1
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Jiang Y, Rex DA, Schuster D, Neely BA, Rosano GL, Volkmar N, Momenzadeh A, Peters-Clarke TM, Egbert SB, Kreimer S, Doud EH, Crook OM, Yadav AK, Vanuopadath M, Hegeman AD, Mayta M, Duboff AG, Riley NM, Moritz RL, Meyer JG. Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry. ACS MEASUREMENT SCIENCE AU 2024; 4:338-417. [PMID: 39193565 PMCID: PMC11348894 DOI: 10.1021/acsmeasuresciau.3c00068] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 05/03/2024] [Accepted: 05/03/2024] [Indexed: 08/29/2024]
Abstract
Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins are hydrolyzed into peptides that are analyzed by mass spectrometry. Proteomics studies can be applied to diverse studies ranging from simple protein identification to studies of proteoforms, protein-protein interactions, protein structural alterations, absolute and relative protein quantification, post-translational modifications, and protein stability. To enable this range of different experiments, there are diverse strategies for proteome analysis. The nuances of how proteomic workflows differ may be challenging to understand for new practitioners. Here, we provide a comprehensive overview of different proteomics methods. We cover from biochemistry basics and protein extraction to biological interpretation and orthogonal validation. We expect this Review will serve as a handbook for researchers who are new to the field of bottom-up proteomics.
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Affiliation(s)
- Yuming Jiang
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Devasahayam Arokia
Balaya Rex
- Center for
Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Dina Schuster
- Department
of Biology, Institute of Molecular Systems
Biology, ETH Zurich, Zurich 8093, Switzerland
- Department
of Biology, Institute of Molecular Biology
and Biophysics, ETH Zurich, Zurich 8093, Switzerland
- Laboratory
of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Benjamin A. Neely
- Chemical
Sciences Division, National Institute of
Standards and Technology, NIST, Charleston, South Carolina 29412, United States
| | - Germán L. Rosano
- Mass
Spectrometry
Unit, Institute of Molecular and Cellular
Biology of Rosario, Rosario, 2000 Argentina
| | - Norbert Volkmar
- Department
of Biology, Institute of Molecular Systems
Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Amanda Momenzadeh
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Trenton M. Peters-Clarke
- Department
of Pharmaceutical Chemistry, University
of California—San Francisco, San Francisco, California, 94158, United States
| | - Susan B. Egbert
- Department
of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2 Canada
| | - Simion Kreimer
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Emma H. Doud
- Center
for Proteome Analysis, Indiana University
School of Medicine, Indianapolis, Indiana, 46202-3082, United States
| | - Oliver M. Crook
- Oxford
Protein Informatics Group, Department of Statistics, University of Oxford, Oxford OX1 3LB, United
Kingdom
| | - Amit Kumar Yadav
- Translational
Health Science and Technology Institute, NCR Biotech Science Cluster 3rd Milestone Faridabad-Gurgaon
Expressway, Faridabad, Haryana 121001, India
| | | | - Adrian D. Hegeman
- Departments
of Horticultural Science and Plant and Microbial Biology, University of Minnesota, Twin Cities, Minnesota 55108, United States
| | - Martín
L. Mayta
- School
of Medicine and Health Sciences, Center for Health Sciences Research, Universidad Adventista del Plata, Libertador San Martin 3103, Argentina
- Molecular
Biology Department, School of Pharmacy and Biochemistry, Universidad Nacional de Rosario, Rosario 2000, Argentina
| | - Anna G. Duboff
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Nicholas M. Riley
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Robert L. Moritz
- Institute
for Systems biology, Seattle, Washington 98109, United States
| | - Jesse G. Meyer
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
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2
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Peters-Clarke TM, Coon JJ, Riley NM. Instrumentation at the Leading Edge of Proteomics. Anal Chem 2024; 96:7976-8010. [PMID: 38738990 DOI: 10.1021/acs.analchem.3c04497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Affiliation(s)
- Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - Nicholas M Riley
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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3
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Agostini M, Traldi P, Hamdan M. Mass Spectrometry Investigation of Some ATP-Binding Cassette (ABC) Proteins. MEDICINA (KAUNAS, LITHUANIA) 2024; 60:200. [PMID: 38399488 PMCID: PMC10890348 DOI: 10.3390/medicina60020200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 02/25/2024]
Abstract
Drug resistance remains one of the main causes of poor outcome in cancer therapy. It is also becoming evident that drug resistance to both chemotherapy and to antibiotics is driven by more than one mechanism. So far, there are at least eight recognized mechanisms behind such resistance. In this review, we choose to discuss one of these mechanisms, which is known to be partially driven by a class of transmembrane proteins known as ATP-binding cassette (ABC) transporters. In normal tissues, ABC transporters protect the cells from the toxic effects of xenobiotics, whereas in tumor cells, they reduce the intracellular concentrations of anticancer drugs, which ultimately leads to the emergence of multidrug resistance (MDR). A deeper understanding of the structures and the biology of these proteins is central to current efforts to circumvent resistance to both chemotherapy, targeted therapy, and antibiotics. Understanding the biology and the function of these proteins requires detailed structural and conformational information for this class of membrane proteins. For many years, such structural information has been mainly provided by X-ray crystallography and cryo-electron microscopy. More recently, mass spectrometry-based methods assumed an important role in the area of structural and conformational characterization of this class of proteins. The contribution of this technique to structural biology has been enhanced by its combination with liquid chromatography and ion mobility, as well as more refined labelling protocols and the use of more efficient fragmentation methods, which allow the detection and localization of labile post-translational modifications. In this review, we discuss the contribution of mass spectrometry to efforts to characterize some members of the ATP-binding cassette (ABC) proteins and why such a contribution is relevant to efforts to clarify the link between the overexpression of these proteins and the most widespread mechanism of chemoresistance.
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Affiliation(s)
| | - Pietro Traldi
- Corso Stati Uniti 4, Istituto di Ricerca Pediatrica Città della Speranza, 35100 Padova, Italy; (M.A.)
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4
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Jiang Y, Rex DAB, Schuster D, Neely BA, Rosano GL, Volkmar N, Momenzadeh A, Peters-Clarke TM, Egbert SB, Kreimer S, Doud EH, Crook OM, Yadav AK, Vanuopadath M, Mayta ML, Duboff AG, Riley NM, Moritz RL, Meyer JG. Comprehensive Overview of Bottom-Up Proteomics using Mass Spectrometry. ARXIV 2023:arXiv:2311.07791v1. [PMID: 38013887 PMCID: PMC10680866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins are hydrolyzed into peptides that are analyzed by mass spectrometry. Proteomics studies can be applied to diverse studies ranging from simple protein identification to studies of proteoforms, protein-protein interactions, protein structural alterations, absolute and relative protein quantification, post-translational modifications, and protein stability. To enable this range of different experiments, there are diverse strategies for proteome analysis. The nuances of how proteomic workflows differ may be challenging to understand for new practitioners. Here, we provide a comprehensive overview of different proteomics methods to aid the novice and experienced researcher. We cover from biochemistry basics and protein extraction to biological interpretation and orthogonal validation. We expect this work to serve as a basic resource for new practitioners in the field of shotgun or bottom-up proteomics.
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Affiliation(s)
- Yuming Jiang
- Department of Computational Biomedicine, Cedars Sinai Medical Center
| | - Devasahayam Arokia Balaya Rex
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Dina Schuster
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland; Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich 8093, Switzerland; Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Benjamin A. Neely
- Chemical Sciences Division, National Institute of Standards and Technology, NIST Charleston · Funded by NIST
| | - Germán L. Rosano
- Mass Spectrometry Unit, Institute of Molecular and Cellular Biology of Rosario, Rosario, Argentina · Funded by Grant PICT 2019-02971 (Agencia I+D+i)
| | - Norbert Volkmar
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Amanda Momenzadeh
- Department of Computational Biomedicine, Cedars Sinai Medical Center, Los Angeles, California, USA
| | | | - Susan B. Egbert
- Department of Chemistry, University of Manitoba, Winnipeg, Cananda
| | - Simion Kreimer
- Smidt Heart Institute, Cedars Sinai Medical Center; Advanced Clinical Biosystems Research Institute, Cedars Sinai Medical Center
| | - Emma H. Doud
- Center for Proteome Analysis, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Oliver M. Crook
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford OX1 3LB, United Kingdom
| | - Amit Kumar Yadav
- Translational Health Science and Technology Institute · Funded by Grant BT/PR16456/BID/7/624/2016 (Department of Biotechnology, India); Grant Translational Research Program (TRP) at THSTI funded by DBT
| | - Muralidharan Vanuopadath
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam-690 525, Kerala, India · Funded by Department of Health Research, Indian Council of Medical Research, Government of India (File No.R.12014/31/2022-HR)
| | - Martín L. Mayta
- School of Medicine and Health Sciences, Center for Health Sciences Research, Universidad Adventista del Plata, Libertador San Martín 3103, Argentina; Molecular Biology Department, School of Pharmacy and Biochemistry, Universidad Nacional de Rosario, Rosario 2000, Argentina
| | - Anna G. Duboff
- Department of Chemistry, University of Washington · Funded by Summer Research Acceleration Fellowship, Department of Chemistry, University of Washington
| | - Nicholas M. Riley
- Department of Chemistry, University of Washington · Funded by National Institutes of Health Grant R00 GM147304
| | - Robert L. Moritz
- Institute for Systems biology, Seattle, WA, USA, 98109 · Funded by National Institutes of Health Grants R01GM087221, R24GM127667, U19AG023122, S10OD026936; National Science Foundation Award 1920268
| | - Jesse G. Meyer
- Department of Computational Biomedicine, Cedars Sinai Medical Center · Funded by National Institutes of Health Grant R21 AG074234; National Institutes of Health Grant R35 GM142502
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5
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Li M, Zhong X, Feng Y, Li L. Novel Isobaric Tagging Reagent Enabled Multiplex Quantitative Glycoproteomics via Electron-Transfer/Higher-Energy Collisional Dissociation (EThcD) Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1874-1882. [PMID: 36095095 PMCID: PMC10160164 DOI: 10.1021/jasms.2c00177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Protein glycosylation, covalent attachment of carbohydrates to polypeptide chains, is a highly important post-translational modification involved in many essential physiological processes. Comprehensive site-specific and quantitative analysis is crucial for revealing the diverse functions and dynamics of glycosylation. To characterize intact glycopeptides, mass spectrometry (MS)-based glycoproteomics employs versatile fragmentation methods, among which electron-transfer/higher-energy collision dissociation (EThcD) has gained great popularity. However, the inherent limitation of EThcD in fragmenting low-charge ions has prevented its widespread applications. Furthermore, there is a need to develop a high-throughput strategy for comparative glycoproteomics with a large cohort of samples. Herein, we developed isobaric N,N-dimethyl leucine-derivatized ethylenediamine (DiLeuEN) tags to increase the charge states of glycopeptides, thereby improving the fragmentation efficiency and allowing for in-depth intact glycopeptide analysis, especially for sialoglycopeptides. Moreover, the unique reporter ions of DiLeuEN-labeled glycopeptides generated in tandem MS spectra enable relative quantification of up to four samples in a single analysis, which represents a new high-throughput method for quantitative glycoproteomics.
