent and relatively new technique that is now being utilized by an increasing number of laboratories is the combination of so-called "native" electrospray ionization (ESI) with mass spectrometry (MS) for the characterization of proteins and their noncovalent complexes. However, native ESI-MS produces species at increasingly higher m/z with increasing molecular weight, leading to substantial differences when compared to traditional mass spectrometric approaches using denaturing ESI solutions. Herein, these differences are explored both theoretically and experimentally to understand the role that charge state and isotopic distributions have on signal-to-noise (S/N) as a function of complex molecular weight and how the reduced collisional cross sections of proteins electrosprayed under native solution conditions can lead to improved data quality in image current mass analyzers, such as Orbitrap and FT-ICR. Quantifying ion signal differences under native and denatured conditions revealed enhanced S/N and a more gradual decay in S/N with increasing mass under native conditions. Charge state and isotopic S/N models, supported by experimental results, indicate that analysis of proteins under native conditions at 100 kDa will be 17 times more sensitive than analysis under denatured conditions at the same mass. Higher masses produce even larger sensitivity gains. Furthermore, reduced cross sections under native conditions lead to lower levels of ion decay within an Orbitrap scan event over long transient acquisition times, enabling isotopic resolution of species with molecular weights well in excess of those typically resolved under denatured conditions.
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Affiliation(s)
- Jared O Kafader
- Departments of Chemistry and Molecular Biosciences, Chemistry of Life Processes Institute, Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Rafael D Melani
- Departments of Chemistry and Molecular Biosciences, Chemistry of Life Processes Institute, Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Luis F Schachner
- Departments of Chemistry and Molecular Biosciences, Chemistry of Life Processes Institute, Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Ashley N Ives
- Departments of Chemistry and Molecular Biosciences, Chemistry of Life Processes Institute, Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Steven M Patrie
- Departments of Chemistry and Molecular Biosciences, Chemistry of Life Processes Institute, Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Neil L Kelleher
- Departments of Chemistry and Molecular Biosciences, Chemistry of Life Processes Institute, Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Philip D Compton
- Departments of Chemistry and Molecular Biosciences, Chemistry of Life Processes Institute, Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
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29
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Fornelli L, Srzentić K, Toby TK, Doubleday PF, Huguet R, Mullen C, Melani RD, Dos Santos Seckler H, DeHart CJ, Weisbrod CR, Durbin KR, Greer JB, Early BP, Fellers RT, Zabrouskov V, Thomas PM, Compton PD, Kelleher NL. Thorough Performance Evaluation of 213 nm Ultraviolet Photodissociation for Top-down Proteomics. Mol Cell Proteomics 2020; 19:405-420. [PMID: 31888965 PMCID: PMC7000117 DOI: 10.1074/mcp.tir119.001638] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 11/29/2019] [Indexed: 11/06/2022] Open
Abstract
Top-down proteomics studies intact proteoform mixtures and offers important advantages over more common bottom-up proteomics technologies, as it avoids the protein inference problem. However, achieving complete molecular characterization of investigated proteoforms using existing technologies remains a fundamental challenge for top-down proteomics. Here, we benchmark the performance of ultraviolet photodissociation (UVPD) using 213 nm photons generated by a solid-state laser applied to the study of intact proteoforms from three organisms. Notably, the described UVPD setup applies multiple laser pulses to induce ion dissociation, and this feature can be used to optimize the fragmentation outcome based on the molecular weight of the analyzed biomolecule. When applied to complex proteoform mixtures in high-throughput top-down proteomics, 213 nm UVPD demonstrated a high degree of complementarity with the most employed fragmentation method in proteomics studies, higher-energy collisional dissociation (HCD). UVPD at 213 nm offered higher average proteoform sequence coverage and degree of proteoform characterization (including localization of post-translational modifications) than HCD. However, previous studies have shown limitations in applying database search strategies developed for HCD fragmentation to UVPD spectra which contains up to nine fragment ion types. We therefore performed an analysis of the different UVPD product ion type frequencies. From these data, we developed an ad hoc fragment matching strategy and determined the influence of each possible ion type on search outcomes. By paring down the number of ion types considered in high-throughput UVPD searches from all types down to the four most abundant, we were ultimately able to achieve deeper proteome characterization with UVPD. Lastly, our detailed product ion analysis also revealed UVPD cleavage propensities and determined the presence of a product ion produced specifically by 213 nm photons. All together, these observations could be used to better elucidate UVPD dissociation mechanisms and improve the utility of the technique for proteomic applications.
