1
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Lanzillotti M, Brodbelt JS. Comparison of Top-Down Protein Fragmentation Induced by 213 and 193 nm UVPD. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:279-285. [PMID: 36594540 DOI: 10.1021/jasms.2c00288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The growing interest in advancing tandem mass spectrometry strategies for top-down proteomics has motivated efforts to optimize ion activation strategies for intact proteins, including the comparison of 193 and 213 nm wavelengths for ultraviolet photodissociation (UVPD). The present study focuses on the performance and outcomes of UVPD for five proteins, ubiquitin, cytochrome C, frataxin, myoglobin, and carbonic anhydrase, with an emphasis on evaluating the similarities and differences in fragmentation promoted by UVPD using 193 nm versus 213 nm photons. Mass spectra were collected as a function of the number of laser pulses, and precursor depletion levels were monitored and controlled to provide consistent energy deposition between 213 and 193 nm UVPD. Fragment ions were confirmed on the basis of their isotopic distributions in m/z space to preserve both charge state and abundance information and were classified on the basis of ion type and frequency. A large portion of the total fragment ion abundance was attributable to preferential cleavages, particularly ones adjacent to proline residues. These cleavages were examined on the basis of the backbone site and abundances, revealing that a and y-2 ions N-terminal to proline residues appeared at disproportionately high abundances in 213 nm UVPD spectra as compared to 193 nm UVPD spectra, highlighting one notable difference in the top-down spectra. We theorize that these fragments are formed more efficiently in 213 nm UVPD than in 193 nm UVPD due to increased absorption of 213 nm photons at the proline amide bond.
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Affiliation(s)
- Michael Lanzillotti
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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2
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Babović M, Shliaha PV, Gibb S, Jensen ON. Effective Amino Acid Sequencing of Intact Filgrastim by Multimodal Mass Spectrometry with Topdownr. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:2087-2093. [PMID: 36263452 DOI: 10.1021/jasms.2c00193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Therapeutic proteins, known as biologicals, are an important and growing class of drugs for treatment of a series of human ailments. Amino acid sequence variants of therapeutic proteins can affect their safety and efficacy. Top-down mass spectrometry is well suited for the sequence analysis of intact therapeutic proteins. Fine-tuning of tandem mass spectrometry (MS/MS) fragmentation conditions is essential for maximizing the amino acid sequence coverage but is often time-consuming. We used topdownr, an automated and integrated multimodal approach to systematically assess high mass accuracy MS/MS fragmentation parameters to characterize filgrastim, a 19 kDa recombinant human granulocyte colony-stimulating factor used in treating neutropenia. A total of 276 different MS/MS conditions were systematically tested, including the following parameters: protein charge state, HCD and CID collision energy, ETD reaction time, ETD supplemental activation, and UVPD activation time. Stringent and accurate evaluation and annotation of the MS/MS data was achieved by requiring a fragment ion mass error of 5 ppm, considering reproducible N- and C-terminal fragment ions only, and excluding internal fragment ion assignments. We report the first EThcD and UVPD MS/MS analysis of intact filgrastim, and these two techniques combined resulted in 98% amino acid sequence coverage. By combining all tested fragmentation modes, we obtained near-complete amino acid sequence coverage (99.4%) of intact filgrastim.
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Affiliation(s)
- Maša Babović
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense, Denmark
| | - Pavel V Shliaha
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense, Denmark
| | - Sebastian Gibb
- Department of Anesthesiology and Intensive Care, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Ole N Jensen
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense, Denmark
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3
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Lambeth TR, Julian RR. Efficient Isothiocyanate Modification of Peptides Facilitates Structural Analysis by Radical-Directed Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1338-1345. [PMID: 34670075 DOI: 10.1021/jasms.1c00237] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Radical-directed dissociation (RDD) is a powerful technique for structural characterization of peptides in mass spectrometry experiments. Prior to analysis, a radical precursor must typically be appended to facilitate generation of a free radical. To explore the use of a radical precursor that can be easily attached in a single step, we modified peptides using a "click" reaction with iodophenyl isothiocyanate. Coupling with amine functional groups proceeds with high yields, producing stable iodophenylthiourea-modified peptides. Photodissociation yields were recorded at 266 and 213 nm for the 2-, 3-, and 4-iodo isomers of the modifier and found to be highest for the 4-iodo isomer in nearly all cases. Fragmentation of the modified peptides following collisional activation revealed favorable losses of the tag, and electronic structure calculations were used to evaluate a potential mechanism involving hydrogen transfer within the thiourea group. Examination of RDD data revealed that 4-iodobenzoic acid, 4-iodophenylthiourea, and 3-iodotyrosine yield similar fragmentation patterns for a given peptide, although differences in fragment abundance are noted. Iodophenyl isothiocyanate labeling in combination with RDD can be used to differentiate isomeric amino acids within peptides, which should facilitate simplified evaluation of isomers present in complex biological samples.
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Affiliation(s)
- Tyler R Lambeth
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Ryan R Julian
- Department of Chemistry, University of California, Riverside, California 92521, United States
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4
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Becher S, Wang H, Leeming MG, Donald WA, Heiles S. Influence of protein ion charge state on 213 nm top-down UVPD. Analyst 2021; 146:3977-3987. [PMID: 34009215 DOI: 10.1039/d1an00571e] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ultraviolet photodissociation (UVPD) is a powerful and rapidly developing method in top-down proteomics. Sequence coverages can exceed those obtained with collision- and electron-induced fragmentation methods. Because of the recent interest in UVPD, factors that influence protein fragmentation and sequence coverage are actively debated in the literature. Here, we performed top-down 213 nm UVPD experiments on a 7 T Fourier-transform ion cyclotron resonance mass spectrometer (FT-ICR MS) for the model proteins ubiquitin, myoglobin and cytochrome c that were electrosprayed from native, denaturing and supercharging solutions in order to investigate the effect of protein charge states on UVPD fragments. By performing UVPD in ultrahigh vacuum, factors associated with collisional cooling and any ion activation during transfer between mass analyzers can be largely eliminated. Sequence coverage increased from <10% for low charge states to >60% for high charge states for all three proteins. This trend is influenced by the overall charge state, i.e., charges per number of amino acid residues, and to a lesser degree by associated structural changes of protein ions of different charge states based on comparisons to published collision-cross section measurements. To rationalize this finding, and correlate sequence ion formation and identity with the number and location of protons, UVPD results were compared to protonation sites predicted based on electrostatic modelling. Assuming confined protonation sites, these results indicate the presence of two general fragmentation types; i.e., charge remote and charge directed. For moderately high protein charge states, fragment ions mostly originate in regions between likely protonation sites (charge remote), whereas sequence ions of highly charge protein ions occur either near backbone amide protonation sites at low-basicity residues (charge directed) or at charge remote sites (i.e., high-basicity residues). Overall, our results suggest that top-down 213 UVPD performance in the zero-pressure limit depends strongly on protein charge states and protonation sites can influence the location of backbone cleavages.