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6
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Chen L, Li X, Xie Y, Liu N, Qin X, Chen X, Bu Y. Modulation of proton-coupled electron transfer reactions in lysine-containing alpha-helixes: alpha-helixes promoting long-range electron transfer. Phys Chem Chem Phys 2022; 24:14592-14602. [PMID: 35667661 DOI: 10.1039/d2cp00666a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The proton-coupled electron transfer (PCET) reaction plays an important role in promoting many biological and chemical reactions. Usually, the rate of the PCET reaction increases with an increase in the electron transfer distance because long-range electron transfer requires more free energy barriers. Our density functional theory calculations here reveal that the mechanism of PCET occurring in lysine-containing alpha(α)-helixes changes with an increasing number of residues in the α-helical structure and the different conformations because of the modulation of the excess electron distribution by the α-helical structures. The rate constants of the corresponding PCET reactions are independent of or substantially shallower dependent on the electron transfer distances along α-helixes. This counter-intuitive behavior can be attributed to the fact that the formation of larger macro-cylindrical dipole moments in longer helixes can promote electron transfer along the α-helix with a low energy barrier. These findings may be useful to gain insights into long-range electron transfer in proteins and design α-helix-based electronics via the regulation of short-range proton transfer.
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Affiliation(s)
- Long Chen
- Chongqing Key Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331, P. R. China.
| | - Xin Li
- Chongqing Key Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331, P. R. China.
| | - Yuxin Xie
- Chongqing Key Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331, P. R. China.
| | - Nian Liu
- Chongqing Key Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331, P. R. China.
| | - Xin Qin
- Chongqing Key Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331, P. R. China.
| | - Xiaohua Chen
- Chongqing Key Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331, P. R. China.
| | - Yuxiang Bu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong, 250100, P. R. China.
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7
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Burt RA, Alghusen IM, John Ephrame S, Villar MT, Artigues A, Slawson C. Mapping the O-GlcNAc Modified Proteome: Applications for Health and Disease. Front Mol Biosci 2022; 9:920727. [PMID: 35664676 PMCID: PMC9161079 DOI: 10.3389/fmolb.2022.920727] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/02/2022] [Indexed: 01/03/2023] Open
Abstract
O-GlcNAc is a pleotropic, enigmatic post-translational modification (PTM). This PTM modifies thousands of proteins differentially across tissue types and regulates diverse cellular signaling processes. O-GlcNAc is implicated in numerous diseases, and the advent of O-GlcNAc perturbation as a novel class of therapeutic underscores the importance of identifying and quantifying the O-GlcNAc modified proteome. Here, we review recent advances in mass spectrometry-based proteomics that will be critical in elucidating the role of this unique glycosylation system in health and disease.
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Affiliation(s)
- Rajan A. Burt
- University of Kansas Medical Center, Medical Scientist Training Program (MSTP), Kansas, KS, United States
| | - Ibtihal M. Alghusen
- Department Biochemistry, University of Kansas Medical Center, Kansas, KS, United States
| | - Sophiya John Ephrame
- Department Biochemistry, University of Kansas Medical Center, Kansas, KS, United States
| | - Maria T. Villar
- Department Biochemistry, University of Kansas Medical Center, Kansas, KS, United States
| | - Antonio Artigues
- Department Biochemistry, University of Kansas Medical Center, Kansas, KS, United States
| | - Chad Slawson
- University of Kansas Medical Center, Medical Scientist Training Program (MSTP), Kansas, KS, United States
- Department Biochemistry, University of Kansas Medical Center, Kansas, KS, United States
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8
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Peters-Clarke TM, Riley NM, Westphall MS, Coon JJ. Practical Effects of Intramolecular Hydrogen Rearrangement in Electron Transfer Dissociation-Based Proteomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:100-110. [PMID: 34874726 PMCID: PMC10291708 DOI: 10.1021/jasms.1c00284] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Ion-ion reactions are valuable tools in mass-spectrometry-based peptide and protein sequencing. To boost the generation of sequence-informative fragment ions from low charge-density precursors, supplemental activation methods, via vibrational and photoactivation, have become widely adopted. However, long-lived radical peptide cations undergo intramolecular hydrogen atom transfer from c-type ions to z•-type ions. Here we investigate the degree of hydrogen transfer for thousands of unique peptide cations where electron transfer dissociation (ETD) was performed and was followed by beam-type collisional activation (EThcD), resonant collisional activation (ETcaD), or concurrent infrared photoirradiation (AI-ETD). We report on the precursor charge density and the local amino acid environment surrounding bond cleavage to illustrate the effects of intramolecular hydrogen atom transfer for various precursor ions. Over 30% of fragments from EThcD spectra comprise distorted isotopic distributions, whereas over 20% of fragments from ETcaD have distorted distributions and less than 15% of fragments derived from ETD and AI-ETD reveal distorted isotopic distributions. Both ETcaD and EThcD give a relatively high degree of hydrogen migration, especially when D, G, N, S, and T residues were directly C-terminal to the cleavage site. Whereas all postactivation methods boost the number of c- and z•-type fragment ions detected, the collision-based approaches produce higher rates of hydrogen migration, yielding fewer spectral identifications when only c- and z•-type ions are considered. Understanding hydrogen rearrangement between c- and z•-type ions will facilitate better spectral interpretation.
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Affiliation(s)
- Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Nicholas M Riley
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Michael S Westphall
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- National Center for Quantitative Biology of Complex Systems, Madison, Wisconsin 53706, United States
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- National Center for Quantitative Biology of Complex Systems, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53515, United States
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9
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Bagal D, Gibson BW. Identification of Proteolysis Products in Protein Therapeutics through TMPP N-Terminal Tagging and Electron Transfer Dissociation Product Triggered Collisional Induced Dissociation Fragmentation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1936-1944. [PMID: 33534996 DOI: 10.1021/jasms.0c00391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Thorough characterization of protein therapeutics is often challenging due to the heterogeneity arising from primary sequence variants, post-translational modifications, proteolytic clipping, or incomplete processing of the signal peptide. Modern mass spectrometry (MS) techniques are now routinely used to characterize such heterogeneous protein populations. Here, we present an LC-MS/MS method using (N-succinimidyloxycarbonylmethyl)-tris (2,4,6-trimethoxyphenyl) phosphonium bromide (TMPP-Ac-OSu) to label any free N-terminal α-amines to rapidly and selectively identify proteolytic clipping events. Electron transfer dissociation (ETD) fragmentation of these chemically tagged peptides generates two unique TMPP product ions, TMPP+ and TMPP-Ac-NH2/c0. The presence of these signature ions following ETD is used to trigger subsequent collisional induced dissociation (CID) fragmentation of the precursor ion. This results in a small subset of CID tandem MS spectra that are used in a customized database search. Using a purified fusion monoclonal antibody (mAb) as an example, we demonstrate how TMPP labeling followed by ETD product ion triggered CID fragmentation is used to accurately identify two undesired clipping sites.
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Affiliation(s)
- Dhanashri Bagal
- Amgen Discovery Research, Discovery Attribute Sciences, South San Francisco, California 94080, United States
| | - Bradford W Gibson
- Amgen Discovery Research, Discovery Attribute Sciences, South San Francisco, California 94080, United States
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10
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Richardson K, Brown J. In Silico Reagent Design for Electron-Transfer Dissociation on a Q-TOF. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2092-2098. [PMID: 33750126 DOI: 10.1021/jasms.0c00483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Electron-transfer dissociation is an important technique capable of probing the primary and higher order structure of a wide variety of biomolecules and yielding information that is often inaccessible using other common MS methods. The source of the electron used to initiate the fragmentation event is a radical anion, and the fragmentation process therefore depends intimately on the electronic properties of both the reagent and analyte ions. A good reagent must ionize easily and be sufficiently robust to survive transport to the reaction location, but must also be capable of donating an electron to analyte cations efficiently enough to overcome competition with other ion-ion reaction channels. Inspired by the work of Gunawardena et al. ( J. Am. Chem. Soc. 2005, 127, 12627), an in silico workflow to allow prescreening of potential electron-transfer reagents for use in glow-discharge sources is described. Approximately 150 candidate molecules have been characterized using this workflow. We discuss in detail the properties of a selected subset of singly and doubly substituted benzenes and introduce five effective new reagents that have been identified as a result of this work.