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Affiliation(s)
- Luca Fornelli
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | - Kristina Srzentić
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | - Timothy K Toby
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | - Peter F Doubleday
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | - Romain Huguet
- Thermo Fisher Scientific, San Jose, California 95134
| | | | - Rafael D Melani
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | - Henrique Dos Santos Seckler
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | - Caroline J DeHart
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | | | - Kenneth R Durbin
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208; Proteinaceous Inc., Evanston, Illinois 60201
| | - Joseph B Greer
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | - Bryan P Early
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | - Ryan T Fellers
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | | | - Paul M Thomas
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | - Philip D Compton
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | - Neil L Kelleher
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208.
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30
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Kafader JO, Beu SC, Early BP, Melani RD, Durbin KR, Zabrouskov V, Makarov AA, Maze JT, Shinholt DL, Yip PF, Kelleher NL, Compton PD, Senko MW. STORI Plots Enable Accurate Tracking of Individual Ion Signals. J Am Soc Mass Spectrom 2019; 30:2200-2203. [PMID: 31512223 PMCID: PMC6852666 DOI: 10.1007/s13361-019-02309-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 07/30/2019] [Accepted: 08/02/2019] [Indexed: 05/08/2023]
Abstract
Charge detection mass spectrometry (CDMS) of low-level signals is currently limited to the analysis of individual ions that generate a persistent signal during the entire observation period. Ions that disintegrate during the observation period produce reduced frequency domain signal amplitudes, which lead to an underestimation of the ion charge state, and thus the ion mass. The charge assignment can only be corrected through an accurate determination of the time of ion disintegration. The traditional mechanisms for temporal signal analysis have severe limitations for temporal resolution, spectral resolution, and signal-to-noise ratios. Selective Temporal Overview of Resonant Ions (STORI) plots provide a new framework to accurately analyze low-level time domain signals of individual ions. STORI plots allow for complete correction of intermittent signals, the differentiation of single and multiple ions at the same frequency, and the association of signals that spontaneously change frequency.
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Affiliation(s)
- Jared O Kafader
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, The Proteomics Center of Excellence at Northwestern University, Evanston, IL, 60208, USA
| | | | - Bryan P Early
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, The Proteomics Center of Excellence at Northwestern University, Evanston, IL, 60208, USA
| | - Rafael D Melani
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, The Proteomics Center of Excellence at Northwestern University, Evanston, IL, 60208, USA
| | - Kenneth R Durbin
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, The Proteomics Center of Excellence at Northwestern University, Evanston, IL, 60208, USA
| | | | | | | | | | - Ping F Yip
- Thermo Fisher Scientific, San Jose, CA, 95134, USA
| | - Neil L Kelleher
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, The Proteomics Center of Excellence at Northwestern University, Evanston, IL, 60208, USA
| | - Philip D Compton
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, The Proteomics Center of Excellence at Northwestern University, Evanston, IL, 60208, USA
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31
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Melani RD, Srzentić K, Gerbasi VR, McGee JP, Huguet R, Fornelli L, Kelleher NL. Direct measurement of light and heavy antibody chains using ion mobility and middle-down mass spectrometry. MAbs 2019; 11:1351-1357. [PMID: 31607219 PMCID: PMC6816405 DOI: 10.1080/19420862.2019.1668226] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The analysis of monoclonal antibodies (mAbs) by a middle-down mass spectrometry (MS) approach is a growing field that attracts the attention of many researchers and biopharmaceutical companies. Usually, liquid fractionation techniques are used to separate mAbs polypeptides chains before MS analysis. Gas-phase fractionation techniques such as high-field asymmetric waveform ion mobility spectrometry (FAIMS) can replace liquid-based separations and reduce both analysis time and cost. Here, we present a rapid FAIMS tandem MS method capable of characterizing the polypeptide sequence of mAbs light and heavy chains in an unprecedented, easy, and fast fashion. This new method uses commercially available instruments and takes ~24 min, which is 40-60% faster than regular liquid chromatography-MS/MS analysis, to acquire fragmentation data using different dissociation methods.
