1
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Mikawy NN, Rojas Ramírez C, DeFiglia SA, Szot CW, Le J, Lantz C, Wei B, Zenaidee MA, Blakney GT, Nesvizhskii AI, Loo JA, Ruotolo BT, Shabanowitz J, Anderson LC, Håkansson K. Are Internal Fragments Observable in Electron Based Top-Down Mass Spectrometry? Mol Cell Proteomics 2024; 23:100814. [PMID: 39029587 PMCID: PMC11388692 DOI: 10.1016/j.mcpro.2024.100814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 06/26/2024] [Accepted: 07/12/2024] [Indexed: 07/21/2024] Open
Abstract
Protein tandem mass spectrometry (MS/MS) often generates sequence-informative fragments from backbone bond cleavages near the termini. This lack of fragmentation in the protein interior is particularly apparent in native top-down mass spectrometry (MS). Improved sequence coverage, critical for reliable annotation of posttranslational modifications and sequence variants, may be obtained from internal fragments generated by multiple backbone cleavage events. However, internal fragment assignments can be error prone due to isomeric/isobaric fragments from different parts of a protein sequence. Also, internal fragment generation propensity depends on the chosen MS/MS activation strategy. Here, we examine internal fragment formation in electron capture dissociation (ECD) and electron transfer dissociation (ETD) following native and denaturing MS, as well as LC/MS of several proteins. Experiments were undertaken on multiple instruments, including quadrupole time-of-flight, Orbitrap, and high-field Fourier-transform ion cyclotron resonance (FT-ICR) across four laboratories. ECD was performed at both ultrahigh vacuum and at similar pressure to ETD conditions. Two complementary software packages were used for data analysis. When feasible, ETD-higher energy collision dissociation MS3 was performed to validate/refute potential internal fragment assignments, including differentiating MS3 fragmentation behavior of radical versus even-electron primary fragments. We show that, under typical operating conditions, internal fragments cannot be confidently assigned in ECD or ETD. On the other hand, such fragments, along with some b-type terminal fragments (not typically observed in ECD/ETD spectra) appear at atypical ECD operating conditions, suggesting they originate from a separate ion-electron activation process. Furthermore, atypical fragment ion types, e.g., x ions, are observed at such conditions as well as upon EThcD, presumably due to vibrational activation of radical z-type ions.
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Affiliation(s)
- Neven N Mikawy
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA; Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Ain-Shams University, Cairo, Egypt
| | - Carolina Rojas Ramírez
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA; Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Steven A DeFiglia
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Carson W Szot
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Jessie Le
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California, USA
| | - Carter Lantz
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California, USA
| | - Benqian Wei
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California, USA
| | - Muhammad A Zenaidee
- Australian Proteome Analysis Facility, Macquarie University, Sydney, New South Wales, Australia
| | - Greg T Blakney
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California, USA
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA
| | - Lissa C Anderson
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida, USA
| | - Kristina Håkansson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA.
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2
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Ivanova B. Special Issue with Research Topics on "Recent Analysis and Applications of Mass Spectra on Biochemistry". Int J Mol Sci 2024; 25:1995. [PMID: 38396673 PMCID: PMC10888122 DOI: 10.3390/ijms25041995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 02/04/2024] [Indexed: 02/25/2024] Open
Abstract
Analytical mass spectrometry applies irreplaceable mass spectrometric (MS) methods to analytical chemistry and chemical analysis, among other areas of analytical science [...].
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Affiliation(s)
- Bojidarka Ivanova
- Lehrstuhl für Analytische Chemie, Institut für Umweltforschung, Fakultät für Chemie und Chemische Biologie, Universität Dortmund, Otto-Hahn-Straße 6, 44221 Dortmund, Germany
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3
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Dunham SD, Brodbelt JS. Enhancing Top-Down Analysis of Proteins by Combining Ultraviolet Photodissociation (UVPD), Proton-Transfer Charge Reduction (PTCR), and Gas-Phase Fractionation to Alleviate the Impact of Nondissociated Precursor Ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:255-265. [PMID: 38150423 DOI: 10.1021/jasms.3c00351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Recent advances in top-down mass spectrometry strategies continue to improve the analysis of intact proteins. 193 nm ultraviolet photodissociation (UVPD) is one method well-suited for top-down analysis. UVPD is often performed using relatively low photon flux in order to limit multiple-generation dissociation of fragment ions and maximize sequence coverage. Consequently, a large portion of the precursor ion survives the UVPD process, dominates the spectrum, and may impede identification of fragment ions. Here, we explore the isolation of subpopulations of fragment ions lower and higher than the precursor ion after UVPD as a means to eliminate the impact of the surviving precursor ion on the detection of low abundance fragment ions. This gas-phase fractionation method improved sequence coverage harvested from fragment ions found in the m/z regions lower and higher than the precursor by an average factor of 1.3 and 2.3, respectively. Combining this gas-phase fractionation method with proton transfer charge reduction (PTCR) further increased the sequence coverage obtained from these m/z regions by another factor of 1.3 and 1.4, respectively. Implementing a post-UVPD fractionation + PTCR strategy with six fractionation events resulted in a sequence coverage of 75% for enolase, the highest reported for 193 nm UVPD.
