151
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Brodie NI, Huguet R, Zhang T, Viner R, Zabrouskov V, Pan J, Petrotchenko EV, Borchers CH. Top-Down Hydrogen-Deuterium Exchange Analysis of Protein Structures Using Ultraviolet Photodissociation. Anal Chem 2018; 90:3079-3082. [PMID: 29336549 DOI: 10.1021/acs.analchem.7b03655] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Top-down hydrogen-deuterium exchange (HDX) analysis using electron capture or transfer dissociation Fourier transform mass spectrometry (FTMS) is a powerful method for the analysis of secondary structure of proteins in solution. The resolution of the method is a function of the degree of fragmentation of backbone bonds in the proteins. While fragmentation is usually extensive near the N- and C-termini, electron capture (ECD) or electron transfer dissociation (ETD) fragmentation methods sometimes lack good coverage of certain regions of the protein, most often in the middle of the sequence. Ultraviolet photodissociation (UVPD) is a recently developed fast-fragmentation technique, which provides extensive backbone fragmentation that can be complementary in sequence coverage to the aforementioned electron-based fragmentation techniques. Here, we explore the application of electrospray ionization (ESI)-UVPD FTMS on an Orbitrap Fusion Lumos Tribrid mass spectrometer to top-down HDX analysis of proteins. We have incorporated UVPD-specific fragment-ion types and fragment-ion mixtures into our isotopic envelope fitting software (HDX Match) for the top-down HDX analysis. We have shown that UVPD data is complementary to ETD, thus improving the overall resolution when used as a combined approach.
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Affiliation(s)
- Nicholas I Brodie
- University of Victoria -Genome British Columbia Proteomics Centre , No. 3101-4464 Markham Street, Vancouver Island Technology Park , Victoria , British Columbia V8Z 7X8 , Canada
| | - Romain Huguet
- Thermo Fisher Scientific , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Terry Zhang
- Thermo Fisher Scientific , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Rosa Viner
- Thermo Fisher Scientific , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Vlad Zabrouskov
- Thermo Fisher Scientific , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Jingxi Pan
- University of Victoria -Genome British Columbia Proteomics Centre , No. 3101-4464 Markham Street, Vancouver Island Technology Park , Victoria , British Columbia V8Z 7X8 , Canada
| | - Evgeniy V Petrotchenko
- University of Victoria -Genome British Columbia Proteomics Centre , No. 3101-4464 Markham Street, Vancouver Island Technology Park , Victoria , British Columbia V8Z 7X8 , Canada
| | - Christoph H Borchers
- University of Victoria -Genome British Columbia Proteomics Centre , No. 3101-4464 Markham Street, Vancouver Island Technology Park , Victoria , British Columbia V8Z 7X8 , Canada.,Department of Biochemistry and Microbiology , University of Victoria , Petch Building, Room 270d, 3800 Finnerty Road , Victoria , British Columbia V8P 5C2 , Canada.,Gerald Bronfman Department of Oncology, Jewish General Hospital , McGill University , 3755 Côte Ste-Catherine Road , Montreal , Quebec H3T 1E2 , Canada.,Proteomics Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital , McGill University , 3755 Côte Ste-Catherine Road , Montreal , Quebec H3T 1E2 , Canada
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152
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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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153
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Greer SM, Brodbelt JS. Top-Down Characterization of Heavily Modified Histones Using 193 nm Ultraviolet Photodissociation Mass Spectrometry. J Proteome Res 2018; 17:1138-1145. [DOI: 10.1021/acs.jproteome.7b00801] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Sylvester M. Greer
- 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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154
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Wang H, Zhong J, Xiao K, Tian Z. Enrichment of intact phosphoproteins using immobilized titanium(IV) affinity chromatography microspheres. SEPARATION SCIENCE PLUS 2018. [DOI: 10.1002/sscp.201700008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hao Wang
- School of Chemical Science & Engineering and Shanghai Key Laboratory of Chemical Assessment and Sustainability; Tongji University; China
| | - Jinqiang Zhong
- School of Chemical Science & Engineering and Shanghai Key Laboratory of Chemical Assessment and Sustainability; Tongji University; China
| | - Kaijie Xiao
- School of Chemical Science & Engineering and Shanghai Key Laboratory of Chemical Assessment and Sustainability; Tongji University; China
| | - Zhixin Tian
- School of Chemical Science & Engineering and Shanghai Key Laboratory of Chemical Assessment and Sustainability; Tongji University; China