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Affiliation(s)
- Rafael D Melani
- Departments of Chemistry, Molecular Biosciences, and Chemical and Biological Engineering; the Chemistry of Life Processes Institute; and the Proteomics Center of Excellence, Northwestern University , Evanston , IL , USA
| | | | - Vincent R Gerbasi
- Departments of Chemistry, Molecular Biosciences, and Chemical and Biological Engineering; the Chemistry of Life Processes Institute; and the Proteomics Center of Excellence, Northwestern University , Evanston , IL , USA
| | - John P McGee
- Departments of Chemistry, Molecular Biosciences, and Chemical and Biological Engineering; the Chemistry of Life Processes Institute; and the Proteomics Center of Excellence, Northwestern University , Evanston , IL , USA
| | | | - Luca Fornelli
- Department of Biology, University of Oklahoma , Norman , OK , USA
| | - Neil L Kelleher
- Departments of Chemistry, Molecular Biosciences, and Chemical and Biological Engineering; the Chemistry of Life Processes Institute; and the Proteomics Center of Excellence, Northwestern University , Evanston , IL , USA
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32
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Schachner LF, Ives AN, McGee JP, Melani RD, Kafader JO, Compton PD, Patrie SM, Kelleher NL. Standard Proteoforms and Their Complexes for Native Mass Spectrometry. J Am Soc Mass Spectrom 2019; 30:1190-1198. [PMID: 30963455 PMCID: PMC6592724 DOI: 10.1007/s13361-019-02191-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 03/04/2019] [Accepted: 03/11/2019] [Indexed: 05/09/2023]
Abstract
Native mass spectrometry (nMS) is a technique growing at the interface of analytical chemistry, structural biology, and proteomics that enables the detection and partial characterization of non-covalent protein assemblies. Currently, the standardization and dissemination of nMS is hampered by technical challenges associated with instrument operation, benchmarking, and optimization over time. Here, we provide a standard operating procedure for acquiring high-quality native mass spectra of 30-300 kDa proteins using an Orbitrap mass spectrometer. By describing reproducible sample preparation, loading, ionization, and nMS analysis, we forward two proteoforms and three complexes as possible standards to advance training and longitudinal assessment of instrument performance. Spectral data for five standards can guide assessment of instrument parameters, data production, and data analysis. By introducing this set of standards and protocols, we aim to help normalize native mass spectrometry practices across labs and provide benchmarks for reproducibility and high-quality data production in the years ahead. Graphical abstract.
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Affiliation(s)
- Luis F Schachner
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, Evanston, IL, 60208, USA
| | - Ashley N Ives
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, Evanston, IL, 60208, USA
| | - John P McGee
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, Evanston, IL, 60208, USA
| | - Rafael D Melani
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, Evanston, IL, 60208, USA
| | - Jared O Kafader
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, Evanston, IL, 60208, USA
| | - Philip D Compton
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, Evanston, IL, 60208, USA
| | - Steven M Patrie
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, Evanston, IL, 60208, USA
| | - Neil L Kelleher
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, Evanston, IL, 60208, USA.