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Affiliation(s)
- Sean D Dunham
- Department of Chemistry, University of Texas, Austin, Texas 787812, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas, Austin, Texas 787812, United States
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4
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Dunham SD, Wei B, Lantz C, Loo JA, Brodbelt JS. Impact of Internal Fragments on Top-Down Analysis of Intact Proteins by 193 nm UVPD. J Proteome Res 2023; 22:170-181. [PMID: 36503236 DOI: 10.1021/acs.jproteome.2c00583] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
193 nm ultraviolet photodissociation (UVPD) allows high sequence coverage to be obtained for intact proteins using terminal fragments alone. However, internal fragments, those that contain neither N- nor C- terminus, are typically ignored, neglecting their potential to bolster characterization of intact proteins. Here, we explore internal fragments generated by 193 nm UVPD for proteins ranging in size from 17-47 kDa and using the ClipsMS algorithm to facilitate searches for internal fragments. Internal fragments were only retained if identified in multiple replicates in order to reduce spurious assignments and to explore the reproducibility of internal fragments generated by UVPD. Inclusion of internal fragment improved sequence coverage by an average of 18% and 32% for UVPD and HCD, respectively, across all proteins and charge states studied. However, only an average of 18% of UVPD internal fragments were identified in two out of three replicates relative to the average number identified across all replicates for all proteins studied. Conversely, for HCD, an average of 63% of internal fragments were retained across replicates. These trends reflect an increased risk of false-positive identifications and a need for caution when considering internal fragments for UVPD. Additionally, proton-transfer charge reduction (PTCR) reactions were performed following UVPD or HCD to assess the impact on internal fragment identifications, allowing up to 20% more fragment ions to be retained across multiple replicates. At this time, it is difficult to recommend the inclusion of the internal fragment when searching UVPD spectra without further work to develop strategies for reducing the possibilities of false-positive identifications. All mass spectra are available in the public repository jPOST with the accession number JPST001885.
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Affiliation(s)
- Sean D Dunham
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Benqian Wei
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Carter Lantz
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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5
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Adams LM, DeHart CJ, Drown BS, Anderson LC, Bocik W, Boja ES, Hiltke TM, Hendrickson CL, Rodriguez H, Caldwell M, Vafabakhsh R, Kelleher NL. Mapping the KRAS proteoform landscape in colorectal cancer identifies truncated KRAS4B that decreases MAPK signaling. J Biol Chem 2022; 299:102768. [PMID: 36470426 PMCID: PMC9808003 DOI: 10.1016/j.jbc.2022.102768] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 11/22/2022] [Accepted: 11/28/2022] [Indexed: 12/07/2022] Open
Abstract
The KRAS gene is one of the most frequently mutated oncogenes in human cancer and gives rise to two isoforms, KRAS4A and KRAS4B. KRAS post-translational modifications (PTMs) have the potential to influence downstream signaling. However, the relationship between KRAS PTMs and oncogenic mutations remains unclear, and the extent of isoform-specific modification is unknown. Here, we present the first top-down proteomics study evaluating both KRAS4A and KRAS4B, resulting in 39 completely characterized proteoforms across colorectal cancer cell lines and primary tumor samples. We determined which KRAS PTMs are present, along with their relative abundance, and that proteoforms of KRAS4A versus KRAS4B are differentially modified. Moreover, we identified a subset of KRAS4B proteoforms lacking the C185 residue and associated C-terminal PTMs. By confocal microscopy, we confirmed that this truncated GFP-KRAS4BC185∗ proteoform is unable to associate with the plasma membrane, resulting in a decrease in mitogen-activated protein kinase signaling pathway activation. Collectively, our study provides a reference set of functionally distinct KRAS proteoforms and the colorectal cancer contexts in which they are present.
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Affiliation(s)
- Lauren M. Adams
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
| | - Caroline J. DeHart
- NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Bryon S. Drown
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA
| | - Lissa C. Anderson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Tallahassee, Florida, USA
| | - William Bocik
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Emily S. Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda Maryland, USA
| | - Tara M. Hiltke
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda Maryland, USA
| | | | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda Maryland, USA
| | - Michael Caldwell
- Division of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA,Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA
| | - Reza Vafabakhsh
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
| | - Neil L. Kelleher
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA,Department of Chemistry, Northwestern University, Evanston, Illinois, USA,Division of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA,Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA,For correspondence: Neil L. Kelleher
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6
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Shaw JB, Cooper-Shepherd DA, Hewitt D, Wildgoose JL, Beckman JS, Langridge JI, Voinov VG. Enhanced Top-Down Protein Characterization with Electron Capture Dissociation and Cyclic Ion Mobility Spectrometry. Anal Chem 2022; 94:3888-3896. [PMID: 35188751 PMCID: PMC8908312 DOI: 10.1021/acs.analchem.1c04870] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Tandem mass spectrometry of denatured, multiply charged high mass protein precursor ions yield extremely dense spectra with hundreds of broad and overlapping product ion isotopic distributions of differing charge states that yield an elevated baseline of unresolved "noise" centered about the precursor ion. Development of mass analyzers and signal processing methods to increase mass resolving power and manipulation of precursor and product ion charge through solution additives or ion-ion reactions have been thoroughly explored as solutions to spectral congestion. Here, we demonstrate the utility of electron capture dissociation (ECD) coupled with high-resolution cyclic ion mobility spectrometry (cIMS) to greatly increase top-down protein characterization capabilities. Congestion of protein ECD spectra was reduced using cIMS of the ECD product ions and "mobility fractions", that is, extracted mass spectra for segments of the 2D mobiligram (m/z versus drift time). For small proteins, such as ubiquitin (8.6 kDa), where mass resolving power was not the limiting factor for characterization, pre-IMS ECD and mobility fractions did not significantly increase protein sequence coverage, but an increase in the number of identified product ions was observed. However, a dramatic increase in performance, measured by protein sequence coverage, was observed for larger and more highly charged species, such as the +35 charge state of carbonic anhydrase (29 kDa). Pre-IMS ECD combined with mobility fractions yielded a 135% increase in the number of annotated isotope clusters and a 75% increase in unique product ions compared to processing without using the IMS dimension. These results yielded 89% sequence coverage for carbonic anhydrase.