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155
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Mehaffey MR, Cammarata MB, Brodbelt JS. Tracking the Catalytic Cycle of Adenylate Kinase by Ultraviolet Photodissociation Mass Spectrometry. Anal Chem 2018; 90:839-846. [PMID: 29188992 PMCID: PMC5750083 DOI: 10.1021/acs.analchem.7b03591] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The complex interplay of dynamic protein plasticity and specific side-chain interactions with substrate molecules that allows enzymes to catalyze reactions has yet to be fully unraveled. Top-down ultraviolet photodissociation (UVPD) mass spectrometry is used to track snapshots of conformational fluctuations in the phosphotransferase adenylate kinase (AK) throughout its active reaction cycle by characterization of complexes containing AK and each of four different adenosine phosphate ligands. Variations in efficiencies of UVPD backbone cleavages were consistently observed for three α-helices and the adenosine binding regions for AK complexes representing different steps of the catalytic cycle, implying that these stretches of the protein sample various structural microstates as the enzyme undergoes global open-to-closed transitions. Focusing on the conformational impact of recruiting or releasing the Mg2+ cofactor highlights two loop regions for which fragmentation increases upon UVPD, signaling an increase in loop flexibility as the metal cation disrupts the loop interactions with the substrate ligands. Additionally, the observation of holo ions and variations in UVPD backbone cleavage efficiency at R138 implicate this conserved active site residue in stabilizing the donor phosphoryl group during catalysis. This study showcases the utility of UVPD-MS to provide insight into conformational fluctuations of single residues for active enzymes.
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Affiliation(s)
- M. Rachel Mehaffey
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712
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156
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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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157
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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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158
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Lyon YA, Riggs D, Fornelli L, Compton PD, Julian RR. The Ups and Downs of Repeated Cleavage and Internal Fragment Production in Top-Down Proteomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:150-157. [PMID: 29038993 PMCID: PMC5786485 DOI: 10.1007/s13361-017-1823-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 09/08/2017] [Accepted: 09/23/2017] [Indexed: 05/10/2023]
Abstract
Analysis of whole proteins by mass spectrometry, or top-down proteomics, has several advantages over methods relying on proteolysis. For example, proteoforms can be unambiguously identified and examined. However, from a gas-phase ion-chemistry perspective, proteins are enormous molecules that present novel challenges relative to peptide analysis. Herein, the statistics of cleaving the peptide backbone multiple times are examined to evaluate the inherent propensity for generating internal versus terminal ions. The raw statistics reveal an inherent bias favoring production of terminal ions, which holds true regardless of protein size. Importantly, even if the full suite of internal ions is generated by statistical dissociation, terminal ions are predicted to account for at least 50% of the total ion current, regardless of protein size, if there are three backbone dissociations or fewer. Top-down analysis should therefore be a viable approach for examining proteins of significant size. Comparison of the purely statistical analysis with actual top-down data derived from ultraviolet photodissociation (UVPD) and higher-energy collisional dissociation (HCD) reveals that terminal ions account for much of the total ion current in both experiments. Terminal ion production is more favored in UVPD relative to HCD, which is likely due to differences in the mechanisms controlling fragmentation. Importantly, internal ions are not found to dominate from either the theoretical or experimental point of view. Graphical abstract ᅟ.
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Affiliation(s)
- Yana A Lyon
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA
| | - Dylan Riggs
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA
| | - Luca Fornelli
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, 2145 N. Sheridan Road, Evanston, IL, 60208, USA
| | - Philip D Compton
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, 2145 N. Sheridan Road, Evanston, IL, 60208, USA
| | - Ryan R Julian
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA.