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Affiliation(s)
- Simon Becher
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, 35392 Giessen, Germany.
| | - Huixin Wang
- Mark Wainwright Analytical Centre, University of New South Wales, New South Wales, Australia
| | - Michael G Leeming
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, Australia
| | - William A Donald
- School of Chemistry, University of New South Wales, Sydney, New South Wales, Australia
| | - Sven Heiles
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, 35392 Giessen, Germany.
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5
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Stiving AQ, Harvey SR, Jones BJ, Bellina B, Brown JM, Barran PE, Wysocki VH. Coupling 193 nm Ultraviolet Photodissociation and Ion Mobility for Sequence Characterization of Conformationally-Selected Peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2313-2320. [PMID: 32959654 PMCID: PMC8127984 DOI: 10.1021/jasms.0c00259] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Ultraviolet photodissociation (UVPD) has emerged as a useful technique for characterizing peptide, protein, and protein complex primary and secondary structure. 193 nm UVPD, specifically, enables extensive covalent fragmentation of the peptide backbone without the requirement of a specific side chain chromophore and with no precursor charge state dependence. We have modified a commercial quadrupole-ion mobility-time-of-flight (Q-IM-TOF) mass spectrometer to include 193 nm UVPD following ion mobility. Ion mobility (IM) is a gas-phase separation technique that enables separation of ions by their size, shape, and charge, providing an orthogonal dimension of separation to mass analysis. Following instrument modifications, we characterized the performance of, and information that could be generated from, this new setup using the model peptides substance P, melittin, and insulin chain B. These experiments show extensive fragmentation across the peptide backbone and a variety of ion types as expected from 193 nm UVPD. Additionally, y-2 ions (along with complementary a+2 and b+2 ions) N-terminal to proline were observed. Combining the IM separation and mobility gating capabilities with UVPD, we demonstrate the ability to accomplish both mass- and mobility-selection of bradykinin des-Arg9 and des-Arg1 peptides followed by complete sequence characterization by UVPD. The new capabilities of this modified instrument demonstrate the utility of combining IM with UVPD because isobaric species cannot be independently selected with a traditional quadrupole alone.
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Affiliation(s)
- Alyssa Q Stiving
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sophie R Harvey
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Benjamin J Jones
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Bruno Bellina
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, and Photon Science Institute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | | | - Perdita E Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, and Photon Science Institute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
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6
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Zhou M, Lantz C, Brown KA, Ge Y, Paša-Tolić L, Loo JA, Lermyte F. Higher-order structural characterisation of native proteins and complexes by top-down mass spectrometry. Chem Sci 2020; 11:12918-12936. [PMID: 34094482 PMCID: PMC8163214 DOI: 10.1039/d0sc04392c] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 10/05/2020] [Indexed: 12/11/2022] Open
Abstract
In biology, it can be argued that if the genome contains the script for a cell's life cycle, then the proteome constitutes an ensemble cast of actors that brings these instructions to life. Their interactions with each other, co-factors, ligands, substrates, and so on, are key to understanding nearly any biological process. Mass spectrometry is well established as the method of choice to determine protein primary structure and location of post-translational modifications. In recent years, top-down fragmentation of intact proteins has been increasingly combined with ionisation of noncovalent assemblies under non-denaturing conditions, i.e., native mass spectrometry. Sequence, post-translational modifications, ligand/metal binding, protein folding, and complex stoichiometry can thus all be probed directly. Here, we review recent developments in this new and exciting field of research. While this work is written primarily from a mass spectrometry perspective, it is targeted to all bioanalytical scientists who are interested in applying these methods to their own biochemistry and chemical biology research.
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Affiliation(s)
- Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory Richland WA 99354 USA
| | - Carter Lantz
- Department of Chemistry and Biochemistry, Department of Biological Chemistry, University of California-Los Angeles Los Angeles CA 90095 USA
| | - Kyle A Brown
- Department of Chemistry, University of Wisconsin-Madison Madison WI 53706 USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison Madison WI 53706 USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison Madison WI 53706 USA
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory Richland WA 99354 USA
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, Department of Biological Chemistry, University of California-Los Angeles Los Angeles CA 90095 USA
| | - Frederik Lermyte
- Department of Chemistry, Institute of Chemistry and Biochemistry, Technical University of Darmstadt 64287 Darmstadt Germany
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège 4000 Liège Belgium
- School of Engineering, University of Warwick Coventry CV4 7AL UK
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7
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Kolbowski L, Belsom A, Rappsilber J. Ultraviolet Photodissociation of Tryptic Peptide Backbones at 213 nm. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1282-1290. [PMID: 32352297 PMCID: PMC7273743 DOI: 10.1021/jasms.0c00106] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/30/2020] [Accepted: 04/30/2020] [Indexed: 05/23/2023]
Abstract
We analyzed the backbone fragmentation behavior of tryptic peptides of a four-protein mixture and of E. coli lysate subjected to ultraviolet photodissociation (UVPD) at 213 nm on a commercially available UVPD-equipped tribrid mass spectrometer. We obtained 15 178 unique high-confidence peptide UVPD spectrum matches by recording a reference beam-type collision-induced dissociation (HCD) spectrum of each precursor, ensuring that our investigation includes a broad selection of peptides, including those that fragmented poorly by UVPD. Type a, b, and y ions were most prominent in UVPD spectra, and median sequence coverage ranged from 5.8% (at 5 ms laser excitation time) to 45.0% (at 100 ms). Overall, the sequence fragment intensity remained relatively low (median: 0.4% (5 ms) to 16.8% (100 ms) of total intensity), and the remaining precursor intensity, high. The sequence coverage and sequence fragment intensity ratio correlated with the precursor charge density, suggesting that UVPD at 213 nm may suffer from newly formed fragments sticking together due to noncovalent interactions. The UVPD fragmentation efficiency therefore might benefit from supplemental activation, as was shown for ETD. Aromatic amino acids, most prominently tryptophan, facilitated UVPD. This points to aromatic tags as possible enhancers of UVPD. Data are available via ProteomeXchange with identifier PXD018176 and on spectrumviewer.org/db/UVPD-213nm-trypPep.