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Affiliation(s)
- Jared B. Shaw
- e-MSion
Inc., 2121 NE Jack London Street, Corvallis, Oregon 97330, United States, (J.S.)
| | | | - Darren Hewitt
- Waters
Corporation, Wilmslow, Cheshire SK9 4AX, U.K.
| | | | - Joseph S. Beckman
- e-MSion
Inc., 2121 NE Jack London Street, 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 Street, Corvallis, Oregon 97330, United States
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7
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Dunham SD, Sanders JD, Holden DD, Brodbelt JS. Improving the Center Section Sequence Coverage of Large Proteins Using Stepped-Fragment Ion Protection Ultraviolet Photodissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:446-456. [PMID: 35119856 DOI: 10.1021/jasms.1c00296] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Ultraviolet photodissociation (UVPD) mass spectrometry has gained attention in recent years for its ability to provide high sequence coverage of intact proteins. However, secondary dissociation of fragment ions, in which fragment ions subjected to multiple laser pulses decompose into small products, is a common phenomenon during UVPD that contributes to limited coverage in the midsection of protein sequences. To counter secondary dissociation, a method involving the application of notched waveforms to modulate the trajectories of fragment ions away from the laser beam, termed fragment ion protection (FIP), was previously developed to reduce the probability of secondary dissociation. This, in turn, increased the number of identified large fragment ions. In the present study, FIP was applied to UVPD of large proteins ranging in size from 29 to 55 kDa, enhancing the abundances of large fragment ions. A stepped-FIP strategy was implemented in which UVPD mass spectra were collected using multiple different amplitudes of the FIP waveforms and then the results from the mass spectra were combined. By using stepped-FIP, the number of fragment ions in the midsections of the sequences increased for all proteins. For example, whereas no fragment ions were identified in the middle section of the sequence for glutamate dehydrogenase (55 kDa, 55+ charge state), 10 sequence ions were identified by using UVPD-FIP.
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Affiliation(s)
- Sean D Dunham
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
| | - James D Sanders
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
| | - Dustin D Holden
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
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8
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Tucholski T, Ge Y. Fourier-transform ion cyclotron resonance mass spectrometry for characterizing proteoforms. MASS SPECTROMETRY REVIEWS 2022; 41:158-177. [PMID: 32894796 PMCID: PMC7936991 DOI: 10.1002/mas.21653] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 08/26/2020] [Accepted: 08/26/2020] [Indexed: 05/05/2023]
Abstract
Proteoforms contribute functional diversity to the proteome and aberrant proteoforms levels have been implicated in biological dysfunction and disease. Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS), with its ultrahigh mass-resolving power, mass accuracy, and versatile tandem MS capabilities, has empowered top-down, middle-down, and native MS-based approaches for characterizing proteoforms and their complexes in biological systems. Herein, we review the features which make FT-ICR MS uniquely suited for measuring proteoform mass with ultrahigh resolution and mass accuracy; obtaining in-depth proteoform sequence coverage with expansive tandem MS capabilities; and unambiguously identifying and localizing post-translational and noncovalent modifications. We highlight examples from our body of work in which we have quantified and comprehensively characterized proteoforms from cardiac and skeletal muscle to better understand conditions such as chronic heart failure, acute myocardial infarction, and sarcopenia. Structural characterization of monoclonal antibodies and their proteoforms by FT-ICR MS and emerging applications, such as native top-down FT-ICR MS and high-throughput top-down FT-ICR MS-based proteomics at 21 T, are also covered. Historically, the information gleaned from FT-ICR MS analyses have helped provide biological insights. We predict FT-ICR MS will continue to enable the study of proteoforms of increasing size from increasingly complex endogenous mixtures and facilitate the benchmarking of sensitive and specific assays for clinical diagnostics. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Trisha Tucholski
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53706
- Human Proteomics Program, University of Wisconsin-Madison, Madison, WI, 53705
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9
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Li C, Chu S, Tan S, Yin X, Jiang Y, Dai X, Gong X, Fang X, Tian D. Towards Higher Sensitivity of Mass Spectrometry: A Perspective From the Mass Analyzers. Front Chem 2021; 9:813359. [PMID: 34993180 PMCID: PMC8724130 DOI: 10.3389/fchem.2021.813359] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 12/06/2021] [Indexed: 01/12/2023] Open
Abstract
Mass spectrometry (MS) is one of the most widely used analytical techniques in many fields. Recent developments in chemical and biological researches have drawn much attention to the measurement of substances with low abundances in samples. Continuous efforts have been made consequently to further improve the sensitivity of MS. Modifications on the mass analyzers of mass spectrometers offer a direct, universal and practical way to obtain higher sensitivity. This review provides a comprehensive overview of the latest developments in mass analyzers for the improvement of mass spectrometers' sensitivity, including quadrupole, ion trap, time-of-flight (TOF) and Fourier transform ion cyclotron (FT-ICR), as well as different combinations of these mass analyzers. The advantages and limitations of different mass analyzers and their combinations are compared and discussed. This review provides guidance to the selection of suitable mass spectrometers in chemical and biological analytical applications. It is also beneficial to the development of novel mass spectrometers.
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Affiliation(s)
- Chang Li
- College of Instrumentation & Electrical Engineering, Jilin University, Changchun, China
| | - Shiying Chu
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, People’s Republic ofChina
| | - Siyuan Tan
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, People’s Republic ofChina
| | - Xinchi Yin
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, People’s Republic ofChina
| | - You Jiang
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, People’s Republic ofChina
| | - Xinhua Dai
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, People’s Republic ofChina
| | - Xiaoyun Gong
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, People’s Republic ofChina
| | - Xiang Fang
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, People’s Republic ofChina
| | - Di Tian
- College of Instrumentation & Electrical Engineering, Jilin University, Changchun, China
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10
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Macias LA, Sipe SN, Santos IC, Bashyal A, Mehaffey MR, Brodbelt JS. Influence of Primary Structure on Fragmentation of Native-Like Proteins by Ultraviolet Photodissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2860-2873. [PMID: 34714071 PMCID: PMC8639798 DOI: 10.1021/jasms.1c00269] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Analysis of native-like protein structures in the gas phase via native mass spectrometry and auxiliary techniques has become a powerful tool for structural biology applications. In combination with ultraviolet photodissociation (UVPD), native top-down mass spectrometry informs backbone flexibility, topology, hydrogen bonding networks, and conformational changes in protein structure. Although it is known that the primary structure affects dissociation of peptides and proteins in the gas phase, its effect on the types and locations of backbone cleavages promoted by UVPD and concomitant influence on structural characterization of native-like proteins is not well understood. Here, trends in the fragmentation of native-like proteins were evaluated by tracking the propensity of 10 fragment types (a, a+1, b, c, x, x+1, y, y-1, Y, and z) in relation to primary structure in a native-top down UVPD data set encompassing >9600 fragment ions. Differing fragmentation trends are reported for the production of distinct fragment types, attributed to a combination of both direct dissociation pathways from excited electronic states and those surmised to involve intramolecular vibrational energy redistribution after internal conversion. The latter pathways were systematically evaluated to evince the role of proton mobility in the generation of "CID-like" fragments through UVPD, providing pertinent insight into the characterization of native-like proteins. Fragmentation trends presented here are envisioned to enhance analysis of the protein higher-order structure or augment scoring algorithms in the high-throughput analysis of intact proteins.