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159
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Riley NM, Westphall MS, Coon JJ. Sequencing Larger Intact Proteins (30-70 kDa) with Activated Ion Electron Transfer Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:140-149. [PMID: 29027149 PMCID: PMC5786479 DOI: 10.1007/s13361-017-1808-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 08/31/2017] [Accepted: 09/02/2017] [Indexed: 05/12/2023]
Abstract
The analysis of intact proteins via mass spectrometry can offer several benefits to proteome characterization, although the majority of top-down experiments focus on proteoforms in a relatively low mass range (<30 kDa). Recent studies have focused on improving the analysis of larger intact proteins (up to ~75 kDa), but they have also highlighted several challenges to be addressed. One major hurdle is the efficient dissociation of larger protein ions, which often to do not yield extensive fragmentation via conventional tandem MS methods. Here we describe the first application of activated ion electron transfer dissociation (AI-ETD) to proteins in the 30-70 kDa range. AI-ETD leverages infrared photo-activation concurrent to ETD reactions to improve sequence-informative product ion generation. This method generates more product ions and greater sequence coverage than conventional ETD, higher-energy collisional dissociation (HCD), and ETD combined with supplemental HCD activation (EThcD). Importantly, AI-ETD provides the most thorough protein characterization for every precursor ion charge state investigated in this study, making it suitable as a universal fragmentation method in top-down experiments. Additionally, we highlight several acquisition strategies that can benefit characterization of larger proteins with AI-ETD, including combination of spectra from multiple ETD reaction times for a given precursor ion, multiple spectral acquisitions of the same precursor ion, and combination of spectra from two different dissociation methods (e.g., AI-ETD and HCD). In all, AI-ETD shows great promise as a method for dissociating larger intact protein ions as top-down proteomics continues to advance into larger mass ranges. Graphical Abstract ᅟ.
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Affiliation(s)
- Nicholas M Riley
- Genome Center of Wisconsin, Madison, WI, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | | | - Joshua J Coon
- Genome Center of Wisconsin, Madison, WI, USA.
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Morgridge Institute for Research, Madison, WI, USA.
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160
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Fort KL, Cramer CN, Voinov VG, Vasil'ev YV, Lopez NI, Beckman JS, Heck AJR. Exploring ECD on a Benchtop Q Exactive Orbitrap Mass Spectrometer. J Proteome Res 2017; 17:926-933. [PMID: 29249155 PMCID: PMC5799867 DOI: 10.1021/acs.jproteome.7b00622] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
As the application of mass spectrometry intensifies in scope and diversity, the need for advanced instrumentation addressing a wide variety of analytical needs also increases. To this end, many modern, top-end mass spectrometers are designed or modified to include a wider range of fragmentation technologies, for example, ECD, ETD, EThcD, and UVPD. Still, the majority of instrument platforms are limited to more conventional methods, such as CID and HCD. While these latter methods have performed well, the less conventional fragmentation methods have been shown to lead to increased information in many applications including middle-down proteomics, top-down proteomics, glycoproteomics, and disulfide bond mapping. We describe the modification of the popular Q Exactive Orbitrap mass spectrometer to extend its fragmentation capabilities to include ECD. We show that this modification allows ≥85% matched ion intensity to originate from ECD fragment ion types as well as provides high sequence coverage (≥60%) of intact proteins and high fragment identification rates with ∼70% of ion signals matched. Finally, the ECD implementation promotes selective disulfide bond dissociation, facilitating the identification of disulfide-linked peptide conjugates. Collectively, this modification extends the capabilities of the Q Exactive Orbitrap mass spectrometer to a range of new applications.
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Affiliation(s)
- Kyle L Fort
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University , Utrecht 3584 CH, The Netherlands.,Netherlands Proteomics Center , Utrecht 3584 CH, The Netherlands
| | - Christian N Cramer
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University , Utrecht 3584 CH, The Netherlands.,Protein Engineering, Global Research Novo Nordisk A/S , Novo Nordisk Park, 2760 Måløv, Denmark.,Proteomics Program, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen , 2200 Copenhagen, Denmark
| | - Valery G Voinov
- e-MSion, Inc. , 2121 NE Jack London Drive, Corvallis, Oregon 97330, United States.,Linus Pauling Institute, Department of Biochemistry and Biophysics, Oregon State University , Corvallis, Oregon 97331, United States
| | - Yury V Vasil'ev
- e-MSion, Inc. , 2121 NE Jack London Drive, Corvallis, Oregon 97330, United States.,Linus Pauling Institute, 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
| | - Joseph S Beckman
- e-MSion, Inc. , 2121 NE Jack London Drive, Corvallis, Oregon 97330, United States.,Linus Pauling Institute, Department of Biochemistry and Biophysics, Oregon State University , Corvallis, Oregon 97331, United States
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University , Utrecht 3584 CH, The Netherlands.,Netherlands Proteomics Center , Utrecht 3584 CH, The Netherlands
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161