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Affiliation(s)
- Lars Kolbowski
- Bioanalytics, Institute of Biotechnology, Technische
Universität Berlin, 13355 Berlin, Germany
- Wellcome Centre for Cell Biology, School of Biological Sciences,
University of Edinburgh, Edinburgh EH9 3BF, United
Kingdom
| | - Adam Belsom
- Bioanalytics, Institute of Biotechnology, Technische
Universität Berlin, 13355 Berlin, Germany
- Wellcome Centre for Cell Biology, School of Biological Sciences,
University of Edinburgh, Edinburgh EH9 3BF, United
Kingdom
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8
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Brodbelt JS, Morrison LJ, Santos I. Ultraviolet Photodissociation Mass Spectrometry for Analysis of Biological Molecules. Chem Rev 2020; 120:3328-3380. [PMID: 31851501 PMCID: PMC7145764 DOI: 10.1021/acs.chemrev.9b00440] [Citation(s) in RCA: 127] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The development of new ion-activation/dissociation methods continues to be one of the most active areas of mass spectrometry owing to the broad applications of tandem mass spectrometry in the identification and structural characterization of molecules. This Review will showcase the impact of ultraviolet photodissociation (UVPD) as a frontier strategy for generating informative fragmentation patterns of ions, especially for biological molecules whose complicated structures, subtle modifications, and large sizes often impede molecular characterization. UVPD energizes ions via absorption of high-energy photons, which allows access to new dissociation pathways relative to more conventional ion-activation methods. Applications of UVPD for the analysis of peptides, proteins, lipids, and other classes of biologically relevant molecules are emphasized in this Review.
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Affiliation(s)
- Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Lindsay J. Morrison
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Inês Santos
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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9
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Fornelli L, Srzentić K, Toby TK, Doubleday PF, Huguet R, Mullen C, Melani RD, Dos Santos Seckler H, DeHart CJ, Weisbrod CR, Durbin KR, Greer JB, Early BP, Fellers RT, Zabrouskov V, Thomas PM, Compton PD, Kelleher NL. Thorough Performance Evaluation of 213 nm Ultraviolet Photodissociation for Top-down Proteomics. Mol Cell Proteomics 2020; 19:405-420. [PMID: 31888965 PMCID: PMC7000117 DOI: 10.1074/mcp.tir119.001638] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 11/29/2019] [Indexed: 11/06/2022] Open
Abstract
Top-down proteomics studies intact proteoform mixtures and offers important advantages over more common bottom-up proteomics technologies, as it avoids the protein inference problem. However, achieving complete molecular characterization of investigated proteoforms using existing technologies remains a fundamental challenge for top-down proteomics. Here, we benchmark the performance of ultraviolet photodissociation (UVPD) using 213 nm photons generated by a solid-state laser applied to the study of intact proteoforms from three organisms. Notably, the described UVPD setup applies multiple laser pulses to induce ion dissociation, and this feature can be used to optimize the fragmentation outcome based on the molecular weight of the analyzed biomolecule. When applied to complex proteoform mixtures in high-throughput top-down proteomics, 213 nm UVPD demonstrated a high degree of complementarity with the most employed fragmentation method in proteomics studies, higher-energy collisional dissociation (HCD). UVPD at 213 nm offered higher average proteoform sequence coverage and degree of proteoform characterization (including localization of post-translational modifications) than HCD. However, previous studies have shown limitations in applying database search strategies developed for HCD fragmentation to UVPD spectra which contains up to nine fragment ion types. We therefore performed an analysis of the different UVPD product ion type frequencies. From these data, we developed an ad hoc fragment matching strategy and determined the influence of each possible ion type on search outcomes. By paring down the number of ion types considered in high-throughput UVPD searches from all types down to the four most abundant, we were ultimately able to achieve deeper proteome characterization with UVPD. Lastly, our detailed product ion analysis also revealed UVPD cleavage propensities and determined the presence of a product ion produced specifically by 213 nm photons. All together, these observations could be used to better elucidate UVPD dissociation mechanisms and improve the utility of the technique for proteomic applications.
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Affiliation(s)
- Luca Fornelli
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | - Kristina Srzentić
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | - Timothy K Toby
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | - Peter F Doubleday
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | - Romain Huguet
- Thermo Fisher Scientific, San Jose, California 95134
| | | | - Rafael D Melani
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | - Henrique Dos Santos Seckler
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | - Caroline J DeHart
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | | | - Kenneth R Durbin
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208; Proteinaceous Inc., Evanston, Illinois 60201
| | - Joseph B Greer
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | - Bryan P Early
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | - Ryan T Fellers
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | | | - Paul M Thomas
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | - Philip D Compton
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208
| | - Neil L Kelleher
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208.
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Zhou M, Liu W, Shaw JB. Charge Movement and Structural Changes in the Gas-Phase Unfolding of Multimeric Protein Complexes Captured by Native Top-Down Mass Spectrometry. Anal Chem 2020; 92:1788-1795. [PMID: 31869201 DOI: 10.1021/acs.analchem.9b03469] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The extent to which noncovalent protein complexes retain native structure in the gas phase is highly dependent on experimental conditions. Energetic collisions with background gas can cause structural changes ranging from unfolding to subunit dissociation. Additionally, recent studies have highlighted the role of charge in such structural changes, but the mechanism is not completely understood. In this study, native top down (native TD) mass spectrometry was used to probe gas-phase structural changes of alcohol dehydrogenase (ADH, 4mer) under varying degrees of in-source activation. Changes in covalent backbone fragments produced by electron capture dissociation (ECD) or 193 nm ultraviolet photodissociation (UVPD) were attributed to structural changes of the ADH 4mer. ECD fragments indicated unfolding started at the N-terminus, and the charge states of UVPD fragments enabled monitoring of charge migration to the unfolded regions. Interestingly, UVPD fragments also indicated that the charge at the "unfolding" N-terminus of ADH decreased at high in-source activation energies after the initial increase. We proposed a possible "refolding-after-unfolding" mechanism, as further supported by monitoring hydrogen elimination from radical a-ions produced by UVPD at the N-terminus of ADH. However, "refolding-after-unfolding" with increasing in-source activation was not observed for charge-reduced ADH, which likely adopted compact structures that are resistant to both charge migration and unfolding. When combined, these results support a charge-directed unfolding mechanism for protein complexes. Overall, an experimental framework was outlined for utilizing native TD to generate structure-informative mass spectral signatures for protein complexes that complement other structure characterization techniques, such as ion mobility and computational modeling.