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Affiliation(s)
| | - Jeffery Brown
- Waters Corporation, Altrincham Road, Wilmslow SK9 4AX, U.K
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11
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Peters-Clarke TM, Schauer KL, Riley NM, Lodge JM, Westphall MS, Coon JJ. Optical Fiber-Enabled Photoactivation of Peptides and Proteins. Anal Chem 2020; 92:12363-12370. [PMID: 32786458 DOI: 10.1021/acs.analchem.0c02087] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Photoactivation and photodissociation have long proven to be useful tools in tandem mass spectrometry, but implementation often involves cumbersome and potentially dangerous configurations. Here, we redress this problem by using a fiber-optic cable to couple an infrared (IR) laser to a mass spectrometer for robust, efficient, and safe photoactivation experiments. Transmitting 10.6 μm IR photons through a hollow-core fiber, we show that such fiber-assisted activated ion-electron transfer dissociation (AI-ETD) and IR multiphoton dissociation (IRMPD) experiments can be carried out as effectively as traditional mirror-based implementations. We report on the transmission efficiency of the hollow-core fiber for conducting photoactivation experiments and perform various intact protein and peptide analyses to illustrate the benefits of fiber-assisted AI-ETD, namely, a simplified system for irradiating the two-dimensional linear ion trap volume concurrent with ETD reactions to limit uninformative nondissociative events and thereby amplify sequence coverage. We also describe a calibration scheme for the routine analysis of IR laser alignment and power through the fiber and into the dual cell quadrupolar linear ion trap. In all, these advances allow for a more robust, straightforward, and safe instrumentation platform, permitting implementation of AI-ETD and IRMPD on commercial mass spectrometers and broadening the accessibility of these techniques.
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Affiliation(s)
- Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kevin L Schauer
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Nicholas M Riley
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Jean M Lodge
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Michael S Westphall
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.,Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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12
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Lodge JM, Schauer KL, Brademan DR, Riley NM, Shishkova E, Westphall MS, Coon JJ. Top-Down Characterization of an Intact Monoclonal Antibody Using Activated Ion Electron Transfer Dissociation. Anal Chem 2020; 92:10246-10251. [PMID: 32608969 DOI: 10.1021/acs.analchem.0c00705] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Monoclonal antibodies (mAbs) are important therapeutic glycoproteins, but their large size and structural complexity make them difficult to rapidly characterize. Top-down mass spectrometry (MS) has the potential to overcome challenges of other common approaches by minimizing sample preparation and preserving endogenous modifications. However, comprehensive mAb characterization requires generation of many, well-resolved fragments and remains challenging. While ETD retains modifications and cleaves disulfide bonds-making it attractive for mAb characterization-it can be less effective for precursors having high m/z values. Activated ion electron transfer dissociation (AI-ETD) uses concurrent infrared photoactivation to promote product ion generation and has proven effective in increasing sequence coverage of intact proteins. Here, we present the first application of AI-ETD to mAb sequencing. For the standard NIST mAb, we observe a high degree of complementarity between fragments generated using standard ETD with a short reaction time and AI-ETD with a long reaction time. Most importantly, AI-ETD reveals disulfide-bound regions that have been intractable, thus far, for sequencing with top-down MS. We conclude AI-ETD has the potential to rapidly and comprehensively analyze intact mAbs.
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13
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Peters-Clarke TM, Quan Q, Brademan DR, Hebert AS, Westphall MS, Coon JJ. Ribonucleic Acid Sequence Characterization by Negative Electron Transfer Dissociation Mass Spectrometry. Anal Chem 2020; 92:4436-4444. [PMID: 32091202 PMCID: PMC7161943 DOI: 10.1021/acs.analchem.9b05388] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Modified oligonucleotides represent a promising avenue for drug development, with small interfering RNAs (siRNA) and microRNAs gaining traction in the therapeutic market. Mass spectrometry (MS)-based analysis offers many benefits for characterizing modified nucleic acids. Negative electron transfer dissociation (NETD) has proven valuable in sequencing oligonucleotide anions, particularly because it can retain modifications while generating sequence-informative fragments. We show that NETD can be successfully implemented on a widely available quadrupole-Orbitrap-linear ion trap mass spectrometer that uses a front-end glow discharge source to generate radical fluoranthene reagent cations. We characterize both unmodified and modified ribonucleic acids and present the first application of activated-ion negative electron transfer dissociation (AI-NETD) to nucleic acids. AI-NETD achieved 100% sequence coverage for both a 6-mer (5'-rGmUrArCmUrG-3') with 2'-O-methyl modifications and a 21-mer (5'-rCrArUrCrCrUrCrUrArGrArGrGrArUrArGrArArUrG-3'), the luciferase antisense siRNA. Both NETD and AI-NETD afforded complete sequence coverage of these molecules while maintaining a relatively low degree of undesired base-loss products and internal products relative to collision-based methods.
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Affiliation(s)
| | - Qiuwen Quan
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Dain R. Brademan
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | | | | | - Joshua J. Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
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14
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Adhikari S, Xia Y, McLuckey SA. Top-Down Analysis of Disulfide-Linked Proteins Using Photoinduced Radical Reactions and ET-DDC. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2019; 444:116173. [PMID: 31372092 PMCID: PMC6675022 DOI: 10.1016/j.ijms.2019.06.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Top-down characterization of proteins via tandem mass spectrometry (MS/MS) can be challenging due to the presence of multiple disulfide bond linkages; which significantly inhibit the backbone cleavage efficiency for the formation of structurally informative fragment ions. In this study, we present a strategy of pairing a solution-phase photoinitiating system with dipolar direct current induced collisional activation of electron transfer products (ET-DDC) of proteins for a top-down MS/MS approach. The photoinitiating system allows for a rapid scission of all the disulfide linkages in the protein (on the time scale of seconds) with high efficiency (near to complete reduction); while ET-DDC collisional activation improves the fragmentation efficiency for the protein via broadband activation of all the first-generation charge reduced precursor ions (e.g., electron transfer no-dissociation or ETnoD products) from electron transfer reactions over a wide mass-to-charge range. As a result, this approach enabled the generation of extensive sequence informative fragment ion yields for a rapid and enhanced structural characterization of disulfide-linked proteins.
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Affiliation(s)
- Sarju Adhikari
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Yu Xia
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Scott A. McLuckey
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
- Address reprint requests to: Dr. Scott A. McLuckey, 560 Oval Drive, Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084, USA, Phone: (765) 494-5270, Fax: (765) 494-0239,
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15
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Penkert M, Hauser A, Harmel R, Fiedler D, Hackenberger CPR, Krause E. Electron Transfer/Higher Energy Collisional Dissociation of Doubly Charged Peptide Ions: Identification of Labile Protein Phosphorylations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1578-1585. [PMID: 31111417 DOI: 10.1007/s13361-019-02240-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/07/2019] [Accepted: 03/16/2019] [Indexed: 06/09/2023]
Abstract
In recent years, labile phosphorylation sites on arginine, histidine, cysteine, and lysine as well as pyrophosphorylation of serine and threonine have gained more attention in phosphoproteomic studies. However, the analysis of these delicate posttranslational modifications via tandem mass spectrometry remains a challenge. Common fragmentation techniques such as collision-induced dissociation (CID) and higher energy collisional dissociation (HCD) are limited due to extensive phosphate-related neutral loss. Electron transfer dissociation (ETD) has shown to preserve labile modifications, but is restricted to higher charge states, missing the most prevalent doubly charged peptides. Here, we report the ability of electron transfer/higher energy collisional dissociation (EThcD) to fragment doubly charged phosphorylated peptides without losing the labile modifications. Using synthetic peptides that contain phosphorylated arginine, histidine, cysteine, and lysine as well as pyrophosphorylated serine residues, we evaluated the optimal fragmentation conditions, demonstrating that EThcD is the method of choice for unambiguous assignment of tryptic, labile phosphorylated peptides. Graphical Abstract.
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Affiliation(s)
- Martin Penkert
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle Str. 10, 13125, Berlin, Germany.
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany.
| | - Anett Hauser
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle Str. 10, 13125, Berlin, Germany
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
| | - Robert Harmel
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle Str. 10, 13125, Berlin, Germany
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
| | - Dorothea Fiedler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle Str. 10, 13125, Berlin, Germany
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
| | - Christian P R Hackenberger
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle Str. 10, 13125, Berlin, Germany
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
| | - Eberhard Krause
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle Str. 10, 13125, Berlin, Germany
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16
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Adhikari S, Dziekonski ET, Londry FA, McLuckey SA. Dipolar DC induced collisional activation of non-dissociated electron-transfer products. JOURNAL OF MASS SPECTROMETRY : JMS 2019; 54:459-465. [PMID: 30869178 PMCID: PMC6520196 DOI: 10.1002/jms.4352] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/03/2019] [Accepted: 03/06/2019] [Indexed: 05/22/2023]
Abstract
The application of electron transfer and dipolar direct current induced collisional activation (ET-DDC) for enhanced sequence coverage of peptide/protein cations is described. A DDC potential is applied across one pair of opposing rods in the high-pressure collision cell of a hybrid quadrupole/time-of-flight tandem mass spectrometer (QqTOF) to induce collisional activation, in conjunction with electron transfer reactions. As a broadband technique, DDC can be employed for the simultaneous collisional activation of all the first-generation charge-reduced precursor ions (eg, electron transfer no-dissociation or ETnoD products) from electron transfer reactions over a relatively broad mass-to-charge range. A systematic study of ET-DDC induced collision activation on peptide/protein cations revealed an increase in the variety (and abundances) of sequence informative fragment ions, mainly c- and z-type fragment ions, relative to products derived directly via electron transfer dissociation (ETD). Compared with ETD, which has low dissociation efficiency for low-charge-state precursor ions, ET-DDC also showed marked improvement, providing a sequence coverage of 80% to 85% for all the charge states of ubiquitin. Overall, this method provides a simple means for the broadband collisional activation of ETnoD ions in the same collision cell in which they are generated for improved structural characterization of polypeptide and protein cations subjected to ETD.