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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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162
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Garcia L, Lemoine J, Dugourd P, Girod M. Fragmentation patterns of chromophore-tagged peptides in visible laser induced dissociation. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:1985-1992. [PMID: 28884878 DOI: 10.1002/rcm.7984] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 08/21/2017] [Accepted: 09/02/2017] [Indexed: 06/07/2023]
Abstract
RATIONALE Tandem mass spectrometry (MS/MS) is the pivotal tool for protein structural characterization and quantification. Identification relies on the fragmentation step of tryptic peptides in bottom-up strategy. Specificity of fragmentation can be obtained using laser-induced dissociation (LID) in the visible range, after tagging of the targeted peptides with an adequate chromophore. Backbone fragmentation is required to obtain specific fragments and confident identification. We present herein a study of fragmentation patterns of chromophore-tagged peptides in LID, showing the potential of LID methodology to provide the maximum number of fragments for further identification and quantification. METHODS A total of 401 cysteine-containing tryptic peptides originating from the human proteome were derivatizated on the thiol group of cysteine with a Dabcyl maleimide chromophore, which has a high photo-absorption cross section at 473 nm. The derivatized peptides were then analyzed by LID at 473 nm on a Q Exactive instrument. RESULTS LID spectra present a characteristic fragment at m/z 252.112 for all precursors. This product ion arises from the internal dissociation of the Dabcyl chromophore. Several peptide-backbone fragment ions are also detected. Results show the quasi absence of fragmentation at the cysteine site. This indicates that part of the energy must be redistributed across the entire system despite excitation initially localized at the chromophore. Indeed, the fragmentation mainly occurs at 3 to 5 amino acids from the derivatized cysteine residue. CONCLUSIONS LID of derivatized cysteine-containing peptides displays the initial fragmentation of the chromophore. As energy is redistributed all along the peptide sequence, fragmentation of the peptide backbone is also observed. Thus, LID of chromophore-tagged peptides produces adequate fragment ions, allowing both good sequence coverage for a greater confidence of identification, and a large choice of transitions for specific quantification.
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Affiliation(s)
- Lény Garcia
- Univ de Lyon, CNRS, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100, Villeurbanne, France
| | - Jérôme Lemoine
- Univ de Lyon, CNRS, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100, Villeurbanne, France
| | - Philippe Dugourd
- Univ de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, VILLEURBANNE, France
| | - Marion Girod
- Univ de Lyon, CNRS, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100, Villeurbanne, France
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163
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Sanders JD, Greer SM, Brodbelt JS. Integrating Carbamylation and Ultraviolet Photodissociation Mass Spectrometry for Middle-Down Proteomics. Anal Chem 2017; 89:11772-11778. [DOI: 10.1021/acs.analchem.7b03396] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- James D. Sanders
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Sylvester M. Greer
- 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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164
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Anderson LC, Håkansson M, Walse B, Nilsson CL. Intact Protein Analysis at 21 Tesla and X-Ray Crystallography Define Structural Differences in Single Amino Acid Variants of Human Mitochondrial Branched-Chain Amino Acid Aminotransferase 2 (BCAT2). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1796-1804. [PMID: 28681360 PMCID: PMC5556139 DOI: 10.1007/s13361-017-1705-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 04/21/2017] [Accepted: 04/29/2017] [Indexed: 05/16/2023]
Abstract
Structural technologies are an essential component in the design of precision therapeutics. Precision medicine entails the development of therapeutics directed toward a designated target protein, with the goal to deliver the right drug to the right patient at the right time. In the field of oncology, protein structural variants are often associated with oncogenic potential. In a previous proteogenomic screen of patient-derived glioblastoma (GBM) tumor materials, we identified a sequence variant of human mitochondrial branched-chain amino acid aminotransferase 2 as a putative factor of resistance of GBM to standard-of-care-treatments. The enzyme generates glutamate, which is neurotoxic. To elucidate structural coordinates that may confer altered substrate binding or activity of the variant BCAT2 T186R, a ~45 kDa protein, we applied combined ETD and CID top-down mass spectrometry in a LC-FT-ICR MS at 21 T, and X-Ray crystallography in the study of both the variant and non-variant intact proteins. The combined ETD/CID fragmentation pattern allowed for not only extensive sequence coverage but also confident localization of the amino acid variant to its position in the sequence. The crystallographic experiments confirmed the hypothesis generated by in silico structural homology modeling, that the Lys59 side-chain of BCAT2 may repulse the Arg186 in the variant protein (PDB code: 5MPR), leading to destabilization of the protein dimer and altered enzyme kinetics. Taken together, the MS and novel 3D structural data give us reason to further pursue BCAT2 T186R as a precision drug target in GBM. Graphical Abstract ᅟ.