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Affiliation(s)
- Luis A Macias
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Sarah N Sipe
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Inês C Santos
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Aarti Bashyal
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - M Rachel Mehaffey
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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11
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Duselis EM, Panepinto MC, Syka JEP, Mullen C, D'Ippolito RA, English AM, Ugrin SA, Shabanowitz J, Hunt DF. Improved Sequence Analysis of Intact Proteins by Parallel Ion Parking during Electron Transfer Dissociation. Anal Chem 2021; 93:15728-15735. [PMID: 34788003 DOI: 10.1021/acs.analchem.1c03652] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Electron transfer dissociation (ETD) is an analytically useful tool for primary structure interrogation of intact proteins, but its utility is limited by higher-order reactions with the products. To inhibit these higher-order reactions, first-generation fragment ions are kinetically excited by applying an experimentally tailored parallel ion parking waveform during ETD (ETD-PIP). In combination with subsequent ion/ion proton transfer reactions, precursor-to-product conversion was maximized as evidenced by the consumption of more than 90% of the 21 kDa Protein G precursor to form ETD product ions. The employment of ETD-PIP increased sequence coverage to 90% from 80% with standard ETD. Additionally, the inhibition of sequential electron transfers was reflected in the high number of complementary ion pairs from ETD-PIP (90%) compared to standard ETD (39%).
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Affiliation(s)
- Elizabeth M Duselis
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Maria C Panepinto
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - John E P Syka
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | | | - Robert A D'Ippolito
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - A Michelle English
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Scott A Ugrin
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Donald F Hunt
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States.,Department of Pathology, University of Virginia, Charlottesville, Virginia 22903, United States
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12
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Baba T, Ryumin P, Duchoslav E, Chen K, Chelur A, Loyd B, Chernushevich I. Dissociation of Biomolecules by an Intense Low-Energy Electron Beam in a High Sensitivity Time-of-Flight Mass Spectrometer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1964-1975. [PMID: 34080873 DOI: 10.1021/jasms.0c00425] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
We report the progress on an electron-activated dissociation (EAD) device coupled to a quadrupole TOF mass spectrometer (QqTOF MS) developed in our group. This device features a new electron beam optics design allowing up to 100 times stronger electron currents in the reaction cell. The electron beam current reached the space-charge limit of 0.5 μA at near-zero electron kinetic energies. These advances enable fast and efficient dissociation of various analytes ranging from singly charged small molecules to multiply protonated proteins. Tunable electron energy provides access to different fragmentation regimes: ECD, hot ECD, and electron-impact excitation of ions from organics (EIEIO). The efficiency of the device was tested on a wide range of precursor charge states. The EAD device was installed in a QqTOF MS employing a novel trap-and-release strategy facilitating spatial mass focusing of ions at the center of the TOF accelerator. This technique increased the sensitivity 6-10 times and allows for the first time comprehensive structural lipidomics on an LC time scale. The system was evaluated for other compound classes such as intact proteins and glycopeptides. Application of hot ECD for the analysis of glycopeptides resulted in rich fragmentation with predominantly peptide backbone fragments; however, glycan fragments attributed to the ECD process were also observed. A standard small protein ubiquitin (8.6 kDa) was sequenced with 90% cleavage coverage at spectrum accumulation times of 100 ms and 98% at 800 ms. Comparable cleavage coverage for a medium-size protein (carbonic anhydrase: 29 kDa) could be achieved, albeit with longer accumulation times.
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Affiliation(s)
- Takashi Baba
- Sciex, 71 Four Valley Drive Concord, Ontario L4K 4V8, Canada
| | - Pavel Ryumin
- Sciex, 71 Four Valley Drive Concord, Ontario L4K 4V8, Canada
| | - Eva Duchoslav
- Sciex, 71 Four Valley Drive Concord, Ontario L4K 4V8, Canada
| | - Keqin Chen
- Sciex, 71 Four Valley Drive Concord, Ontario L4K 4V8, Canada
| | - Anjali Chelur
- Sciex, 71 Four Valley Drive Concord, Ontario L4K 4V8, Canada
| | - Bill Loyd
- Sciex, 71 Four Valley Drive Concord, Ontario L4K 4V8, Canada
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13
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Weisbrod CR, Anderson LC, Hendrickson CL, Schaffer LV, Shortreed MR, Smith LM, Shabanowitz J, Hunt DF. Advanced Strategies for Proton-Transfer Reactions Coupled with Parallel Ion Parking on a 21 T FT-ICR MS for Intact Protein Analysis. Anal Chem 2021; 93:9119-9128. [PMID: 34165955 DOI: 10.1021/acs.analchem.1c00847] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proton-transfer reactions (PTRs) have emerged as a powerful tool for the study of intact proteins. When coupled with m/z-selective kinetic excitation, such as parallel ion parking (PIP), one can exert exquisite control over rates of reaction with a high degree of specificity. This allows one to "concentrate", in the gas phase, nearly all the signals from an intact protein charge state envelope into a single charge state, improving the signal-to-noise ratio (S/N) by 10× or more. While this approach has been previously reported, here we show that implementing these technologies on a 21 T FT-ICR MS provides a tremendous advantage for intact protein analysis. Advanced strategies for performing PTR with PIP were developed to complement this unique instrument, including subjecting all analyte ions entering the mass spectrometer to PTR and PIP. This experiment, which we call "PTR-MS1-PIP", generates a pseudo-MS1 spectrum derived from ions that are exposed to the PTR reagent and PIP waveforms but have not undergone any prior true mass filtering or ion isolation. The result is an extremely rapid and significant improvement in the spectral S/N of intact proteins. This permits the observation of many more proteoforms and reduces ion injection periods for subsequent tandem mass spectrometry characterization. Additionally, the product ion parking waveform has been optimized to enhance the PTR rate without compromise to the parking efficiency. We demonstrate that this process, called "rapid park", can improve reaction rates by 5-10× and explore critical factors discovered to influence this process. Finally, we demonstrate how coupling PTR-MS1 and rapid park provides a 10-fold reduction in ion injection time, improving the rate of tandem MS sequencing.