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Affiliation(s)
- Mowei Zhou
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , 3335 Innovation Boulevard , Richland , Washington 99354 , United States
| | - Weijing Liu
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , 3335 Innovation Boulevard , Richland , Washington 99354 , United States
| | - Jared B Shaw
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , 3335 Innovation Boulevard , Richland , Washington 99354 , United States
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11
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Theisen A, Black R, Corinti D, Brown JM, Bellina B, Barran PE. Initial Protein Unfolding Events in Ubiquitin, Cytochrome c and Myoglobin Are Revealed with the Use of 213 nm UVPD Coupled to IM-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:24-33. [PMID: 29949061 PMCID: PMC6318241 DOI: 10.1007/s13361-018-1992-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/08/2018] [Accepted: 05/09/2018] [Indexed: 05/11/2023]
Abstract
The initial stages of protein unfolding may reflect the stability of the entire fold and can also reveal which parts of a protein can be perturbed, without restructuring the rest. In this work, we couple UVPD with activated ion mobility mass spectrometry to measure how three model proteins start to unfold. Ubiquitin, cytochrome c and myoglobin ions produced via nESI from salty solutions are subjected to UV irradiation pre-mobility separation; experiments are conducted with a range of source conditions which alter the conformation of the precursor ion as shown by the drift time profiles. For all three proteins, the compact structures result in less fragmentation than more extended structures which emerge following progressive in-source activation. Cleavage sites are found to differ between conformational ensembles, for example, for the dominant charge state of cytochrome c [M + 7H]7+, cleavage at Phe10, Thr19 and Val20 was only observed in activating conditions whilst cleavage at Ala43 is dramatically enhanced. Mapping the photo-cleaved fragments onto crystallographic structures provides insight into the local structural changes that occur as protein unfolding progresses, which is coupled to global restructuring observed in the drift time profiles. Graphical Abstract.
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Affiliation(s)
- Alina Theisen
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology and Photon Science Institute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Rachelle Black
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology and Photon Science Institute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", 00185, Rome, Italy
| | - Jeffery M Brown
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow, SK9 4AX, UK
| | - Bruno Bellina
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology and Photon Science Institute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Perdita E Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology and Photon Science Institute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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12
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Bonner J, Talbert LE, Akkawi N, Julian RR. Simplified identification of disulfide, trisulfide, and thioether pairs with 213 nm UVPD. Analyst 2018; 143:5176-5184. [PMID: 30264084 PMCID: PMC6197924 DOI: 10.1039/c8an01582a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Disulfide heterogeneity and other non-native crosslinks introduced during therapeutic antibody production and storage could have considerable negative effects on clinical efficacy, but tracking these modifications remains challenging. Analysis must also be carried out cautiously to avoid introduction of disulfide scrambling or reduction, necessitating the use of low pH digestion with less specific proteases. Herein we demonstrate that 213 nm ultraviolet photodissociation streamlines disulfide elucidation through bond-selective dissociation of sulfur-sulfur and carbon-sulfur bonds in combination with less specific backbone dissociation. Importantly, both types of fragmentation can be initiated in a single MS/MS activation stage. In addition to disulfide mapping, it is also shown that thioethers and trisulfides can be identified by characteristic fragmentation patterns. The photochemistry resulting from 213 nm excitation facilitates a simplified, two-tiered data processing approach that allows observation of all native disulfide bonds, scrambled disulfide bonds, and non-native sulfur-based linkages in a pepsin digest of Rituximab. Native disulfides represented the majority of bonds according to ion count, but the highly solvent-exposed heavy/light interchain disulfides were found to be most prone to modification. Production and storage methods that facilitate non-native links are discussed. Due to the importance of heavy and light chain connectivity for antibody structure and function, this region likely requires particular attention in terms of its influence on maintaining structural fidelity.
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Affiliation(s)
- James Bonner
- Department of Chemistry, University of California, Riverside, California 92521, USA.
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13
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Talbert LE, Julian RR. Directed-Backbone Dissociation Following Bond-Specific Carbon-Sulfur UVPD at 213 nm. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1760-1767. [PMID: 29623659 PMCID: PMC6087500 DOI: 10.1007/s13361-018-1934-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 02/16/2018] [Accepted: 02/23/2018] [Indexed: 05/22/2023]
Abstract
Ultraviolet photodissociation or UVPD is an increasingly popular option for tandem-mass spectrometry experiments. UVPD can be carried out at many wavelengths, and it is important to understand how the results will be impacted by this choice. Here, we explore the utility of 213 nm photons for initiating bond-selective fragmentation. It is found that bonds previously determined to be labile at 266 nm, including carbon-iodine and sulfur-sulfur bonds, can also be cleaved with high selectivity at 213 nm. In addition, many carbon-sulfur bonds that are not subject to direct dissociation at 266 nm can be selectively fragmented at 213 nm. This capability can be used to site-specifically create alaninyl radicals that direct backbone dissociation at the radical site, creating diagnostic d-ions. Furthermore, the additional carbon-sulfur bond fragmentation capability leads to signature triplets for fragmentation of disulfide bonds. Absorption of amide bonds can enhance dissociation of nearby labile carbon-sulfur bonds and can be used for stochastic backbone fragmentation typical of UVPD experiments at shorter wavelengths. Several potential applications of the bond-selective fragmentation chemistry observed at 213 nm are discussed. Graphical Abstract ᅟ.
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Affiliation(s)
- Lance E Talbert
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA
| | - Ryan R Julian
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA.
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14
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Han Y, Anderson K, Hobbie EK, Boudjouk P, Kilin DS. Unraveling Photodimerization of Cyclohexasilane from Molecular Dynamics Studies. J Phys Chem Lett 2018; 9:4349-4354. [PMID: 30004709 DOI: 10.1021/acs.jpclett.8b01691] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Photoinduced reactions of a pair of cyclohexasilane (CHS) monomers are explored by time-dependent excited-state molecular dynamics (TDESMD) calculations. In TDESMD trajectories, one observes vivid reaction events including dimerization and fragmentation. A general reaction pathway is identified as (i) ring-opening formation of a dimer, (ii) rearrangement induced by bond breaking, and (iii) decomposition through the elimination of small fragments. The identified pathway supports the chemistry proposed for the fabrication of silicon-based materials using CHS as a precursor. In addition, we find dimers have smaller HOMO-LUMO gaps and exhibit a red shift and line-width broadening in the computed photoluminescence spectra compared with a pair of CHS monomers.