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Affiliation(s)
- Sarju Adhikari
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | | | | | - Scott A. McLuckey
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
- Address reprint requests to: Dr. Scott A. McLuckey, 560 Oval Drive, Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084, USA, Phone: (765) 494-5270, Fax: (765) 494-0239,
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17
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Affiliation(s)
- Clement
M. Potel
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Simone Lemeer
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
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18
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Shaw JB, Malhan N, Vasil'ev YV, Lopez NI, Makarov A, Beckman JS, Voinov VG. Sequencing Grade Tandem Mass Spectrometry for Top-Down Proteomics Using Hybrid Electron Capture Dissociation Methods in a Benchtop Orbitrap Mass Spectrometer. Anal Chem 2018; 90:10819-10827. [PMID: 30118589 DOI: 10.1021/acs.analchem.8b01901] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Compared to traditional collision induced dissociation methods, electron capture dissociation (ECD) provides more comprehensive characterization of large peptides and proteins as well as preserves labile post-translational modifications. However, ECD experiments are generally restricted to the high magnetic fields of FTICR-MS that enable the reaction of large polycations and electrons. Here, we demonstrate the use of an electromagnetostatic ECD cell to perform ECD and hybrid ECD methods utilizing 193 nm photons (ECuvPD) or collisional activation (EChcD) in a benchtop quadrupole-Orbitrap mass spectrometer. The electromagnetostatic ECD cell was designed to replace the transfer octapole between the quadrupole and C-trap. This implementation enabled facile installation of the ECD cell, and ions could be independently subjected to ECD, UVPD, HCD, or any combination. Initial benchmarking and characterization of fragmentation propensities for ECD, ECuvPD, and EChcD were performed using ubiquitin (8.6 kDa). ECD yielded extensive sequence coverage for low charge states of ubiquitin as well as for the larger protein carbonic anhydrase II (29 kDa), indicating pseudo-activated ion conditions. Additionally, relatively high numbers of d- and w-ions enable differentiation of isobaric isoleucine and leucine residues and suggest a distribution of electron energies yield hot-ECD type fragmentation. We report the most comprehensive characterization to date for model proteins up to 29 kDa and a monoclonal antibody at the subunit level. ECD, ECuvPD, and EChcD yielded 93, 95, and 91% sequence coverage, respectively, for carbonic anhydrase II (29 kDa), and targeted online analyses of monoclonal antibody subunits yielded 86% overall antibody sequence coverage.
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Affiliation(s)
- Jared B Shaw
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , 3335 Innovation Bouelvard , Richland , Washington 99354 , United States
| | - Neha Malhan
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , 3335 Innovation Bouelvard , Richland , Washington 99354 , United States
| | - Yury V Vasil'ev
- e-MSion Inc. , 2121 NE Jack London Drive , Corvallis , Oregon 97330 , United States.,Linus Pauling Institute and the Department of Biochemistry and Biophysics , Oregon State University , Corvallis , Oregon 97331 , United States
| | - Nathan I Lopez
- e-MSion Inc. , 2121 NE Jack London Drive , Corvallis , Oregon 97330 , United States.,Linus Pauling Institute and the Department of Biochemistry and Biophysics , Oregon State University , Corvallis , Oregon 97331 , United States
| | - Alexander Makarov
- Thermo Fisher Scientific (Bremen) GmbH , Hanna-Kunath Str. 11 , 28199 Bremen , Germany
| | - Joseph S Beckman
- e-MSion Inc. , 2121 NE Jack London Drive , Corvallis , Oregon 97330 , United States.,Linus Pauling Institute and the Department of Biochemistry and Biophysics , Oregon State University , Corvallis , Oregon 97331 , United States
| | - Valery G Voinov
- e-MSion Inc. , 2121 NE Jack London Drive , Corvallis , Oregon 97330 , United States.,Linus Pauling Institute and the Department of Biochemistry and Biophysics , Oregon State University , Corvallis , Oregon 97331 , United States
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19
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Rush MJ, Riley NM, Westphall MS, Coon JJ. Top-Down Characterization of Proteins with Intact Disulfide Bonds Using Activated-Ion Electron Transfer Dissociation. Anal Chem 2018; 90:8946-8953. [PMID: 29949341 PMCID: PMC6434944 DOI: 10.1021/acs.analchem.8b01113] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Here we report the fragmentation of disulfide linked intact proteins using activated-ion electron transfer dissociation (AI-ETD) for top-down protein characterization. This fragmentation method is then compared to the alternative methods of beam-type collisional activation (HCD), electron transfer dissociation (ETD), and electron transfer and higher-energy collision dissociation (EThcD). We analyzed multiple precursor charge states of the protein standards bovine insulin, α-lactalbumin, lysozyme, β-lactoglobulin, and trypsin inhibitor. In all cases, we found that AI-ETD provides a boost in protein sequence coverage information and the generation of fragment ions from within regions enclosed by disulfide bonds. AI-ETD shows the largest improvement over the other techniques when analyzing highly disulfide linked and low charge density precursor ions. This substantial improvement is attributed to the concurrent irradiation of the gas phase ions while the electron-transfer reaction is taking place, mitigating nondissociative electron transfer, helping unfold the gas phase protein during the electron transfer event, and preventing disulfide bond reformation. We also show that AI-ETD is able to yield comparable sequence coverage information when disulfide bonds are left intact relative to proteins that have been reduced and alkylated. This work demonstrates that AI-ETD is an effective fragmentation method for the analysis of proteins with intact disulfide bonds, dramatically enhancing sequence ion generation and total sequence coverage compared to HCD and ETD.
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Affiliation(s)
- Matthew J.P. Rush
- Genome Center of Wisconsin, Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Nicholas M. Riley
- Genome Center of Wisconsin, Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
| | | | - Joshua J. Coon
- Genome Center of Wisconsin, Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
- Department of Biomolecular Chemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
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20
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Riley NM, Sikora JW, Seckler HS, Greer JB, Fellers RT, LeDuc RD, Westphall MS, Thomas PM, Kelleher NL, Coon JJ. The Value of Activated Ion Electron Transfer Dissociation for High-Throughput Top-Down Characterization of Intact Proteins. Anal Chem 2018; 90:8553-8560. [PMID: 29924586 DOI: 10.1021/acs.analchem.8b01638] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
High-throughput top-down proteomic experiments directly identify proteoforms in complex mixtures, making high quality tandem mass spectra necessary to deeply characterize proteins with many sources of variation. Collision-based dissociation methods offer expedient data acquisition but often fail to extensively fragment proteoforms for thorough analysis. Electron-driven dissociation methods are a popular alternative approach, especially for precursor ions with high charge density. Combining infrared photoactivation concurrent with electron transfer dissociation (ETD) reactions, i.e., activated ion ETD (AI-ETD), can significantly improve ETD characterization of intact proteins, but benefits of AI-ETD have yet to be quantified in high-throughput top-down proteomics. Here, we report the first application of AI-ETD to LC-MS/MS characterization of intact proteins (<20 kDa), highlighting improved proteoform identification the method offers over higher energy-collisional dissociation (HCD), standard ETD, and ETD followed by supplemental HCD activation (EThcD). We identified 935 proteoforms from 295 proteins from human colorectal cancer cell line HCT116 using AI-ETD compared to 1014 proteoforms, 915 proteoforms, and 871 proteoforms with HCD, ETD, and EThcD, respectively. Importantly, AI-ETD outperformed each of the three other methods in MS/MS success rates and spectral quality metrics (e.g., sequence coverage achieved and proteoform characterization scores). In all, this four-method analysis offers the most extensive comparisons to date and demonstrates that AI-ETD both increases identifications over other ETD methods and improves proteoform characterization via higher sequence coverage, positioning it as a premier method for high-throughput top-down proteomics.
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Affiliation(s)
| | - Jacek W Sikora
- National Resource for Translational and Developmental Proteomics, Departments of Chemistry and Molecular Biosciences , Northwestern University , Evanston , Illinois 60208 , United States
| | - Henrique S Seckler
- National Resource for Translational and Developmental Proteomics, Departments of Chemistry and Molecular Biosciences , Northwestern University , Evanston , Illinois 60208 , United States
| | - Joseph B Greer
- National Resource for Translational and Developmental Proteomics, Departments of Chemistry and Molecular Biosciences , Northwestern University , Evanston , Illinois 60208 , United States
| | - Ryan T Fellers
- National Resource for Translational and Developmental Proteomics, Departments of Chemistry and Molecular Biosciences , Northwestern University , Evanston , Illinois 60208 , United States
| | - Richard D LeDuc
- National Resource for Translational and Developmental Proteomics, Departments of Chemistry and Molecular Biosciences , Northwestern University , Evanston , Illinois 60208 , United States
| | | | - Paul M Thomas
- National Resource for Translational and Developmental Proteomics, Departments of Chemistry and Molecular Biosciences , Northwestern University , Evanston , Illinois 60208 , United States
| | - Neil L Kelleher
- National Resource for Translational and Developmental Proteomics, Departments of Chemistry and Molecular Biosciences , Northwestern University , Evanston , Illinois 60208 , United States
| | - Joshua J Coon
- Morgridge Institute for Research , Madison , Wisconsin 53706 , United States
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21
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Affiliation(s)
- Nicholas
M. Riley
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Genome
Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Joshua J. Coon
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Genome
Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department
of Biomolecular Chemistry, University of
Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Morgridge
Institute for Research, Madison, Wisconsin 53715, United States
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22
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Riley NM, Westphall MS, Coon JJ. Sequencing Larger Intact Proteins (30-70 kDa) with Activated Ion Electron Transfer Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:140-149. [PMID: 29027149 PMCID: PMC5786479 DOI: 10.1007/s13361-017-1808-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 08/31/2017] [Accepted: 09/02/2017] [Indexed: 05/12/2023]
Abstract
The analysis of intact proteins via mass spectrometry can offer several benefits to proteome characterization, although the majority of top-down experiments focus on proteoforms in a relatively low mass range (<30 kDa). Recent studies have focused on improving the analysis of larger intact proteins (up to ~75 kDa), but they have also highlighted several challenges to be addressed. One major hurdle is the efficient dissociation of larger protein ions, which often to do not yield extensive fragmentation via conventional tandem MS methods. Here we describe the first application of activated ion electron transfer dissociation (AI-ETD) to proteins in the 30-70 kDa range. AI-ETD leverages infrared photo-activation concurrent to ETD reactions to improve sequence-informative product ion generation. This method generates more product ions and greater sequence coverage than conventional ETD, higher-energy collisional dissociation (HCD), and ETD combined with supplemental HCD activation (EThcD). Importantly, AI-ETD provides the most thorough protein characterization for every precursor ion charge state investigated in this study, making it suitable as a universal fragmentation method in top-down experiments. Additionally, we highlight several acquisition strategies that can benefit characterization of larger proteins with AI-ETD, including combination of spectra from multiple ETD reaction times for a given precursor ion, multiple spectral acquisitions of the same precursor ion, and combination of spectra from two different dissociation methods (e.g., AI-ETD and HCD). In all, AI-ETD shows great promise as a method for dissociating larger intact protein ions as top-down proteomics continues to advance into larger mass ranges. Graphical Abstract ᅟ.