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Affiliation(s)
- Chad R Weisbrod
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800 E. Paul Dirac Dr., Tallahassee, Florida 32310, United States
| | - Lissa C Anderson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800 E. Paul Dirac Dr., Tallahassee, Florida 32310, United States
| | - Christopher L Hendrickson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800 E. Paul Dirac Dr., Tallahassee, Florida 32310, United States
| | - Leah V Schaffer
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Michael R Shortreed
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Donald F Hunt
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
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14
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Shen X, Xu T, Hakkila B, Hare M, Wang Q, Wang Q, Beckman JS, Sun L. Capillary Zone Electrophoresis-Electron-Capture Collision-Induced Dissociation on a Quadrupole Time-of-Flight Mass Spectrometer for Top-Down Characterization of Intact Proteins. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1361-1369. [PMID: 33749270 PMCID: PMC8576897 DOI: 10.1021/jasms.0c00484] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Mass spectrometry (MS)-based denaturing top-down proteomics (dTDP) requires high-capacity separation and extensive gas-phase fragmentation of proteoforms. Herein, we coupled capillary zone electrophoresis (CZE) to electron-capture collision-induced dissociation (ECciD) on an Agilent 6545 XT quadrupole time-of-flight (Q-TOF) mass spectrometer for dTDP for the first time. During ECciD, the protein ions were first fragmented using ECD, followed by further activation and fragmentation by applying a CID potential. In this pilot study, we optimized the CZE-ECciD method for small proteins (lower than 20 kDa) regarding the charge state of protein parent ions for fragmentation and the CID potential applied to maximize the protein backbone cleavage coverage and the number of sequence-informative fragment ions. The CZE-ECciD Q-TOF platform provided extensive backbone cleavage coverage for three standard proteins lower than 20 kDa from only single charge states in a single CZE-MS/MS run in the targeted MS/MS mode, including ubiquitin (97%, +7, 8.6 kDa), superoxide dismutase (SOD, 87%, +17, 16 kDa), and myoglobin (90%, +16, 17 kDa). The CZE-ECciD method produced comparable cleavage coverage of small proteins (i.e., myoglobin) with direct-infusion MS studies using electron transfer dissociation (ETD), activated ion-ETD, and combinations of ETD and collision-based fragmentation on high-end orbitrap mass spectrometers. The results render CZE-ECciD a new tool for dTDP to enhance both separation and gas-phase fragmentation of proteoforms.
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Affiliation(s)
- Xiaojing Shen
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Tian Xu
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Blake Hakkila
- e-MSion, Inc., 2121 NE Jack London Drive, Corvallis, Oregon 97330, United States
| | - Mike Hare
- e-MSion, Inc., 2121 NE Jack London Drive, Corvallis, Oregon 97330, United States
| | - Qianjie Wang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Qianyi Wang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - 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
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
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15
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Cejkov M, Greer T, Johnson RO, Zheng X, Li N. Electron Transfer Dissociation Parameter Optimization Using Design of Experiments Increases Sequence Coverage of Monoclonal Antibodies. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:762-771. [PMID: 33596068 DOI: 10.1021/jasms.0c00458] [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
Middle-down analysis of monoclonal antibodies (mAbs) by tandem mass spectrometry (MS2) can provide detailed insight into their primary structure with minimal sample preparation. The middle-down approach uses an enzyme to cleave mAbs into Fc/2, LC, and Fd subunits that are then analyzed by reversed phase liquid chromatography tandem mass spectrometry (RPLC-MS2). As maximum sequence coverage is desired to obtain meaningful structural information at the subunit level, a host of dissociation methods have been developed, and sometimes combined, to bolster fragmentation and increase the number of identified fragments. Here, we present a design of experiments (DOE) approach to optimize MS2 parameters, in particular those that may influence electron transfer dissociation (ETD) efficiency to increase the sequence coverage of antibody subunits. Applying this approach to the NIST monoclonal antibody standard (NISTmAb) using three RPLC-MS2 runs resulted in high sequence coverages of 67%, 67%, and 52% for Fc/2, LC, and Fd subunits, respectively. In addition, we apply this DOE strategy to model the parameters required to maximize the number of fragments produced in "low", "medium", and "high" mass ranges, which ultimately resulted in even higher sequence coverages of NISTmAb subunits (75%, 78%, and 64% for Fc/2, LC, and Fd subunits, respectively). The DOE approach provides high sequence coverage percentages utilizing only one fragmentation method, ETD, and could be extended to other state-of-the-art techniques that combine multiple fragmentation mechanisms to increase coverage.
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Affiliation(s)
- Milos Cejkov
- Analytical Chemistry, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, New York 10591-6707, United States
| | - Tyler Greer
- Analytical Chemistry, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, New York 10591-6707, United States
| | - Reid O'Brien Johnson
- Analytical Chemistry, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, New York 10591-6707, United States
| | - Xiaojing Zheng
- Analytical Chemistry, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, New York 10591-6707, United States
| | - Ning Li
- Analytical Chemistry, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, New York 10591-6707, United States
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16
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Weisbrod CR, Anderson LC, Greer JB, DeHart CJ, Hendrickson CL. Increased Single-Spectrum Top-Down Protein Sequence Coverage in Trapping Mass Spectrometers with Chimeric Ion Loading. Anal Chem 2020; 92:12193-12200. [PMID: 32812743 DOI: 10.1021/acs.analchem.0c01064] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Fourier transform mass spectrometers routinely provide high mass resolution, mass measurement accuracy, and mass spectral dynamic range. In this work, we utilize 21 T Fourier transform ion cyclotron resonance (FT-ICR) to analyze product ions derived from the application of multiple dissociation techniques and/or multiple precursor ions within a single transient acquisition. This ion loading technique, which we call, "chimeric ion loading", saves valuable acquisition time, decreases sample consumption, and improves top-down protein sequence coverage. In the analysis of MCF7 cell lysate, we show collision-induced dissociation (CID) and electron-transfer dissociation (ETD) on each precursor on a liquid chromatography-mass spectrometry (LC-MS) timescale and improve mean sequence coverage dramatically (CID-only 15% vs chimeric 33%), even during discovery-based acquisition. This approach can also be utilized to multiplex the acquisition of product ion spectra of multiple charge states from a single protein precursor or multiple ETD/proton-transfer reactions (PTR) reaction periods. The analytical utility of chimeric ion loading is demonstrated for top-down proteomics, but it is also likely to be impactful for tandem mass spectrometry applications in other areas.