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Affiliation(s)
- Lissa C Anderson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800 E. Paul Dirac Dr., Tallahassee, FL, 32310, USA
| | - Maria Håkansson
- SARomics Biostructures AB, Medicon Village, SE-223 81, Lund, Sweden
| | - Björn Walse
- SARomics Biostructures AB, Medicon Village, SE-223 81, Lund, Sweden
| | - Carol L Nilsson
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch, 301 University Blvd., Galveston, TX, 77555-1074, USA.
- Institute of Clinical Sciences-Lund, Lund University, SE-221 85, Lund, Sweden.
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165
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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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166
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Weisbrod CR, Kaiser NK, Syka JEP, Early L, Mullen C, Dunyach JJ, English AM, Anderson LC, Blakney GT, Shabanowitz J, Hendrickson CL, Marshall AG, Hunt DF. Front-End Electron Transfer Dissociation Coupled to a 21 Tesla FT-ICR Mass Spectrometer for Intact Protein Sequence Analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1787-1795. [PMID: 28721671 PMCID: PMC5711562 DOI: 10.1007/s13361-017-1702-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 04/21/2017] [Accepted: 04/29/2017] [Indexed: 05/13/2023]
Abstract
High resolution mass spectrometry is a key technology for in-depth protein characterization. High-field Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) enables high-level interrogation of intact proteins in the most detail to date. However, an appropriate complement of fragmentation technologies must be paired with FTMS to provide comprehensive sequence coverage, as well as characterization of sequence variants, and post-translational modifications. Here we describe the integration of front-end electron transfer dissociation (FETD) with a custom-built 21 tesla FT-ICR mass spectrometer, which yields unprecedented sequence coverage for proteins ranging from 2.8 to 29 kDa, without the need for extensive spectral averaging (e.g., ~60% sequence coverage for apo-myoglobin with four averaged acquisitions). The system is equipped with a multipole storage device separate from the ETD reaction device, which allows accumulation of multiple ETD fragment ion fills. Consequently, an optimally large product ion population is accumulated prior to transfer to the ICR cell for mass analysis, which improves mass spectral signal-to-noise ratio, dynamic range, and scan rate. We find a linear relationship between protein molecular weight and minimum number of ETD reaction fills to achieve optimum sequence coverage, thereby enabling more efficient use of instrument data acquisition time. Finally, real-time scaling of the number of ETD reactions fills during method-based acquisition is shown, and the implications for LC-MS/MS top-down analysis are discussed. Graphical Abstract ᅟ.
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Affiliation(s)
- Chad R Weisbrod
- National High Magnetic Field Laboratory (NHMFL), 1800 East Paul Dirac Dr., Tallahassee, FL, 32310, USA.
| | - Nathan K Kaiser
- National High Magnetic Field Laboratory (NHMFL), 1800 East Paul Dirac Dr., Tallahassee, FL, 32310, USA
| | | | - Lee Early
- Thermo Fisher Scientific, San Jose, CA, 95134, USA
| | | | | | - A Michelle English
- Department of Chemistry, University of Virginia, McCormick Road, P.O. Box 400319, Charlottesville, VA, 22904-4319, USA
| | - Lissa C Anderson
- National High Magnetic Field Laboratory (NHMFL), 1800 East Paul Dirac Dr., Tallahassee, FL, 32310, USA
| | - Greg T Blakney
- National High Magnetic Field Laboratory (NHMFL), 1800 East Paul Dirac Dr., Tallahassee, FL, 32310, USA
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, McCormick Road, P.O. Box 400319, Charlottesville, VA, 22904-4319, USA
| | - Christopher L Hendrickson
- National High Magnetic Field Laboratory (NHMFL), 1800 East Paul Dirac Dr., Tallahassee, FL, 32310, USA
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, FL, 32306, USA
| | - Alan G Marshall
- National High Magnetic Field Laboratory (NHMFL), 1800 East Paul Dirac Dr., Tallahassee, FL, 32310, USA
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, FL, 32306, USA
| | - Donald F Hunt
- Department of Chemistry, University of Virginia, McCormick Road, P.O. Box 400319, Charlottesville, VA, 22904-4319, USA
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
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167
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Greer SM, Holden DD, Fellers R, Kelleher NL, Brodbelt JS. Modulation of Protein Fragmentation Through Carbamylation of Primary Amines. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1587-1599. [PMID: 28374316 PMCID: PMC5624212 DOI: 10.1007/s13361-017-1648-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 02/28/2017] [Accepted: 03/02/2017] [Indexed: 05/23/2023]
Abstract