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Affiliation(s)
- Nicholas M Riley
- Genome Center of Wisconsin, Madison, WI, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | | | - Joshua J Coon
- Genome Center of Wisconsin, Madison, WI, USA.
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Morgridge Institute for Research, Madison, WI, USA.
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23
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Riley NM, Hebert AS, Dürnberger G, Stanek F, Mechtler K, Westphall MS, Coon JJ. Phosphoproteomics with Activated Ion Electron Transfer Dissociation. Anal Chem 2017; 89:6367-6376. [PMID: 28383256 PMCID: PMC5555596 DOI: 10.1021/acs.analchem.7b00212] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The ability to localize phosphosites to specific amino acid residues is crucial to translating phosphoproteomic data into biological meaningful contexts. In a companion manuscript ( Anal. Chem. 2017 , DOI: 10.1021/acs.analchem.7b00213 ), we described a new implementation of activated ion electron transfer dissociation (AI-ETD) on a quadrupole-Orbitrap-linear ion trap hybrid MS system (Orbitrap Fusion Lumos), which greatly improved peptide fragmentation and identification over ETD and other supplemental activation methods. Here we present the performance of AI-ETD for identifying and localizing sites of phosphorylation in both phosphopeptides and intact phosphoproteins. Using 90 min analyses we show that AI-ETD can identify 24,503 localized phosphopeptide spectral matches enriched from mouse brain lysates, which more than triples identifications from standard ETD experiments and outperforms ETcaD and EThcD as well. AI-ETD achieves these gains through improved quality of fragmentation and MS/MS success rates for all precursor charge states, especially for doubly protonated species. We also evaluate the degree to which phosphate neutral loss occurs from phosphopeptide product ions due to the infrared photoactivation of AI-ETD and show that modifying phosphoRS (a phosphosite localization algorithm) to include phosphate neutral losses can significantly improve localization in AI-ETD spectra. Finally, we demonstrate the utility of AI-ETD in localizing phosphosites in α-casein, an ∼23.5 kDa phosphoprotein that showed eight of nine known phosphorylation sites occupied upon intact mass analysis. AI-ETD provided the greatest sequence coverage for all five charge states investigated and was the only fragmentation method to localize all eight phosphosites for each precursor. Overall, this work highlights the analytical value AI-ETD can bring to both bottom-up and top-down phosphoproteomics.
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Affiliation(s)
- Nicholas M. Riley
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Alexander S. Hebert
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Gerhard Dürnberger
- Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, A-1030 Vienna, Austria
- GMI, Gregor Mendel Institute of Molecular Plant Biology, Dr. Bohr Gasse 3, A-1030 Vienna, Austria
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Dr. Bohr Gasse 3, A-1030 Vienna, Austria
| | - Florian Stanek
- Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, A-1030 Vienna, Austria
| | - Karl Mechtler
- Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, A-1030 Vienna, Austria
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Dr. Bohr Gasse 3, A-1030 Vienna, Austria
| | - Michael S. Westphall
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Joshua J. Coon
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Morgridge Institute for Research, Madison, Wisconsin, USA
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24
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Riley NM, Westphall MS, Hebert AS, Coon JJ. Implementation of Activated Ion Electron Transfer Dissociation on a Quadrupole-Orbitrap-Linear Ion Trap Hybrid Mass Spectrometer. Anal Chem 2017; 89:6358-6366. [PMID: 28383247 DOI: 10.1021/acs.analchem.7b00213] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Using concurrent IR photoactivation during electron transfer dissociation (ETD) reactions, i.e., activated ion ETD (AI-ETD), significantly increases dissociation efficiency resulting in improved overall performance. Here we describe the first implementation of AI-ETD on a quadrupole-Orbitrap-quadrupole linear ion trap (QLT) hybrid MS system (Orbitrap Fusion Lumos) and demonstrate the substantial benefits it offers for peptide characterization. First, we show that AI-ETD can be implemented in a straightforward manner by fastening the laser and guiding optics to the instrument chassis itself, making alignment with the trapping volume of the QLT simple and robust. We then characterize the performance of AI-ETD using standard peptides in addition to a complex mixtures of tryptic peptides using LC-MS/MS, showing not only that AI-ETD can nearly double the identifications achieved with ETD alone but also that it outperforms the other available supplemental activation methods (ETcaD and EThcD). Finally, we introduce a new activation scheme called AI-ETD+ that combines AI-ETD in the high pressure cell of the QLT with a short infrared multiphoton dissociation (IRMPD) activation in the low-pressure cell. This reaction scheme introduces no addition time to the scan duty cycle but generates MS/MS spectra rich in b/y-type and c/z•-type product ions. The extensive generation of fragment ions in AI-ETD+ substantially increases peptide sequence coverage while also improving peptide identifications over all other ETD methods, making it a valuable new tool for hybrid fragmentation approaches.
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Affiliation(s)
| | | | | | - Joshua J Coon
- Morgridge Institute for Research , Madison, Wisconsin 53715, United States
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25
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Lermyte F, Sobott F. A broader view on ion heating in traveling-wave devices using fragmentation of CsI clusters and extent of H˙ migration as molecular thermometers. Analyst 2017; 142:3388-3399. [DOI: 10.1039/c7an00161d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Traveling-wave-dependent ion ‘heating’ is observed during mass spectrometry experiments under both ion mobility and electron transfer dissociation conditions and investigated using novel molecular ‘thermometers’.
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Affiliation(s)
- Frederik Lermyte
- Biomolecular & Analytical Mass Spectrometry Group
- Department of Chemistry
- University of Antwerp
- Antwerp
- Belgium
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry Group
- Department of Chemistry
- University of Antwerp
- Antwerp
- Belgium
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Bagal D, Kast E, Cao P. Rapid Distinction of Leucine and Isoleucine in Monoclonal Antibodies Using Nanoflow LCMSn. Anal Chem 2016; 89:720-727. [DOI: 10.1021/acs.analchem.6b03261] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dhanashri Bagal
- Discovery Attribute Sciences, Amgen, South San
Francisco, California 94080, United States
| | - Eddie Kast
- Discovery Attribute Sciences, Amgen, South San
Francisco, California 94080, United States
| | - Ping Cao
- Discovery Attribute Sciences, Amgen, South San
Francisco, California 94080, United States
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27
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Affiliation(s)
- Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
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28
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Fukuda T, Hike H, Usui F, Bando Y, Nishimura T, Kodama T, Kawamura T. An improvement on mass spectrometry-based epigenetic analysis of large histone-derived peptides by using the Ionization Variable Unit interface. Anal Biochem 2015; 486:14-6. [DOI: 10.1016/j.ab.2015.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 05/31/2015] [Accepted: 06/01/2015] [Indexed: 11/28/2022]
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29
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Riley NM, Westphall MS, Coon JJ. Activated Ion Electron Transfer Dissociation for Improved Fragmentation of Intact Proteins. Anal Chem 2015; 87:7109-16. [PMID: 26067513 PMCID: PMC9488116 DOI: 10.1021/acs.analchem.5b00881] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Here we report the first implementation of activated ion electron transfer dissociation (AI-ETD) for top down protein characterization, showing that AI-ETD definitively extends the m/z range over which ETD can be effective for fragmentation of intact proteins. AI-ETD, which leverages infrared photon bombardment concurrent to the ETD reaction to mitigate nondissociative electron transfer, was performed using a novel multipurpose dissociation cell that can perform both beam-type collisional dissociation and ion-ion reactions on an ion trap-Orbitrap hybrid mass spectrometer. AI-ETD increased the number of c- and z-type product ions for all charge states over ETD alone, boosting product ion yield by nearly 4-fold for low charge density precursors. AI-ETD also outperformed HCD, generating more matching fragments for all proteins at all charge states investigated. In addition to generating more unique fragment ions, AI-ETD provided greater protein sequence coverage compared to both HCD and ETD. In all, the effectiveness of AI-ETD across the entirety of the m/z spectrum demonstrates its efficacy for robust fragmentation of intact proteins.