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Affiliation(s)
- Yulun Han
- Department of Chemistry and Biochemistry , North Dakota State University , Fargo , North Dakota 58102 , United States
| | - Kenneth Anderson
- Department of Chemistry and Biochemistry , North Dakota State University , Fargo , North Dakota 58102 , United States
| | - Erik K Hobbie
- Department of Chemistry and Biochemistry , North Dakota State University , Fargo , North Dakota 58102 , United States
| | - Philip Boudjouk
- Department of Chemistry and Biochemistry , North Dakota State University , Fargo , North Dakota 58102 , United States
| | - Dmitri S Kilin
- Department of Chemistry and Biochemistry , North Dakota State University , Fargo , North Dakota 58102 , United States
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15
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Holden DD, Sanders JD, Weisbrod CR, Mullen C, Schwartz JC, Brodbelt JS. Implementation of Fragment Ion Protection (FIP) during Ultraviolet Photodissociation (UVPD) Mass Spectrometry. Anal Chem 2018; 90:8583-8591. [PMID: 29927232 DOI: 10.1021/acs.analchem.8b01723] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Ultraviolet photodissociation (UVPD) is a nonselective activation method in which both precursor and fragment ions may absorb photons and dissociate. Photoactivation of fragment ions may result in secondary or multiple generations of dissociation, which decreases the signal-to-noise ratio (S/N) of larger fragment ions owing to the prevalent subdivision of the ion current into many smaller, often less informative, fragment ions. Here we report the use of dipolar excitation waveforms to displace fragment ions out of the laser beam path, thus alleviating the extent of secondary dissociation during 193 nm UVPD. This fragment ion protection (FIP) strategy increases S/N of larger fragment ions and improves the sequence coverage obtained for proteins via retaining information deeper into the midsection of protein sequences.
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Affiliation(s)
- Dustin D Holden
- Department of Chemistry , University of Texas at Austin , Austin , Texas 78712 , United States
| | - James D Sanders
- Department of Chemistry , University of Texas at Austin , Austin , Texas 78712 , United States
| | - Chad R Weisbrod
- Thermo Fisher Scientific Inc. , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Christopher Mullen
- Thermo Fisher Scientific Inc. , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Jae C Schwartz
- Thermo Fisher Scientific Inc. , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Jennifer S Brodbelt
- Department of Chemistry , University of Texas at Austin , Austin , Texas 78712 , United States
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16
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Morrison LJ, Chai W, Rosenberg JA, Henkelman G, Brodbelt JS. Characterization of hydrogen bonding motifs in proteins: hydrogen elimination monitoring by ultraviolet photodissociation mass spectrometry. Phys Chem Chem Phys 2018; 19:20057-20074. [PMID: 28722742 DOI: 10.1039/c7cp04073c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Determination of structure and folding of certain classes of proteins remains intractable by conventional structural characterization strategies and has spurred the development of alternative methodologies. Mass spectrometry-based approaches have a unique capacity to differentiate protein heterogeneity due to the ability to discriminate populations, whether minor or major, featuring modifications or complexation with non-covalent ligands on the basis of m/z. Cleavage of the peptide backbone can be further utilized to obtain residue-specific structural information. Here, hydrogen elimination monitoring (HEM) upon ultraviolet photodissociation (UVPD) of proteins transferred to the gas phase via nativespray ionization is introduced as an innovative approach to deduce backbone hydrogen bonding patterns. Using well-characterized peptides and a series of proteins, prediction of the engagement of the amide carbonyl oxygen of the protein backbone in hydrogen bonding using UVPD-HEM is demonstrated to show significant agreement with the hydrogen-bonding motifs derived from molecular dynamics simulations and X-ray crystal structures.
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17
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Halim MA, MacAleese L, Lemoine J, Antoine R, Dugourd P, Girod M. Ultraviolet, Infrared, and High-Low Energy Photodissociation of Post-Translationally Modified Peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:270-283. [PMID: 28980177 DOI: 10.1007/s13361-017-1794-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 08/17/2017] [Accepted: 08/18/2017] [Indexed: 06/07/2023]
Abstract
Mass spectrometry-based methods have made significant progress in characterizing post-translational modifications in peptides and proteins; however, certain aspects regarding fragmentation methods must still be improved. A good technique is expected to provide excellent sequence information, locate PTM sites, and retain the labile PTM groups. To address these issues, we investigate 10.6 μm IRMPD, 213 nm UVPD, and combined UV and IR photodissociation, known as HiLoPD (high-low photodissociation), for phospho-, sulfo-, and glyco-peptide cations. IRMPD shows excellent backbone fragmentation and produces equal numbers of N- and C-terminal ions. The results reveal that 213 nm UVPD and HiLoPD methods can provide diverse backbone fragmentation producing a/x, b/y, and c/z ions with excellent sequence coverage, locate PTM sites, and offer reasonable retention efficiency for phospho- and glyco-peptides. Excellent sequence coverage is achieved for sulfo-peptides and the position of the SO3 group can be pinpointed; however, widespread SO3 losses are detected irrespective of the methods used herein. Based on the overall performance achieved, we believe that 213 nm UVPD and HiLoPD can serve as alternative options to collision activation and electron transfer dissociations for phospho- and glyco-proteomics. Graphical Abstract ᅟ.
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Affiliation(s)
- Mohammad A Halim
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Lyon, France
| | - Luke MacAleese
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Lyon, France
| | - Jérôme Lemoine
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1, ENS Lyon, 69622, Villeurbanne, Cedex, France
| | - Rodolphe Antoine
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Lyon, France
| | - Philippe Dugourd
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Lyon, France.