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33
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Kafader JO, Melani RD, Senko MW, Makarov AA, Kelleher NL, Compton PD. Measurement of Individual Ions Sharply Increases the Resolution of Orbitrap Mass Spectra of Proteins. Anal Chem 2019; 91:2776-2783. [PMID: 30609364 DOI: 10.1021/acs.analchem.8b04519] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
It is well-known that with Orbitrap-based Fourier-transform-mass-spectrometry (FT-MS) analysis, longer-time-domain signals are needed to better resolve species of interest. Unfortunately, increasing the signal-acquisition period comes at the expense of increasing ion decay, which lowers signal-to-noise ratios and ultimately limits resolution. This is especially problematic for intact proteins, including antibodies, which demonstrate rapid decay because of their larger collisional cross-sections, and result in more frequent collisions with background gas molecules. Provided here is a method that utilizes numerous low-ion-count spectra and single-ion processing to reconstruct a conventional m/ z spectrum. This technique has been applied to proteins varying in molecular weight from 8 to 150 kDa, with a resolving power of 677 000 achieved for transients of carbonic anhydrase (29 kDa) with a duration of only ∼250 ms. A resolution improvement ranging from 10- to 20-fold was observed for all proteins, providing isotopic resolution where none was previously present.
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Affiliation(s)
- Jared O Kafader
- Departments of Chemistry and Molecular Biosciences, The Chemistry of Life Processes Institute , The Proteomics Center of Excellence at Northwestern University , Evanston , Illinois 60208 , United States
| | - Rafael D Melani
- Departments of Chemistry and Molecular Biosciences, The Chemistry of Life Processes Institute , The Proteomics Center of Excellence at Northwestern University , Evanston , Illinois 60208 , United States
| | - Michael W Senko
- Thermo Fisher Scientific , San Jose , California 95134 , United States
| | | | - Neil L Kelleher
- Departments of Chemistry and Molecular Biosciences, The Chemistry of Life Processes Institute , The Proteomics Center of Excellence at Northwestern University , Evanston , Illinois 60208 , United States
| | - Philip D Compton
- Departments of Chemistry and Molecular Biosciences, The Chemistry of Life Processes Institute , The Proteomics Center of Excellence at Northwestern University , Evanston , Illinois 60208 , United States
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Abstract
The protein composition of animal venoms is usually determined by peptide-centric proteomics approaches (bottom-up proteomics). However, this technique cannot, in most cases, distinguish among toxin proteoforms, herein called toxiforms, because of the protein inference problem. Top-down proteomics (TDP) analyzes intact proteins without digestion and provides high quality data to identify and characterize toxiforms. Denaturing top-down proteomics is the most disseminated subarea of TDP, which performs qualitative and quantitative analyzes of proteoforms up to ~30 kDa in high-throughput and automated fashion. On the other hand, native top-down proteomics provides access to information on large proteins (> 50 kDA) and protein interactions preserving non-covalent bonds and physiological complex stoichiometry. The use of native and denaturing top-down venomics introduced novel and useful techniques to toxinology, allowing an unprecedented characterization of venom proteins and protein complexes at the toxiform level. The collected data contribute to a deep understanding of venom natural history, open new possibilities to study the toxin evolution, and help in the development of better biotherapeutics.
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Affiliation(s)
- Rafael D. Melani
- Proteomics Unit, Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Av. Athos da Silveira Ramos, 149, CT A-542, Cidade Universitária, Rio de Janeiro, RJ CEP 21941-909 Brazil
| | - Fabio C. S. Nogueira
- Proteomics Unit, Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Av. Athos da Silveira Ramos, 149, CT A-542, Cidade Universitária, Rio de Janeiro, RJ CEP 21941-909 Brazil
| | - Gilberto B. Domont
- Proteomics Unit, Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Av. Athos da Silveira Ramos, 149, CT A-542, Cidade Universitária, Rio de Janeiro, RJ CEP 21941-909 Brazil
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35
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Melani RD, Skinner OS, Fornelli L, Domont GB, Compton PD, Kelleher NL. Mapping Proteoforms and Protein Complexes From King Cobra Venom Using Both Denaturing and Native Top-down Proteomics. Mol Cell Proteomics 2016; 15:2423-34. [PMID: 27178327 DOI: 10.1074/mcp.m115.056523] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Indexed: 11/06/2022] Open
Abstract
Characterizing whole proteins by top-down proteomics avoids a step of inference encountered in the dominant bottom-up methodology when peptides are assembled computationally into proteins for identification. The direct interrogation of whole proteins and protein complexes from the venom of Ophiophagus hannah (king cobra) provides a sharply clarified view of toxin sequence variation, transit peptide cleavage sites and post-translational modifications (PTMs) likely critical for venom lethality. A tube-gel format for electrophoresis (called GELFrEE) and solution isoelectric focusing were used for protein fractionation prior to LC-MS/MS analysis resulting in 131 protein identifications (18 more than bottom-up) and a total of 184 proteoforms characterized from 14 protein toxin families. Operating both GELFrEE and mass spectrometry to preserve non-covalent interactions generated detailed information about two of the largest venom glycoprotein complexes: the homodimeric l-amino acid oxidase (∼130 kDa) and the multichain toxin cobra venom factor (∼147 kDa). The l-amino acid oxidase complex exhibited two clusters of multiproteoform complexes corresponding to the presence of 5 or 6 N-glycans moieties, each consistent with a distribution of N-acetyl hexosamines. Employing top-down proteomics in both native and denaturing modes provides unprecedented characterization of venom proteoforms and their complexes. A precise molecular inventory of venom proteins will propel the study of snake toxin variation and the targeted development of new antivenoms or other biotherapeutics.