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Affiliation(s)
- Nicholas M. Riley
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
- Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Michael S. Westphall
- Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Joshua J. Coon
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
- Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53706, United States
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Riley NM, Rush MJP, Rose CM, Richards AL, Kwiecien NW, Bailey DJ, Hebert AS, Westphall MS, Coon JJ. The Negative Mode Proteome with Activated Ion Negative Electron Transfer Dissociation (AI-NETD). Mol Cell Proteomics 2015; 14:2644-60. [PMID: 26193884 DOI: 10.1074/mcp.m115.049726] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Indexed: 01/15/2023] Open
Abstract
The field of proteomics almost uniformly relies on peptide cation analysis, leading to an underrepresentation of acidic portions of proteomes, including relevant acidic posttranslational modifications. Despite the many benefits negative mode proteomics can offer, peptide anion analysis remains in its infancy due mainly to challenges with high-pH reversed-phase separations and a lack of robust fragmentation methods suitable for peptide anion characterization. Here, we report the first implementation of activated ion negative electron transfer dissociation (AI-NETD) on the chromatographic timescale, generating 7,601 unique peptide identifications from Saccharomyces cerevisiae in single-shot nLC-MS/MS analyses of tryptic peptides-a greater than 5-fold increase over previous results with NETD alone. These improvements translate to identification of 1,106 proteins, making this work the first negative mode study to identify more than 1,000 proteins in any system. We then compare the performance of AI-NETD for analysis of peptides generated by five proteases (trypsin, LysC, GluC, chymotrypsin, and AspN) for negative mode analyses, identifying as many as 5,356 peptides (1,045 proteins) with LysC and 4,213 peptides (857 proteins) with GluC in yeast-characterizing 1,359 proteins in total. Finally, we present the first deep-sequencing approach for negative mode proteomics, leveraging offline low-pH reversed-phase fractionation prior to online high-pH separations and peptide fragmentation with AI-NETD. With this platform, we identified 3,467 proteins in yeast with trypsin alone and characterized a total of 3,730 proteins using multiple proteases, or nearly 83% of the expressed yeast proteome. This work represents the most extensive negative mode proteomics study to date, establishing AI-NETD as a robust tool for large-scale peptide anion characterization and making the negative mode approach a more viable platform for future proteomic studies.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Joshua J Coon
- From the ‡Department of Chemistry, §Genome Center, and ¶Department of Biomolecular Chemistry University of Wisconsin, Madison, Wisconsin, 53706
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Hoffmann WD, Jackson GP. Charge transfer dissociation (CTD) mass spectrometry of peptide cations using kiloelectronvolt helium cations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1939-43. [PMID: 25231159 DOI: 10.1007/s13361-014-0989-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 07/23/2014] [Accepted: 07/27/2014] [Indexed: 05/04/2023]
Abstract
A kiloelectronvolt beam of helium ions is used to ionize and fragment precursor peptide ions starting in the 1+ charge state. The electron affinity of helium cations (24.6 eV) exceeds the ionization potential of protonated peptides and can therefore be used to abstract an electron from--or charge exchange with--the isolated precursor ions. Kiloelectronvolt energies are used, (1) to overcome the Coulombic repulsion barrier between the cationic reactants, (2) to overcome ion-defocussing effects in the ion trap, and (3) to provide additional activation energy. Charge transfer dissociation (CTD) of the [M+H](+) precursor of Substance P gives product ions such as [M+H](2+•) and a dominant series of a ions in both the 1+ and 2+ charge states. These observations, along with the less-abundant a + 1 ions, are consistent with ultraviolet photodissociation (UVPD) results of others and indicate that C-C(α) cleavages are possible through charge exchange with helium ions. Although the efficiencies and timescale of CTD are not yet suitable for on-line chromatography, this new approach to ion activation provides an additional potential tool for the interrogation of gas phase ions.
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Affiliation(s)
- William D Hoffmann
- Department of Forensic and Investigative Science, West Virginia University, Morgantown, WV, 26506, USA
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Robb DB, Brown JM, Morris M, Blades MW. Tandem mass spectrometry using the atmospheric pressure electron capture dissociation ion source. Anal Chem 2014; 86:4439-46. [PMID: 24694021 DOI: 10.1021/ac5002959] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Atmospheric pressure electron capture dissociation (AP-ECD) is an emerging technique capable of being adopted to virtually any electrospray mass spectrometer, without modification of the main instrument. To date, however, because the electron capture reactions occur in the ion source, AP-ECD has been limited by its apparent inability to select precursors prior to fragmentation, i.e., to perform tandem mass spectrometry (MS/MS) experiments. In this paper we demonstrate a novel AP-ECD-MS/MS method using an AP-ECD source on a Xevo G2-S quadrupole time-of-flight (Q-TOF) mass spectrometer from Waters Micromass. The method takes advantage of the tendency for electron capture reactions to generate charge-reduced "ECnoD" products, species that have captured an electron and have had a covalent bond cleaved yet do not immediately dissociate into separate products and so retain the mass of the precursor ion. In the method, ECnoD products from the AP-ECD source are isolated in the quadrupole mass filter and induced to dissociate through supplemental activation in the collision cell, and then the liberated ECD fragment ions are mass analyzed using the high-resolution TOF. In this manner, true MS/MS spectra may be obtained with AP-ECD even though all of the precursors in the source are subjected to electron capture reactions in parallel. Here, using a late-model Q-TOF instrument otherwise incapable of performing electron-based fragmentation, we present AP-ECD-MS/MS results for a group of model peptides and show that informative, high-sequence-coverage spectra are readily attainable with the method.
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Affiliation(s)
- Damon B Robb
- University of British Columbia , Department of Chemistry, Vancouver, BC V6T 1Z1, Canada
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Anusiewicz I, Skurski P, Simons J. Refinements to the Utah–Washington Mechanism of Electron Capture Dissociation. J Phys Chem B 2014; 118:7892-901. [DOI: 10.1021/jp5004819] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Iwona Anusiewicz
- Department
of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Piotr Skurski
- Department
of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Jack Simons
- Chemistry
Department and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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Williams JP, Pringle S, Richardson K, Gethings L, Vissers JPC, De Cecco M, Houel S, Chakraborty AB, Yu YQ, Chen W, Brown JM. Characterisation of glycoproteins using a quadrupole time-of-flight mass spectrometer configured for electron transfer dissociation. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:2383-2390. [PMID: 24097394 DOI: 10.1002/rcm.6684] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 07/08/2013] [Accepted: 07/08/2013] [Indexed: 06/02/2023]
Abstract
RATIONALE Electron transfer dissociation (ETD) within ion trapping mass spectrometers has proven to be a useful tool for the characterisation of post-translational modifications. In this study, we describe the implementation of ETD upon a modified quadrupole time-of-flight (Q-ToF) system and methods for the analysis of glycoproteins. METHODS Liquid chromatography electrospray ionisation mass spectrometry (LC/ESI-MS) was performed using a hybrid quadrupole/ion mobility/oa-ToF mass spectrometer equipped with ETD functionality. 1,4-Dicyanobenzene reagent anions necessary for the ETD reaction were generated from a glow discharge region located within the ESI source block. ETD reactions occurred in the stacked ring travelling wave ion guide (located after the quadrupole mass filter and prior to the oa-ToF mass analyser). LC/ETD was performed upon 'super-charged' tryptic glycopeptide ions produced from the recombinant monoclonal antibody trastuzumab. LC/ETD was also performed on ions from the smaller glycopeptides obtained from erythropoietin. RESULTS ETD performed upon the quadruply 'super-charged' N-linked glycopeptide ions of trastuzumab and the triply charged O-linked glycopeptide ions of erythropoietin provided both glycosylation site assignments and full sequence information, respectively. Tandem mass (MS/MS) spectra employing collision-induced dissociation (CID) were dominated by oxonium product ions hampering full peptide sequence characterisation. CONCLUSIONS LC/ETD on the Q-ToF system proved effective at characterising a number of different N-linked glyco-forms of the tryptic peptide, EEQYNSTYR, from trastuzumab as well as glyco-forms from the O-linked tryptic peptide, EASIPPDAASAAPLR, from erythropoietin. The data demonstrates that the glycopeptide site heterogeneity of trastuzumab and erythropoietin can be accurately characterised. In addition, the post-column mixing of the super-charging reagent, m-NBA, is an effective method to increase the precursor ion charge state and to improve ETD reaction efficiency.
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Ledvina AR, Rose CM, McAlister GC, Syka JE, Westphall MS, Griep-Raming J, Schwartz JC, Coon JJ. Activated ion ETD performed in a modified collision cell on a hybrid QLT-Oribtrap mass spectrometer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1623-33. [PMID: 23677544 PMCID: PMC3776012 DOI: 10.1007/s13361-013-0621-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 03/19/2013] [Accepted: 03/20/2013] [Indexed: 05/12/2023]
Abstract
We describe the implementation and characterization of activated ion electron transfer dissociation (AI-ETD) on a hybrid QLT-Orbitrap mass spectrometer. AI-ETD was performed using a collision cell that was modified to enable ETD reactions, in addition to normal collisional activation. The instrument manifold was modified to enable irradiation of ions along the axis of this modified cell with IR photons from a CO2 laser. Laser power settings were optimized for both charge (z) and mass to charge (m/z) and the instrument control firmware was updated to allow for automated adjustments to the level of irradiation. This implementation of AI-ETD yielded 1.6-fold more unique identifications than ETD in an nLC-MS/MS analysis of tryptic yeast peptides. Furthermore, we investigated the application of AI-ETD on large scale analysis of phosphopeptides, where laser power aids ETD, but can produce b- and y-type ions because of the phosphoryl moiety's high IR adsorption. nLC-MS/MS analysis of phosphopeptides derived from human embryonic stem cells using AI-ETD yielded 2.4-fold more unique identifications than ETD alone, demonstrating a promising advance in ETD sequencing of PTM containing peptides.
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Affiliation(s)
- Aaron R. Ledvina
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
- Genome Center, University of Wisconsin, Madison, Wisconsin 53706
| | - Christopher M. Rose
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
- Genome Center, University of Wisconsin, Madison, Wisconsin 53706
| | - Graeme C. McAlister
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
- Genome Center, University of Wisconsin, Madison, Wisconsin 53706
| | | | | | | | | | - Joshua J. Coon
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin 53706
- Genome Center, University of Wisconsin, Madison, Wisconsin 53706
- To whom correspondence should be addressed.