| | - Marion Girod
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1, ENS Lyon, 69622, Villeurbanne, Cedex, France
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18
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Becher S, Spengler B, Heiles S. Effects of wavelength, fluence, and dose on fragmentation pathways and photoproduct ion yield in 213 nm and 266 nm ultraviolet photodissociation experiments. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2018; 24:54-65. [PMID: 29141443 DOI: 10.1177/1469066717741747] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Ultraviolet photodissociation tandem mass spectrometry is a powerful tool to investigate the structure of biomolecules, due to its ability to generate rich fragmentation patterns or bond selective cleavage, as a function of used laser wavelength, laser fluence, dose (number of accumulated laser pulses), and available chromophores. Herein, we report first results obtained with a newly developed two-wavelength (266 nm and 213 nm) ultraviolet photodissociation setup coupled to a Fourier-transform ion cyclotron resonance mass spectrometer. Photoproduct yields for protonated 3-iodo-l-tyrosine were up to ∼75%. Dose and fluence dependent measurements for protonated 3-iodo-l-tyrosine, doubly charged protonated bradykinin and Fe(II) attached to 1,2-dioleoyl-sn-glycero-3-phosphocholine reveal that the ultraviolet photodissociation mechanism for photoproduct formation qualitatively differs between these model systems. Three derived photodissociation models were used to interpret the experimental results and show that while protonated 3-iodo-l-tyrosine and Fe(II) attached to 1,2-dioleoyl-sn-glycero-3-phosphocholine most likely dissociates via a single-photon process, fragmentation of doubly charged bradykinin ions was found to be most consistent with sequential two-photon dissociation (213 nm). The introduced dissociation models present an easy means to study the mechanism of ultraviolet photodissociation processes for a variety of analytes without prior knowledge of their photochemistry or to optimize experimental conditions by adjusting laser fluence or number of laser pulses.
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Affiliation(s)
- Simon Becher
- 426460 Institute of Inorganic and Analytical Chemistry, Justus Liebig University , Giessen, Germany
| | - Bernhard Spengler
- 426460 Institute of Inorganic and Analytical Chemistry, Justus Liebig University , Giessen, Germany
| | - Sven Heiles
- 426460 Institute of Inorganic and Analytical Chemistry, Justus Liebig University , Giessen, Germany
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19
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Mistarz UH, Bellina B, Jensen PF, Brown JM, Barran PE, Rand KD. UV Photodissociation Mass Spectrometry Accurately Localize Sites of Backbone Deuteration in Peptides. Anal Chem 2017; 90:1077-1080. [DOI: 10.1021/acs.analchem.7b04683] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Ulrik H. Mistarz
- Department
of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Bruno Bellina
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
of Biotechnology, and Photon Science Institute, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Pernille F. Jensen
- Department
of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Jeffery M. Brown
- Waters Corporation, Stamford
Avenue, Altrincham Road, Wilmslow, SK9 4AX, United Kingdom
| | - Perdita E. Barran
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
of Biotechnology, and Photon Science Institute, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Kasper D. Rand
- Department
of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
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20
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R Julian R. The Mechanism Behind Top-Down UVPD Experiments: Making Sense of Apparent Contradictions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1823-1826. [PMID: 28702929 PMCID: PMC5711567 DOI: 10.1007/s13361-017-1721-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/15/2017] [Accepted: 05/22/2017] [Indexed: 05/21/2023]
Abstract
Top-down ultraviolet photodissociation (UVPD) allows greater sequence coverage than any other currently available method, often fracturing the vast majority of peptide bonds in whole proteins. At the same time, UVPD can be used to dissociate noncovalent complexes assembled from multiple proteins without breaking any covalent bonds. Although the utility of these experiments is unquestioned, the mechanism underlying these seemingly contradictory results has been the subject of many discussions. Herein, some fundamental considerations of photochemistry are briefly summarized within the context of a proposed mechanism that rationalizes the experimental results obtained by UVPD. Considerations for future instrument design, in terms of wavelength choice and power, are briefly discussed. Graphical Abstract ᅟ.
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Affiliation(s)
- Ryan R Julian
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA.
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21
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Cotham VC, Horton AP, Lee J, Georgiou G, Brodbelt JS. Middle-Down 193-nm Ultraviolet Photodissociation for Unambiguous Antibody Identification and its Implications for Immunoproteomic Analysis. Anal Chem 2017; 89:6498-6504. [PMID: 28517930 DOI: 10.1021/acs.analchem.7b00564] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Mass spectrometry (MS) has emerged as a powerful tool within the growing field of immunoproteomics, which aims to understand antibody-mediated immunity at the molecular-level based on the direct determination of serological antibody repertoire. To date, these methods have relied on the use of high-resolution bottom-up proteomic strategies that require effective sampling and characterization of low abundance peptides derived from the antigen-binding domains of polyclonal antibody mixtures. Herein, we describe a method that uses restricted Lys-C enzymatic digestion to increase the average mass of proteolytic IgG peptides (≥4.5 kDa) and produce peptides which uniquely derive from single antibody species. This enhances the capacity to discriminate between very similar antibodies present within polyclonal mixtures. Furthermore, our use of 193-nm ultraviolet photodissociation (UVPD) improves spectral coverage of the antibody sequence relative to conventional collision- and electron-based fragmentation methods. We apply these methods to both a monoclonal and an antibody mixture. By identifying from a database search of approximately 15 000 antibody sequences those which compose the mixture, we demonstrate the analytical potential of middle-down UVPD for MS-based serological repertoire analysis.
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Affiliation(s)
- Victoria C Cotham
- Department of Chemistry, ‡Center for Systems and Synthetic Biology, §Department of Biomedical Engineering, ∥Department of Chemical Engineering, ⊥Institute for Cellular and Molecular Biology, #Department of Molecular Biosciences, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Andrew P Horton
- Department of Chemistry, ‡Center for Systems and Synthetic Biology, §Department of Biomedical Engineering, ∥Department of Chemical Engineering, ⊥Institute for Cellular and Molecular Biology, #Department of Molecular Biosciences, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Jiwon Lee
- Department of Chemistry, ‡Center for Systems and Synthetic Biology, §Department of Biomedical Engineering, ∥Department of Chemical Engineering, ⊥Institute for Cellular and Molecular Biology, #Department of Molecular Biosciences, The University of Texas at Austin , Austin, Texas 78712, United States
| | - George Georgiou
- Department of Chemistry, ‡Center for Systems and Synthetic Biology, §Department of Biomedical Engineering, ∥Department of Chemical Engineering, ⊥Institute for Cellular and Molecular Biology, #Department of Molecular Biosciences, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, ‡Center for Systems and Synthetic Biology, §Department of Biomedical Engineering, ∥Department of Chemical Engineering, ⊥Institute for Cellular and Molecular Biology, #Department of Molecular Biosciences, The University of Texas at Austin , Austin, Texas 78712, United States
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22
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Schwob L, Lalande M, Rangama J, Egorov D, Hoekstra R, Pandey R, Eden S, Schlathölter T, Vizcaino V, Poully JC. Single-photon absorption of isolated collagen mimetic peptides and triple-helix models in the VUV-X energy range. Phys Chem Chem Phys 2017; 19:18321-18329. [DOI: 10.1039/c7cp02527k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
By monitoring ionization and fragmentation after single-photon absorption, we show that an isolated collagen triple helix model is stabilized by proline hydroxylation.