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Affiliation(s)
- Rafael D Melani
- From the ‡Proteomics Unit, Rio de Janeiro Proteomics Network, Departamento de Bioquímica. Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-909, Brazil; §Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, 60208
| | - Owen S Skinner
- §Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, 60208
| | - Luca Fornelli
- §Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, 60208
| | - Gilberto B Domont
- From the ‡Proteomics Unit, Rio de Janeiro Proteomics Network, Departamento de Bioquímica. Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-909, Brazil;
| | - Philip D Compton
- §Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, 60208
| | - Neil L Kelleher
- §Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, 60208
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36
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Skinner OS, Havugimana PC, Haverland NA, Fornelli L, Early BP, Greer JB, Fellers RT, Durbin KR, Do Vale LHF, Melani RD, Seckler HS, Nelp MT, Belov ME, Horning SR, Makarov AA, LeDuc RD, Bandarian V, Compton PD, Kelleher NL. An informatic framework for decoding protein complexes by top-down mass spectrometry. Nat Methods 2016; 13:237-40. [PMID: 26780093 PMCID: PMC4767540 DOI: 10.1038/nmeth.3731] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 11/30/2015] [Indexed: 12/22/2022]
Abstract
Efforts to map the human protein interactome have resulted in information about thousands of multi-protein assemblies housed in public repositories, but the molecular characterization and stoichiometry of their protein subunits remains largely unknown. Here, we report a computational search strategy that supports hierarchical top-down analysis for precise identification and scoring of multi-proteoform complexes by native mass spectrometry.
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Affiliation(s)
- Owen S. Skinner
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA
| | - Pierre C. Havugimana
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA
| | | | - Luca Fornelli
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA
| | - Bryan P. Early
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA
| | - Joseph B. Greer
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA
| | - Ryan T. Fellers
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA
| | - Kenneth R. Durbin
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
| | - Luis H. F. Do Vale
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA
- Brazilian Center for Protein Research, University of Brasilia, Brasilia, Federal District, Brazil
| | - Rafael D. Melani
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA
| | | | - Micah T. Nelp
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA
| | | | | | | | - Richard D. LeDuc
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA
| | - Vahe Bandarian
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA
| | - Philip D. Compton
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA
| | - Neil L. Kelleher
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
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37
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Melani RD, Seckler HS, Skinner OS, Do Vale LHF, Catherman AD, Havugimana PC, Valle de Sousa M, Domont GB, Kelleher NL, Compton PD. CN-GELFrEE - Clear Native Gel-eluted Liquid Fraction Entrapment Electrophoresis. J Vis Exp 2016:53597. [PMID: 26967310 DOI: 10.3791/53597] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Protein complexes perform an array of crucial cellular functions. Elucidating their non-covalent interactions and dynamics is paramount for understanding the role of complexes in biological systems. While the direct characterization of biomolecular assemblies has become increasingly important in recent years, native fractionation techniques that are compatible with downstream analysis techniques, including mass spectrometry, are necessary to further expand these studies. Nevertheless, the field lacks a high-throughput, wide-range, high-recovery separation method for native protein assemblies. Here, we present clear native gel-eluted liquid fraction entrapment electrophoresis (CN-GELFrEE), which is a novel separation modality for non-covalent protein assemblies. CN-GELFrEE separation performance was demonstrated by fractionating complexes extracted from mouse heart. Fractions were collected over 2 hr and displayed discrete bands ranging from ~30 to 500 kDa. A consistent pattern of increasing molecular weight bandwidths was observed, each ranging ~100 kDa. Further, subsequent reanalysis of native fractions via SDS-PAGE showed molecular-weight shifts consistent with the denaturation of protein complexes. Therefore, CN-GELFrEE was proved to offer the ability to perform high-resolution and high-recovery native separations on protein complexes from a large molecular weight range, providing fractions that are compatible with downstream protein analyses.