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Mentinova M, Crizer DM, Baba T, McGee WM, Glish GL, McLuckey SA. Cation recombination energy/coulomb repulsion effects in ETD/ECD as revealed by variation of charge per residue at fixed total charge. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1676-89. [PMID: 23568028 PMCID: PMC3795911 DOI: 10.1007/s13361-013-0606-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 02/25/2013] [Accepted: 02/28/2013] [Indexed: 05/11/2023]
Abstract
Electron capture dissociation (ECD) and electron transfer dissociation (ETD) experiments in electrodynamic ion traps operated in the presence of a bath gas in the 1-10 mTorr range have been conducted on a common set of doubly protonated model peptides of the form X(AG)nX (X = lysine, arginine, or histidine, n = 1, 2, or 4). The partitioning of reaction products was measured using thermal electrons, anions of azobenzene, and anions of 1,3-dinitrobenzene as reagents. Variation of n alters the charge per residue of the peptide cation, which affects recombination energy. The ECD experiments showed that H-atom loss is greatest for the n = 1 peptides and decreases as n increases. Proton transfer in ETD, on the other hand, is expected to increase as charge per residue decreases (i.e., as n increases). These opposing tendencies were apparent in the data for the K(AG)nK peptides. H-atom loss appeared to be more prevalent in ECD than in ETD and is rationalized on the basis of either internal energy differences, differences in angular momentum transfer associated with the electron capture versus electron transfer processes, or a combination of the two. The histidine peptides showed the greatest extent of charge reduction without dissociation, the arginine peptides showed the greatest extent of side-chain cleavages, and the lysine peptides generally showed the greatest extent of partitioning into the c/z•-product ion channels. The fragmentation patterns for the complementary c- and z•-ions for ETD and ECD were found to be remarkably similar, particularly for the peptides with X = lysine.
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Affiliation(s)
- Marija Mentinova
- Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084, USA
| | - David M. Crizer
- Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084, USA
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Takashi Baba
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - William M. McGee
- Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084, USA
| | - Gary L. Glish
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Scott A. McLuckey
- Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084, USA
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Shaw JB, Kaplan DA, Brodbelt JS. Activated ion negative electron transfer dissociation of multiply charged peptide anions. Anal Chem 2013; 85:4721-8. [PMID: 23577957 DOI: 10.1021/ac4005315] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We report the implementation and evaluation of activated ion negative electron transfer dissociation (AI-NETD) in order to enhance the analytical capabilities of NETD for the elucidation of doubly deprotonated peptide anions. The analytical figures-of-merit and fragmentation characteristics are compared for NETD alone and with supplemental collisional activation of the charge reduced precursors or infrared photoactivation of the entire ion population during the NETD reaction period. The addition of supplemental collisional activation of charge reduced precursor ions or infrared photoactivation of the entire ion population concomitant with the NETD reaction period significantly improves sequencing capabilities for peptide anions as evidenced by the greater abundances of product ions and overall sequence coverage. Neither of these two AI-NETD methods significantly alters the net fragmentation efficiencies relative to NETD; however, the sequence ion conversion percentages with respect to formation of diagnostic product ions are notably higher. Supplemental infrared photoactivation outperforms collisional activation for most of the peptide fragmentation metrics evaluated.
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Affiliation(s)
- Jared B Shaw
- Department of Chemistry and Biochemistry, University of Texas, Austin, Texas 78712, United States
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Liu J, McLuckey SA. Electron Transfer Dissociation: Effects of Cation Charge State on Product Partitioning in Ion/Ion Electron Transfer to Multiply Protonated Polypeptides. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2012; 330-332:174-181. [PMID: 23264749 PMCID: PMC3525064 DOI: 10.1016/j.ijms.2012.07.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The effect of cation charge state on product partitioning in the gas-phase ion/ion electron transfer reactions of multiply protonated tryptic peptides, model peptides, and relatively large peptides with singly charged radical anions has been examined. In particular, partitioning into various competing channels, such as proton transfer (PT) versus electron transfer (ET), electron transfer with subsequent dissociation (ETD) versus electron transfer with no dissociation (ET,noD), and fragmentation of backbone bonds versus fragmentation of side chains, was measured quantitatively as a function of peptide charge state to allow insights to be drawn about the fundamental aspects of ion/ion reactions that lead to ETD. The ET channel increases relative to the PT channel, ETD increases relative to ET,noD, and fragmentation at backbone bonds increases relative to side-chain cleavages as cation charge state increases. The increase in ET versus PT with charge state is consistent with a Landau-Zener based curve-crossing model. An optimum charge state for ET is predicted by the model for the ground state-to-ground state reaction. However, when the population of excited product ion states is considered, it is possible that a decrease in ET efficiency as charge state increases will not be observed due to the possibility of the population of excited electronic states of the products. Several factors can contribute to the increase in ETD versus ET,noD and backbone cleavage versus side-chain losses. These factors include an increase in reaction exothermicity and charge state dependent differences in precursor and product ion structures, stabilities, and sites of protonation.
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Affiliation(s)
| | - Scott A. McLuckey
- Address reprint requests to: Dr. S.A. McLuckey, 560 Oval Drive, Department of Chemistry, Purdue University, West Lafayette, IN, USA 47907-2084, Phone: (765) 494-5270, Fax: (765) 494-0239,
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Frese CK, Altelaar AFM, van den Toorn H, Nolting D, Griep-Raming J, Heck AJR, Mohammed S. Toward full peptide sequence coverage by dual fragmentation combining electron-transfer and higher-energy collision dissociation tandem mass spectrometry. Anal Chem 2012; 84:9668-73. [PMID: 23106539 DOI: 10.1021/ac3025366] [Citation(s) in RCA: 224] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Increasing peptide sequence coverage by tandem mass spectrometry improves confidence in database search-based peptide identification and facilitates mapping of post-translational modifications and de novo sequencing. Inducing 2-fold fragmentation by combining electron-transfer and higher-energy collision dissociation (EThcD) generates dual fragment ion series and facilitates extensive peptide backbone fragmentation. After an initial electron-transfer dissociation step, all ions including the unreacted precursor ions are subjected to collision induced dissociation which yields b/y- and c/z-type fragment ions in a single spectrum. This new fragmentation scheme provides richer spectra and substantially increases the peptide sequence coverage and confidence in peptide identification.
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Imamura H, Wakabayashi M, Ishihama Y. Analytical strategies for shotgun phosphoproteomics: Status and prospects. Semin Cell Dev Biol 2012; 23:836-42. [DOI: 10.1016/j.semcdb.2012.05.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 05/29/2012] [Indexed: 12/17/2022]
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Hersberger KE, Håkansson K. Characterization of O-sulfopeptides by negative ion mode tandem mass spectrometry: superior performance of negative ion electron capture dissociation. Anal Chem 2012; 84:6370-7. [PMID: 22770115 DOI: 10.1021/ac301536r] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Positive ion mode collision-activated dissociation tandem mass spectrometry (CAD MS/MS) of O-sulfopeptides precludes determination of sulfonated sites due to facile proton-driven loss of the highly labile sulfonate groups. A previously proposed method for localizing peptide and protein O-sulfonation involves derivatization of nonsulfonated tyrosines followed by positive ion CAD MS/MS of the corresponding modified sulfopeptides for diagnostic sulfonate loss. This indirect method relies upon specific and complete derivatization of nonsulfonated tyrosines. Alternative MS/MS activation methods, including positive ion metastable atom-activated dissociation (MAD) and metal-assisted electron transfer dissociation (ETD) or electron capture dissociation (ECD) provide varying degrees of sulfonate retention. Sulfonate retention has also been reported following negative ion MAD and electron detachment dissociation (EDD), which also operates in negative ion mode in which sulfonate groups are less labile than in positive ion mode. However, an MS/MS activation technique that can effectively preserve sulfonate groups while providing extensive backbone fragmentation (translating to sequence information, including sulfonated sites) with little to no noninformative small molecule neutral loss has not previously been realized. Here, we report that negative ion CAD, EDD, and negative ETD (NETD) result in sulfonate retention mainly at higher charge states with varying degrees of fragmentation efficiency and sequence coverage. Similar to previous observations from CAD of sulfonated glycosaminoglycan anions, higher charge states translate to a higher probability of deprotonation at the sulfonate groups thus yielding charge-localized fragmentation without loss of the sulfonate groups. However, consequently, higher sulfonate retention comes at the price of lower sequence coverage in negative ion CAD. Fragmentation efficiency/sequence coverage averaged 19/6% and 33/20% in EDD and NETD, respectively, both of which are only applicable to multiply-charged anions. In contrast, the recently introduced negative ion ECD showed an average fragmentation efficiency of 69% and an average sequence coverage of 82% with complete sulfonate retention from singly- and doubly-deprotonated sulfopeptide anions.
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Affiliation(s)
- Katherine E Hersberger
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, USA
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Berkout VD, Doroshenko VM. ECD-like peptide fragmentation at atmospheric pressure. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2012; 325-327:113-120. [PMID: 23175626 PMCID: PMC3501133 DOI: 10.1016/j.ijms.2012.06.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Fragmentation of multiply-charged peptide ions via interaction with products of gas discharge at atmospheric pressure conditions was studied using ion mobility separation - fragmentation cell - linear ion trap mass spectrometer. The observed fragmentation spectra mainly consisted of c- type ions that are specific to electron capture dissociation. Experiments with different gases flowing through the discharge and different discharge polarities suggested that fragmentation proceeds via capture of free electrons. Fragmentation of a model phosphorylated peptide using this technique produced c- type fragments with an intact phosphorylation group. High field asymmetric waveform ion mobility separation of a peptide mixture prior to the fragmentation cell demonstrated the feasibility of conducting MS/MS-like experiments at atmospheric pressure conditions.