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Affiliation(s)
- Chad R Weisbrod
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800 E. Paul Dirac Dr., Tallahassee, Florida 32310, United States
| | - Lissa C Anderson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800 E. Paul Dirac Dr., Tallahassee, Florida 32310, United States
| | - Joseph B Greer
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois 60208, United States
| | - Caroline J DeHart
- NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Christopher L Hendrickson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800 E. Paul Dirac Dr., Tallahassee, Florida 32310, United States.,Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, Florida 32306, United States
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17
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Lee KW, Eakins GS, Carlsen MS, McLuckey SA. Ion trap operational modes for ion/ion reactions yielding high mass-to-charge product ions. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2020; 451:116313. [PMID: 32351313 PMCID: PMC7189770 DOI: 10.1016/j.ijms.2020.116313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
To better probe large biomolecular complexes, developments in mass spectrometry (MS) have focused on improving technologies used to generate, transmit, and measure high m/z ions. The additional tandem-MS (MSn) capabilities of ion trap mass spectrometers (ITMS) facilitate experiments that facilitate probing complex biomolecular ions. In particular, charge reduction using gas-phase ion/ion reactions increase separation of charge states generated via electrospray ionization (ESI), which increases confidence in charge state assignments and therefore masses determined from the observed charge states. Current ITMS technologies struggle to generate and measure low charge states of large (>50 kDa) proteins and complexes because of power limitations associated with conventional high-frequency sine wave operation. Other approaches, including frequency scanning techniques and use of digital waveforms, reduce or eliminate some of these limitations. The work presented here studies five different operational modes for a quadrupole ion trap (QIT) mass spectrometer used to generate and measure low charge states of bovine serum albumin (BSA), pyruvate kinase (PK), and GroEL. While digital operation of a QIT presents limitations during the ion/ion reaction period of the experiment, it generally provided the best spectra in terms of resolution and signal at m/z > 50,000.
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Affiliation(s)
| | | | | | - Scott A. McLuckey
- Corresponding author. 560 Oval Drive, Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA, (S.A. McLuckey)
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18
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Gallagher KJ, Palasser M, Hughes S, Mackay CL, Kilgour DPA, Clarke DJ. Isotope Depletion Mass Spectrometry (ID-MS) for Accurate Mass Determination and Improved Top-Down Sequence Coverage of Intact Proteins. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:700-710. [PMID: 32003978 DOI: 10.1021/jasms.9b00119] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Top-down mass spectrometry (MS) is an increasingly important technique for protein characterization. However, in many biological MS experiments, the practicality of applying top-down methodologies is still limited at higher molecular mass. In large part, this is due to the detrimental effect resulting from the partitioning of the mass spectral signal into an increasing number of isotopic peaks as molecular mass increases. Reducing the isotopologue distribution of proteins via depletion of heavy stable isotopes was first reported over 20 years ago (Marshall, A. G.; Senko, M. W.; Li, W.; Li, M.; Dillon, S., Guan, S.; Logan, T. M.. Protein Molecular Mass to 1 Da by 13C, 15N Double-Depletion and FT-ICR Mass Spectrometry. J. Am. Chem. Soc. 1997, 119, 433-434.) and has been demonstrated for several small proteins. Here we extend this approach, introducing a new highly efficient method for the production of recombinant proteins depleted in 13C and 15N and demonstrating its advantages for top-down analysis of larger proteins (up to ∼50 kDa). FT-ICR MS of isotopically depleted proteins reveals dramatically reduced isotope distributions with monoisotopic signal observed up to 50 kDa. In top-down fragmentation experiments, the reduced spectral complexity alleviates fragment-ion signal overlap, the presence of monoisotopic signals allows assignment with higher mass accuracy, and the dramatic increase in signal-to-noise ratio (up to 7-fold) permits vastly reduced acquisition times. These compounding benefits allow the assignment of ∼3-fold more fragment ions than comparable analyses of proteins with natural isotopic abundances. Finally, we demonstrate greatly increased sequence coverage in time-limited top-down experiments-highlighting advantages for top-down LC-MS/MS workflows and top-down proteomics.