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Affiliation(s)
- Lucas Schwob
- CIMAP
- UMR 6252 (CEA/CNRS/ENSICAEN/Université de Caen Normandie)
- Caen
- France
| | - Mathieu Lalande
- CIMAP
- UMR 6252 (CEA/CNRS/ENSICAEN/Université de Caen Normandie)
- Caen
- France
| | - Jimmy Rangama
- CIMAP
- UMR 6252 (CEA/CNRS/ENSICAEN/Université de Caen Normandie)
- Caen
- France
| | - Dmitrii Egorov
- Zernike Institute for Advanced Materials
- University of Groningen
- Nijenborgh 4
- 9747AG Groningen
- The Netherlands
| | - Ronnie Hoekstra
- Zernike Institute for Advanced Materials
- University of Groningen
- Nijenborgh 4
- 9747AG Groningen
- The Netherlands
| | - Rahul Pandey
- Dept. of Physical Sciences
- The Open University
- Walton Hall
- Milton Keynes
- UK
| | - Samuel Eden
- Dept. of Physical Sciences
- The Open University
- Walton Hall
- Milton Keynes
- UK
| | - Thomas Schlathölter
- Zernike Institute for Advanced Materials
- University of Groningen
- Nijenborgh 4
- 9747AG Groningen
- The Netherlands
| | - Violaine Vizcaino
- CIMAP
- UMR 6252 (CEA/CNRS/ENSICAEN/Université de Caen Normandie)
- Caen
- France
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23
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Holden DD, Brodbelt JS. Improving Performance Metrics of Ultraviolet Photodissociation Mass Spectrometry by Selective Precursor Ejection. Anal Chem 2016; 89:837-846. [PMID: 28105830 DOI: 10.1021/acs.analchem.6b03777] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Confident protein identifications derived from high-throughput bottom-up and top-down proteomics workflows depend on acquisition of thousands of tandem mass spectrometry (MS/MS) spectra with adequate signal-to-noise and accurate mass assignments of the fragment ions. Ultraviolet photodissociation (UVPD) using 193 nm photons has proven to be well-suited for activation and fragmentation of peptides and proteins in ion trap mass spectrometers, but the spectral signal-to-noise ratio (S/N) is typically lower than that obtained from collisional activation methods. The lower S/N is attributed to the dispersion of ion current among numerous fragment ion channels (a,b,c,x,y,z ions). In addition, frequently UVPD is performed such that a relatively large population of precursor ions remains undissociated after the UV photoactivation period in order to prevent overdissociation into small uninformative or internal fragment ions. Here we report a method to improve spectral S/N and increase the accuracy of mass assignments of UVPD mass spectra via resonance ejection of undissociated precursor ions after photoactivation. This strategy, termed precursor ejection UVPD or PE-UVPD, allows the ion trap to be filled with more ions prior to UVPD while at the same time alleviating the space charge problems that would otherwise contribute to the skewing of mass assignments and reduction of S/N. Here we report the performance gains by implementation of PE-UVPD for peptide analysis in an ion trap mass spectrometer.
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Affiliation(s)
- Dustin D Holden
- Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
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24
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Holden DD, Makarov A, Schwartz JC, Sanders JD, Zhuk E, Brodbelt JS. Ultraviolet Photodissociation Induced by Light‐Emitting Diodes in a Planar Ion Trap. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605850] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Dustin D. Holden
- Department of Chemistry The University of Texas at Austin 105 E. 24th St Austin TX 78712 USA
| | - Alexander Makarov
- Thermo Fisher Scientific (Bremen) GmbH Hanna-Kunath-Strasse 11 28199 Bremen Germany
| | - Jae C. Schwartz
- Thermo Fisher Scientific Inc. 355 River Oaks Pkwy San Jose CA 95134 USA
| | - James D. Sanders
- Department of Chemistry The University of Texas at Austin 105 E. 24th St Austin TX 78712 USA
| | - Eugene Zhuk
- Thermo Fisher Scientific Inc. 355 River Oaks Pkwy San Jose CA 95134 USA
| | - Jennifer S. Brodbelt
- Department of Chemistry The University of Texas at Austin 105 E. 24th St Austin TX 78712 USA
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25
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Holden DD, Makarov A, Schwartz JC, Sanders JD, Zhuk E, Brodbelt JS. Ultraviolet Photodissociation Induced by Light-Emitting Diodes in a Planar Ion Trap. Angew Chem Int Ed Engl 2016; 55:12417-21. [PMID: 27605434 DOI: 10.1002/anie.201605850] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 08/02/2016] [Indexed: 11/09/2022]
Abstract
The first application of light-emitting diodes (LEDs) for ultraviolet photodissociation (UVPD) mass spectrometry is reported. LEDs provide a compact, low cost light source and have been incorporated directly into the trapping cell of an Orbitrap mass spectrometer. MS/MS efficiencies of over 50 % were obtained using an extended irradiation period, and UVPD was optimized by modulating the ion trapping parameters to maximize the overlap between the ion cloud and the irradiation volume.
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Affiliation(s)
- Dustin D Holden
- Department of Chemistry, The University of Texas at Austin, 105 E. 24th St, Austin, TX, 78712, USA
| | - Alexander Makarov
- Thermo Fisher Scientific (Bremen) GmbH, Hanna-Kunath-Strasse 11, 28199, Bremen, Germany
| | - Jae C Schwartz
- Thermo Fisher Scientific Inc., 355 River Oaks Pkwy, San Jose, CA, 95134, USA
| | - James D Sanders
- Department of Chemistry, The University of Texas at Austin, 105 E. 24th St, Austin, TX, 78712, USA
| | - Eugene Zhuk
- Thermo Fisher Scientific Inc., 355 River Oaks Pkwy, San Jose, CA, 95134, USA
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, 105 E. 24th St, Austin, TX, 78712, USA.