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43
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Cook SL, Zimmermann CM, Singer D, Fedorova M, Hoffmann R, Jackson GP. Comparison of CID, ETD and metastable atom-activated dissociation (MAD) of doubly and triply charged phosphorylated tau peptides. JOURNAL OF MASS SPECTROMETRY : JMS 2012; 47:786-794. [PMID: 22707171 DOI: 10.1002/jms.3023] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The fragmentation behavior of the 2+ and 3+ charge states of eleven different phosphorylated tau peptides was studied using collision-induced dissociation (CID), electron transfer dissociation (ETD) and metastable atom-activated dissociation (MAD). The synthetic peptides studied contain up to two known phosphorylation sites on serine or threonine residues, at least two basic residues, and between four and eight potential sites of phosphorylation. CID produced mainly b-/y-type ions with abundant neutral losses of the phosphorylation modification. ETD produced c-/z-type ions in highest abundance but also showed numerous y-type ions at a frequency about 50% that of the z-type ions. The major peaks observed in the ETD spectra correspond to the charge-reduced product ions and small neutral losses from the charge-reduced peaks. ETD of the 2+ charge state of each peptide generally produced fewer backbone cleavages than the 3+ charge state, consistent with previous reports. Regardless of charge state, MAD achieved more extensive backbone cleavage than CID or ETD, while retaining the modification(s) in most cases. In all but one case, unambiguous modification site determination was achieved with MAD. MAD produced 15-20% better sequence coverage than CID and ETD for both the 2+ and 3+ charge states and very different fragmentation products indicating that the mechanism of fragmentation in MAD is unique and complementary to CID and ETD.
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Affiliation(s)
- Shannon L Cook
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Ohio University, Athens, Ohio 45701-2979, USA
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44
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Robb DB, Rogalski JC, Kast J, Blades MW. Liquid chromatography-atmospheric pressure electron capture dissociation mass spectrometry for the structural analysis of peptides and proteins. Anal Chem 2012; 84:4221-6. [PMID: 22494041 DOI: 10.1021/ac300648g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Atmospheric pressure electron capture dissociation (AP-ECD) is an emerging technique with the potential to be a more accessible alternative to conventional ECD/electron transfer dissociation (ETD) methods because it can be implemented using a stand-alone ion source device suitable for use with any existing or future electrospray ionization mass spectrometer. With AP-ECD, no modification of the main instrument is required, so it may easily be retrofitted to instruments not originally equipped with ECD/ETD capabilities. Here, we present our first purpose-built AP-ECD source and demonstrate its use in conjunction with capillary LC for the analysis of substance P, a tryptic digest of bovine serum albumin, and a phosphopeptide mixture. Quality ECD spectra were obtained for all the samples at the low femtomole level, proving that LC-AP-ECD-MS is suitable for the structural analysis of peptides and protein digests, in this case using an unmodified quadrupole time-of-flight mass spectrometer built ca. 2002.
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Affiliation(s)
- Damon B Robb
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1.
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45
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Mechref Y. Use of CID/ETD mass spectrometry to analyze glycopeptides. CURRENT PROTOCOLS IN PROTEIN SCIENCE 2012; Chapter 12:12.11.1-12.11.11. [PMID: 22470127 PMCID: PMC3673024 DOI: 10.1002/0471140864.ps1211s68] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Collision-induced dissociation (CID) tandem mass spectrometry (MS/MS) does not allow the characterization of glycopeptides because of the fragmentation of glycan structures and limited fragmentation of peptide backbones. Electron transfer dissociation (ETD) MS/MS, on the other hand, offers a complementary approach, prompting only peptide backbone fragmentation while keeping post-translational modifications intact. Characterization of glycopeptides using both CID and ETD is summarized in this unit. While CID provides information related to the composition of glycan moieties attached to a peptide backbone, ETD permits de novo sequencing of peptides. Radical anion transfer of electrons to the peptide backbone in ETD induces cleavage of the N-Cα bond. The glycan moiety is retained on the peptide backbone, largely unaffected by the ETD process, thus allowing the identification of the amino acid sequence of a glycopeptide and its glycosylation site. This unit discusses the use of both CID and ETD for better characterization of glycopeptides.
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Affiliation(s)
- Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas
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46
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Świerszcz I, Skurski P, Simons J. Dipole and Coulomb Forces in Electron Capture Dissociation and Electron Transfer Dissociation Mass Spectroscopy. J Phys Chem A 2012; 116:1828-37. [DOI: 10.1021/jp210915c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Piotr Skurski
- Department
of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952
Gdańsk, Poland
- Chemistry
Department and Henry
Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Jack Simons
- Chemistry
Department and Henry
Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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47
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Rand KD, Pringle SD, Morris M, Brown JM. Site-Specific Analysis of Gas-Phase Hydrogen/Deuterium Exchange of Peptides and Proteins by Electron Transfer Dissociation. Anal Chem 2012; 84:1931-40. [DOI: 10.1021/ac202918j] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Kasper D. Rand
- The Department of
Pharmaceutics
and Analytical Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Steven D. Pringle
- Waters
MS Technologies Centre, Micromass U.K. Ltd., Floats Rd, Wythenshawe, Manchester
M23 9LZ, U.K
| | - Michael Morris
- Waters
MS Technologies Centre, Micromass U.K. Ltd., Floats Rd, Wythenshawe, Manchester
M23 9LZ, U.K
| | - Jeffery M. Brown
- Waters
MS Technologies Centre, Micromass U.K. Ltd., Floats Rd, Wythenshawe, Manchester
M23 9LZ, U.K
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48
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Girod M, Brunet C, Antoine R, Lemoine J, Dugourd P, Charles L. Efficient structural characterization of poly(methacrylic acid) by activated-electron photodetachment dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:7-11. [PMID: 22048905 DOI: 10.1007/s13361-011-0279-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Revised: 10/04/2011] [Accepted: 10/12/2011] [Indexed: 05/31/2023]
Abstract
Characterization of end-groups in poly(methacrylic acid) (PMAA) was achieved using tandem mass spectrometry after activated-electron photodetachment dissociation (activated-EPD). In this technique, multiply deprotonated PMAA oligomers produced in the negative-ion mode of electrospray ionization were oxidized into radical anions upon electron photodetachment using a 220 nm laser wavelength, and further activated by collision. In contrast to conventional collision induced dissociation of negatively charged PMAA, which mainly consists of multiple dehydration steps, fragmentation of odd-electron species is shown to proceed via a radical-induced decarboxylation, followed by reactions involving backbone bond cleavages, giving rise to product ions containing one or the other oligomer termination. A single radical-induced mechanism accounts for the four main fragment series observed in MS/MS. The relative position of the radical and of the anionic center in distonic precursor ions determines the nature of the reaction products. Experiments performed using PMAA sodium salts allowed us to account for relative abundances of product ions in series obtained from PMAA, revealing that ion stability is ensured by hydrogen bonds within pairs of MAA units.
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Affiliation(s)
- Marion Girod
- Université de Lyon, 69622 Villeurbanne cedex, France
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49
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Gupta K, Kumar M, Chandrashekara K, Krishnan KS, Balaram P. Combined electron transfer dissociation-collision-induced dissociation fragmentation in the mass spectrometric distinction of leucine, isoleucine, and hydroxyproline residues in Peptide natural products. J Proteome Res 2011; 11:515-22. [PMID: 22111579 DOI: 10.1021/pr200091v] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Distinctions between isobaric residues have been a major challenge in mass spectrometric peptide sequencing. Here, we propose a methodology for distinction among isobaric leucine, isoleucine, and hydroxyproline, a commonly found post-translationally modified amino acid with a nominal mass of 113 Da, through a combined electron transfer dissociation-collision-induced dissociation approach. While the absence of c and z(•) ions, corresponding to the Yyy-Xxx (Xxx = Leu, Ile, or Hyp) segment, is indicative of the presence of hydroxyproline, loss of isopropyl (Δm = 43 Da) or ethyl radicals (Δm = 29 Da), through collisional activation of z radical ions, are characteristic of leucine or isoleucine, respectively. Radical migration processes permit distinctions even in cases where the specific z(•) ions, corresponding to the Yyy-Leu or -Ile segments, are absent or of low intensity. This tandem mass spectrometric (MS(n)) method has been successfully implemented in a liquid chromatography-MS(n) platform to determine the identity of 23 different isobaric residues from a mixture of five different peptides. The approach is convenient for distinction of isobaric residues from any crude peptide mixture, typically encountered in natural peptide libraries or proteomic analysis.
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Affiliation(s)
- Kallol Gupta
- Molecular Biophysics Unit, Indian Institute of Science , Bangalore 560012, India
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50
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Robb DB, Rogalski JC, Kast J, Blades MW. A new ion source and procedures for atmospheric pressure-electron capture dissociation of peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:1699-1706. [PMID: 21952883 DOI: 10.1007/s13361-011-0202-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Revised: 06/23/2011] [Accepted: 06/28/2011] [Indexed: 05/31/2023]
Abstract
We introduce a new atmospheric pressure-electron capture dissociation (AP-ECD) source in which conventional nanospray emitters are coupled with the source block and photoionization lamp of a PhotoSpray APPI source. We also introduce procedures for data collection and processing, aimed at maximizing the signal-to-background ratio of ECD products. Representative data from Substance P are presented to demonstrate the performance of the technique. Further, we demonstrate the effects of two important experimental variables, source temperature and vacuum-interface declustering potential (DP), on the method. Last, we show that even when a high source temperature is used to maximize efficiency, AP-ECD fragments of a model phosphorylated peptide retain the modification.
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Affiliation(s)
- Damon B Robb
- Department of Chemistry, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada.
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