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Affiliation(s)
- Kelly J Gallagher
- The EastChem School of Chemistry, University of Edinburgh, Joseph Black Building, Brewster Road, Edinburgh EH9 3FJ, U.K
| | - Michael Palasser
- The EastChem School of Chemistry, University of Edinburgh, Joseph Black Building, Brewster Road, Edinburgh EH9 3FJ, U.K
| | - Sam Hughes
- The EastChem School of Chemistry, University of Edinburgh, Joseph Black Building, Brewster Road, Edinburgh EH9 3FJ, U.K
| | - C Logan Mackay
- The EastChem School of Chemistry, University of Edinburgh, Joseph Black Building, Brewster Road, Edinburgh EH9 3FJ, U.K
| | - David P A Kilgour
- Chemistry and Forensics, Nottingham Trent University, Rosalind Franklin Building, Clifton Lane, Nottingham NG11 8NS, U.K
| | - David J Clarke
- The EastChem School of Chemistry, University of Edinburgh, Joseph Black Building, Brewster Road, Edinburgh EH9 3FJ, U.K
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19
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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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20
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Foreman DJ, McLuckey SA. Recent Developments in Gas-Phase Ion/Ion Reactions for Analytical Mass Spectrometry. Anal Chem 2020; 92:252-266. [PMID: 31693342 PMCID: PMC6949396 DOI: 10.1021/acs.analchem.9b05014] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- David J Foreman
- Department of Chemistry , Purdue University , West Lafayette , Indiana 47907-2084 , United States
| | - Scott A McLuckey
- Department of Chemistry , Purdue University , West Lafayette , Indiana 47907-2084 , United States
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21
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Hinkle JD, D'Ippolito RA, Panepinto MC, Wang WH, Bai DL, Shabanowitz J, Hunt DF. Unambiguous Sequence Characterization of a Monoclonal Antibody in a Single Analysis Using a Nonspecific Immobilized Enzyme Reactor. Anal Chem 2019; 91:13547-13554. [PMID: 31584792 DOI: 10.1021/acs.analchem.9b02666] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Accurate sequence characterization is essential for the development of therapeutic antibodies by the pharmaceutical industry. Presented here is a methodology to obtain comprehensive sequence analysis of a monoclonal antibody. An enzyme reactor of immobilized Aspergillopepsin I, a highly stable nonspecific protease, was used to cleave reduced antibody subunits into a peptide profile ranging from 1 to 20 kDa. Utilizing the Thermo Orbitrap Fusion's unique instrument architecture combined with state-of-the-art instrument control software allowed for dynamic instrument methods that optimally characterize eluting peptides based on their size and charge density. Using a data-dependent instrument method, both collisional dissociation and electron transfer dissociation were used to fragment the appropriate charge state of analyte peptides. The instrument layout also allowed for scans to be taken in parallel using both the ion trap and Orbitrap concurrently, thus allowing larger peptides to be analyzed in high resolution using the Orbitrap while simultaneously analyzing tryptic-like peptides using the ion trap. We harnessed these capabilities to develop a custom method to optimally fragment the eluting peptides based on their mass and charge density. Using this approach, we obtained 100% sequence coverage of the total antibody in a single chromatographic analysis, enabling unambiguous sequence assignment of all residues.
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Affiliation(s)
- Joshua D Hinkle
- Department of Chemistry , University of Virginia , Charlottesville , Virginia 22904 , United States
| | - Robert A D'Ippolito
- Department of Chemistry , University of Virginia , Charlottesville , Virginia 22904 , United States
| | - Maria C Panepinto
- Department of Chemistry , University of Virginia , Charlottesville , Virginia 22904 , United States
| | - Wei-Han Wang
- Department of Chemistry , University of Virginia , Charlottesville , Virginia 22904 , United States
| | - Dina L Bai
- Department of Chemistry , University of Virginia , Charlottesville , Virginia 22904 , United States
| | - Jeffrey Shabanowitz
- Department of Chemistry , University of Virginia , Charlottesville , Virginia 22904 , United States
| | - Donald F Hunt
- Department of Chemistry , University of Virginia , Charlottesville , Virginia 22904 , United States.,Department of Pathology , University of Virginia , Charlottesville , Virginia 22908 , United States
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22
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Vincent D, Binos S, Rochfort S, Spangenberg G. Top-Down Proteomics of Medicinal Cannabis. Proteomes 2019; 7:proteomes7040033. [PMID: 31554318 PMCID: PMC6958505 DOI: 10.3390/proteomes7040033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/06/2019] [Accepted: 09/20/2019] [Indexed: 02/02/2023] Open
Abstract
The revised legislation on medicinal cannabis has triggered a surge of research studies in this space. Yet, cannabis proteomics is lagging. In a previous study, we optimised the protein extraction of mature buds for bottom-up proteomics. In this follow-up study, we developed a top-down mass spectrometry (MS) proteomics strategy to identify intact denatured protein from cannabis apical buds. After testing different source-induced dissociation (SID), collision-induced dissociation (CID), higher-energy collisional dissociation (HCD), and electron transfer dissociation (ETD) parameters on infused known protein standards, we devised three LC-MS/MS methods for top-down sequencing of cannabis proteins. Different MS/MS modes produced distinct spectra, albeit greatly overlapping between SID, CID, and HCD. The number of fragments increased with the energy applied; however, this did not necessarily translate into greater sequence coverage. Some precursors were more amenable to fragmentation than others. Sequence coverage decreased as the mass of the protein increased. Combining all MS/MS data maximised amino acid (AA) sequence coverage, achieving 73% for myoglobin. In this experiment, most cannabis proteins were smaller than 30 kD. A total of 46 cannabis proteins were identified with 136 proteoforms bearing different post-translational modifications (PTMs), including the excision of N-terminal M, the N-terminal acetylation, methylation, and acetylation of K resides, and phosphorylation. Most identified proteins are involved in photosynthesis, translation, and ATP production. Only one protein belongs to the phytocannabinoid biosynthesis, olivetolic acid cyclase.
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Affiliation(s)
- Delphine Vincent
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, Victoria 3083, Australia.
| | - Steve Binos
- Thermo Fisher Scientific, Bio21 Institute, The University of Melbourne, 30 Flemington Rd, Parkville, Victoria 3052, Australia.
| | - Simone Rochfort
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, Victoria 3083, Australia.
| | - German Spangenberg
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, Victoria 3083, Australia.