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26
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Halim MA, Girod M, MacAleese L, Lemoine J, Antoine R, Dugourd P. Combined Infrared Multiphoton Dissociation with Ultraviolet Photodissociation for Ubiquitin Characterization. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1435-42. [PMID: 27287047 PMCID: PMC5031736 DOI: 10.1007/s13361-016-1419-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 05/10/2016] [Accepted: 05/11/2016] [Indexed: 05/10/2023]
Abstract
Herein we report the successful implementation of the consecutive and simultaneous photodissociation with high (213 nm) and low (10.6 μm) energy photons (HiLoPD, high-low photodissociation) on ubiquitin in a quadrupole-Orbitrap mass spectrometer. Absorption of high-energy UV photon is dispersed over the whole protein and stimulates extensive C-Cα backbone fragmentation, whereas low-energy IR photon gradually increases the internal energy and thus preferentially dissociates the most labile amide (C-N) bonds. We noticed that simultaneous irradiation of UV and IR lasers on intact ubiquitin in a single MS/MS experiment provides a rich and well-balanced fragmentation array of a/x, b/y, and z ions. Moreover, secondary fragmentation from a/x and z ions leads to the formation of satellite side-chain ions (d, v, and w) and can help to distinguish isomeric residues in a protein. Implementation of high-low photodissociation in a high-resolution mass spectrometer may offer considerable benefits to promote a comprehensive portrait of protein characterization. Graphical Abstract ᅟ.
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Affiliation(s)
- Mohammad A Halim
- Institut Lumière Matière, Université Lyon 1 - CNRS, Université de Lyon, 69622, Villeurbanne, France
| | - Marion Girod
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1, ENS Lyon, 69100, Villeurbanne, France
| | - Luke MacAleese
- Institut Lumière Matière, Université Lyon 1 - CNRS, Université de Lyon, 69622, Villeurbanne, France
| | - Jérôme Lemoine
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1, ENS Lyon, 69100, Villeurbanne, France
| | - Rodolphe Antoine
- Institut Lumière Matière, Université Lyon 1 - CNRS, Université de Lyon, 69622, Villeurbanne, France
| | - Philippe Dugourd
- Institut Lumière Matière, Université Lyon 1 - CNRS, Université de Lyon, 69622, Villeurbanne, France.
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27
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Morrison LJ, Brodbelt JS. 193 nm Ultraviolet Photodissociation Mass Spectrometry of Tetrameric Protein Complexes Provides Insight into Quaternary and Secondary Protein Topology. J Am Chem Soc 2016; 138:10849-59. [PMID: 27480400 DOI: 10.1021/jacs.6b03905] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein-protein interfaces and architecture are critical to the function of multiprotein complexes. Mass spectrometry-based techniques have emerged as powerful strategies for characterization of protein complexes, particularly for heterogeneous mixtures of structures. In the present study, activation and dissociation of three tetrameric protein complexes (streptavidin, transthyretin, and hemoglobin) in the gas phase was undertaken by 193 nm ultraviolet photodissociation (UVPD) for the characterization of higher order structure. High pulse energy UVPD resulted in the production of dimers and low charged monomers exhibiting symmetrical charge partitioning among the subunits (the so-called symmetrical dissociation pathways), consistent with the subunit organization of the complexes. In addition, UVPD promoted backbone cleavages of the monomeric subunits, the abundances of which corresponded to the more flexible loop regions of the proteins.
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Affiliation(s)
- Lindsay J Morrison
- 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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Tuna D, Lu Y, Koslowski A, Thiel W. Semiempirical Quantum-Chemical Orthogonalization-Corrected Methods: Benchmarks of Electronically Excited States. J Chem Theory Comput 2016; 12:4400-22. [DOI: 10.1021/acs.jctc.6b00403] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Deniz Tuna
- Max-Planck-Institut für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany
| | - You Lu
- Max-Planck-Institut für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany
| | - Axel Koslowski
- Max-Planck-Institut für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany
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Halim MA, Girod M, MacAleese L, Lemoine J, Antoine R, Dugourd P. 213 nm Ultraviolet Photodissociation on Peptide Anions: Radical-Directed Fragmentation Patterns. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:474-86. [PMID: 26545767 DOI: 10.1007/s13361-015-1297-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 10/13/2015] [Accepted: 10/16/2015] [Indexed: 05/25/2023]
Abstract
Characterization of acidic peptides and proteins is greatly hindered due to lack of suitable analytical techniques. Here we present the implementation of 213 nm ultraviolet photodissociation (UVPD) in high-resolution quadrupole-Orbitrap mass spectrometer in negative polarity for peptide anions. Radical-driven backbone fragmentation provides 22 distinctive fragment ion types, achieving the complete sequence coverage for all reported peptides. Hydrogen-deficient radical anion not only promotes the cleavage of Cα-C bond but also stimulates the breaking of N-Cα and C-N bonds. Radical-directed loss of small molecules and specific side chain of amino acids are detected in these experiments. Radical containing side chain of amino acids (Tyr, Ser, Thr, and Asp) may possibly support the N-Cα backbone fragmentation. Proline comprising peptides exhibit the unusual fragment ions similar to reported earlier. Interestingly, basic amino acids such as Arg and Lys also stimulated the formation of abundant b and y ions of the related peptide anions. Loss of hydrogen atom from the charge-reduced radical anion and fragment ions are rationalized by time-dependent density functional theory (TDDFT) calculation, locating the potential energy surface (PES) of ππ* and repulsive πσ* excited states of a model amide system.
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Affiliation(s)
- Mohammad A Halim
- Institut Lumière Matière, Université Lyon 1 - CNRS, Université de Lyon, 69622, Villeurbanne Cedex, France
| | - Marion Girod
- Institut des Sciences Analytiques, Université Lyon 1 - CNRS, Université de Lyon, 69622, Villeurbanne Cedex, France
| | - Luke MacAleese
- Institut Lumière Matière, Université Lyon 1 - CNRS, Université de Lyon, 69622, Villeurbanne Cedex, France
| | - Jérôme Lemoine
- Institut des Sciences Analytiques, Université Lyon 1 - CNRS, Université de Lyon, 69622, Villeurbanne Cedex, France
| | - Rodolphe Antoine
- Institut Lumière Matière, Université Lyon 1 - CNRS, Université de Lyon, 69622, Villeurbanne Cedex, France
| | - Philippe Dugourd
- Institut Lumière Matière, Université Lyon 1 - CNRS, Université de Lyon, 69622, Villeurbanne Cedex, France.
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Greer SM, Parker WR, Brodbelt JS. Impact of Protease on Ultraviolet Photodissociation Mass Spectrometry for Bottom-up Proteomics. J Proteome Res 2015; 14:2626-32. [DOI: 10.1021/acs.jproteome.5b00165] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sylvester M. Greer
- Department of Chemistry, University of Texas at Austin, 105
East 24th Street, Austin, Texas 78712, United States
| | - W. Ryan Parker
- Department of Chemistry, University of Texas at Austin, 105
East 24th Street, Austin, Texas 78712, United States
| | - Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, 105
East 24th Street, Austin, Texas 78712, United States
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