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Affiliation(s)
- Rafael D Melani
- Departments of Chemistry and Molecular Biosciences, Chemistry of Life Processes Institute, Proteomics Center of Excellence, Robert H. Lurie Comprehensive Cancer Center, Northwestern University; Institute of Chemistry, Proteomics Unit, Federal University of Rio de Janeiro
| | - Henrique S Seckler
- Departments of Chemistry and Molecular Biosciences, Chemistry of Life Processes Institute, Proteomics Center of Excellence, Robert H. Lurie Comprehensive Cancer Center, Northwestern University
| | - Owen S Skinner
- Departments of Chemistry and Molecular Biosciences, Chemistry of Life Processes Institute, Proteomics Center of Excellence, Robert H. Lurie Comprehensive Cancer Center, Northwestern University
| | - Luis H F Do Vale
- Departments of Chemistry and Molecular Biosciences, Chemistry of Life Processes Institute, Proteomics Center of Excellence, Robert H. Lurie Comprehensive Cancer Center, Northwestern University; Department of Cell Biology, Brazilian Center for Protein Research, Laboratory of Biochemistry and Protein Chemistry, University of Brasilia
| | - Adam D Catherman
- Departments of Chemistry and Molecular Biosciences, Chemistry of Life Processes Institute, Proteomics Center of Excellence, Robert H. Lurie Comprehensive Cancer Center, Northwestern University
| | - Pierre C Havugimana
- Departments of Chemistry and Molecular Biosciences, Chemistry of Life Processes Institute, Proteomics Center of Excellence, Robert H. Lurie Comprehensive Cancer Center, Northwestern University
| | - Marcelo Valle de Sousa
- Department of Cell Biology, Brazilian Center for Protein Research, Laboratory of Biochemistry and Protein Chemistry, University of Brasilia
| | - Gilberto B Domont
- Institute of Chemistry, Proteomics Unit, Federal University of Rio de Janeiro
| | - Neil L Kelleher
- Departments of Chemistry and Molecular Biosciences, Chemistry of Life Processes Institute, Proteomics Center of Excellence, Robert H. Lurie Comprehensive Cancer Center, Northwestern University
| | - Philip D Compton
- Departments of Chemistry and Molecular Biosciences, Chemistry of Life Processes Institute, Proteomics Center of Excellence, Robert H. Lurie Comprehensive Cancer Center, Northwestern University;
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Melani RD, Araujo GD, Carvalho PC, Goto L, Nogueira FC, Junqueira M, Domont GB. Seeing beyond the tip of the iceberg: A deep analysis of the venome of the Brazilian Rattlesnake, Crotalus durissus terrificus. EuPA Open Proteomics 2015. [DOI: 10.1016/j.euprot.2015.05.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Abstract
Eight cassava (Manihot esculenta Crantz) cultivars, of which four are indigenous to the Amazon region, along with an interspecific hybrid, were assessed for their carotenoid content. They were propagated and are maintained in the living Manihot collection at the University of Brasília. The cultivar "Amarelinha do Amapá", which was collected from the State of Amapá, was found to have a very high content of beta-carotene: 27 mg per 100 mg, which is more than 50-fold higher than in other cassava cultivars. This cultivar, which also has excellent palatability, could be an important source of beta-carotene for cassava breeding.
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