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23
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He L, Anderson LC, Barnidge DR, Murray DL, Dasari S, Dispenzieri A, Hendrickson CL, Marshall AG. Classification of Plasma Cell Disorders by 21 Tesla Fourier Transform Ion Cyclotron Resonance Top-Down and Middle-Down MS/MS Analysis of Monoclonal Immunoglobulin Light Chains in Human Serum. Anal Chem 2019; 91:3263-3269. [DOI: 10.1021/acs.analchem.8b03294] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Lidong He
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32310, United States
| | - Lissa C. Anderson
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Dr., Tallahassee, Florida 32310, United States
| | | | | | | | | | - Christopher L. Hendrickson
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32310, United States
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Dr., Tallahassee, Florida 32310, United States
| | - Alan G. Marshall
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32310, United States
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Dr., Tallahassee, Florida 32310, United States
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24
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Wang Z, Liu X, Muther J, James JA, Smith K, Wu S. Top-down Mass Spectrometry Analysis of Human Serum Autoantibody Antigen-Binding Fragments. Sci Rep 2019; 9:2345. [PMID: 30787393 PMCID: PMC6382847 DOI: 10.1038/s41598-018-38380-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 12/18/2018] [Indexed: 12/26/2022] Open
Abstract
Detecting autoimmune diseases at an early stage is crucial for effective treatment and disease management to slow disease progression and prevent irreversible organ damage. In many autoimmune diseases, disease-specific autoantibodies are produced by B cells in response to soluble autoantigens due to defects in B cell tolerance mechanisms. Autoantibodies accrue early in disease development, and several are so disease-specific they serve as classification criteria. In this study, we established a high-throughput, sensitive, intact serum autoantibody analysis platform based on the optimization of a one dimensional ultra-high-pressure liquid chromatography top-down mass spectrometry platform (1D UPLC-TDMS). This approach has been successfully applied to a 12 standard monoclonal antibody antigen-binding fragment (Fab) mixture, demonstrating the feasibility to separate and sequence intact antibodies with high sequence coverage and high sensitivity. We then applied the optimized platform to characterize total serum antibody Fabs in a systemic lupus erythematosus (SLE) patient sample and compared it to healthy control samples. From this analysis, we show that the SLE sample has many dominant antibody Fab-related mass features unlike the healthy controls. To our knowledge, this is the first top-down demonstration of serum autoantibody pool analysis. Our proposed approach holds great promise for discovering novel serum autoantibody biomarkers that are of interest for diagnosis, prognosis, and tolerance induction, as well as improving our understanding of pathogenic autoimmune processes.
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Affiliation(s)
- Zhe Wang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA
| | - Xiaowen Liu
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Jennifer Muther
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Judith A James
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
- Departments of Medicine and Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Kenneth Smith
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA.
| | - Si Wu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA.
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25
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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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26
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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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27
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Park SG, Anderson GA, Bruce JE. Characterization of Harmonic Signal Acquisition with Parallel Dipole and Multipole Detectors. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1394-1402. [PMID: 29691781 PMCID: PMC6537869 DOI: 10.1007/s13361-018-1954-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 03/01/2018] [Accepted: 03/21/2018] [Indexed: 05/22/2023]
Abstract
Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) is a powerful instrument for the study of complex biological samples due to its high resolution and mass measurement accuracy. However, the relatively long signal acquisition periods needed to achieve high resolution can serve to limit applications of FTICR-MS. The use of multiple pairs of detector electrodes enables detection of harmonic frequencies present at integer multiples of the fundamental cyclotron frequency, and the obtained resolving power for a given acquisition period increases linearly with the order of harmonic signal. However, harmonic signal detection also increases spectral complexity and presents challenges for interpretation. In the present work, ICR cells with independent dipole and harmonic detection electrodes and preamplifiers are demonstrated. A benefit of this approach is the ability to independently acquire fundamental and multiple harmonic signals in parallel using the same ions under identical conditions, enabling direct comparison of achieved performance as parameters are varied. Spectra from harmonic signals showed generally higher resolving power than spectra acquired with fundamental signals and equal signal duration. In addition, the maximum observed signal to noise (S/N) ratio from harmonic signals exceeded that of fundamental signals by 50 to 100%. Finally, parallel detection of fundamental and harmonic signals enables deconvolution of overlapping harmonic signals since observed fundamental frequencies can be used to unambiguously calculate all possible harmonic frequencies. Thus, the present application of parallel fundamental and harmonic signal acquisition offers a general approach to improve utilization of harmonic signals to yield high-resolution spectra with decreased acquisition time. Graphical Abstract ᅟ.
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Affiliation(s)
- Sung-Gun Park
- Department of Genome Sciences, University of Washington, Seattle, WA, 98109, USA
| | | | - James E Bruce
- Department of Genome Sciences, University of Washington, Seattle, WA, 98109, USA.
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28
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Jiang T, Hoover ME, Holt MV, Freitas MA, Marshall AG, Young NL. Middle-Down Characterization of the Cell Cycle Dependence of Histone H4 Posttranslational Modifications and Proteoforms. Proteomics 2018; 18:e1700442. [PMID: 29667342 PMCID: PMC8087174 DOI: 10.1002/pmic.201700442] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 02/28/2018] [Indexed: 12/12/2022]
Abstract
Post-translational modifications (PTMs) of histones are important epigenetic regulatory mechanisms that are often dysregulated in cancer. We employ middle-down proteomics to investigate the PTMs and proteoforms of histone H4 during cell cycle progression. We use pH gradient weak cation exchange-hydrophilic interaction liquid chromatography (WCX-HILIC) for on-line liquid chromatography-mass spectrometry analysis to separate and analyze the proteoforms of histone H4. This procedure provides enhanced separation of proteoforms, including positional isomers, and simplifies downstream data analysis. We use ultrahigh mass accuracy and resolution Fourier transform-ion cyclotron resonance (FT-ICR) mass spectrometer to unambiguously distinguish between acetylation and tri-methylation (∆m = 0.036 Da). In total, we identify and quantify 233 proteoforms of histone H4 in two breast cancer cell lines. We observe significant increases in S1 phosphorylation during mitosis, implicating an important role in mitotic chromatin condensation. A decrease of K20 unmodified proteoforms is observed as the cell cycle progresses, corresponding to an increase of K20 mono- and di-methylation. Acetylation at K5, K8, K12, and K16 declines as cells traverse from S phase to mitosis, suggesting cell cycle-dependence and an important role during chromatin replication and condensation. These new insights into the epigenetics of the cell cycle may provide new diagnostic and prognostic biomarkers.
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Affiliation(s)
- Tingting Jiang
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, FL, 32306, USA
| | - Michael E Hoover
- Department of Cancer Biology and Genetics, Ohio State University, 460 West 12th Avenue, Columbus, OH, 43210, USA
| | - Matthew V Holt
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Michael A Freitas
- Department of Cancer Biology and Genetics, Ohio State University, 460 West 12th Avenue, Columbus, OH, 43210, USA
| | - Alan G Marshall
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, FL, 32306, USA
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, FL, 32310, USA
| | - Nicolas L Young
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
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29
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Affiliation(s)
- Bifan Chen
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kyle A. Brown
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Ziqing Lin
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Human Proteomics Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Human Proteomics Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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30
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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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