We evaluate the impact of carbamylation of the primary amines of the side-chains of Lys and the N-termini on the fragmentation of intact protein ions and the chromatographic properties of a mixture of E. coli ribosomal proteins. The fragmentation patterns of the six unmodified and carbamylated proteins obtained by higher energy collision dissociation (HCD) and ultraviolet photodissociation (UVPD) were compared. Carbamylation significantly reduced the total number of protons retained by the protein owing to the conversion of basic primary amines to non-basic carbamates. Carbamylation caused a significant negative impact on fragmentation of the protein by HCD (i.e., reduced sequence coverage and fewer diagnostic fragment ions) consistent with the mobile proton model, which correlates peptide fragmentation with charge distribution and the opportunity for charge-directed pathways. In addition, fragmentation was enhanced near the N- and C-termini upon HCD of carbamylated proteins. For LCMS/MS analysis of E. coli ribosomal proteins, the retention times increased by 16 min on average upon carbamylation, an outcome attributed to the increased hydrophobicity of the proteins after carbamylation. As noted for both the six model proteins and the ribosomal proteins, carbamylation had relatively little impact on the distribution or types of fragment ions product by UVPD, supporting the proposition that the mechanism of UVPD for intact proteins does not reflect the mobile proton model. Graphical Abstract ᅟ.
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Affiliation(s)
- Sylvester M Greer
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Dustin D Holden
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Ryan Fellers
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, 60208, USA
| | - Neil L Kelleher
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, 60208, USA
- Departments of Chemistry, Molecular Biosciences, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, 60208, USA
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA.
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168
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Kar UK, Simonian M, Whitelegge JP. Integral membrane proteins: bottom-up, top-down and structural proteomics. Expert Rev Proteomics 2017; 14:715-723. [PMID: 28737967 DOI: 10.1080/14789450.2017.1359545] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
INTRODUCTION Integral membrane proteins and lipids constitute the bilayer membranes that surround cells and sub-cellular compartments, and modulate movements of molecules and information between them. Since membrane protein drug targets represent a disproportionately large segment of the proteome, technical developments need timely review. Areas covered: Publically available resources such as Pubmed were surveyed. Bottom-up proteomics analyses now allow efficient extraction and digestion such that membrane protein coverage is essentially complete, making up around one third of the proteome. However, this coverage relies upon hydrophilic loop regions while transmembrane domains are generally poorly covered in peptide-based strategies. Top-down mass spectrometry where the intact membrane protein is fragmented in the gas phase gives good coverage in transmembrane regions, and membrane fractions are yielding to high-throughput top-down proteomics. Exciting progress in native mass spectrometry of membrane protein complexes is providing insights into subunit stoichiometry and lipid binding, and cross-linking strategies are contributing critical in-vivo information. Expert commentary: It is clear from the literature that integral membrane proteins have yielded to advanced techniques in protein chemistry and mass spectrometry, with applications limited only by the imagination of investigators. Key advances toward translation to the clinic are emphasized.
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Affiliation(s)
- Upendra K Kar
- a Department of Pharmaceutical Sciences, College of Pharmacy , University of Arkansas for Medical Sciences , Little Rock , AR , USA
| | - Margaret Simonian
- b NPI-Semel Institute , University of California Los Angeles , Los Angeles , CA , USA
| | - Julian P Whitelegge
- b NPI-Semel Institute , University of California Los Angeles , Los Angeles , CA , USA
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169
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Quick MM, Mehaffey MR, Johns RW, Parker WR, Brodbelt JS. SITS Derivatization of Peptides to Enhance 266 nm Ultraviolet Photodissociation (UVPD). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1462-1472. [PMID: 28315237 DOI: 10.1007/s13361-017-1650-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/01/2017] [Accepted: 03/03/2017] [Indexed: 06/06/2023]
Abstract
N-terminal derivatization of peptides with the chromogenic reagent 4-acetamido-4-isothiocyanatostilbene-2,2-disulfonic acid (SITS) is demonstrated to enhance the efficiency of 266 nm ultraviolet photodissociation (UVPD). Attachment of the chromophore results in a mass shift of 454 Da and provides significant gains in the number and abundances of diagnostic fragment ions upon UVPD. Activation of SITS-tagged peptides with 266 nm UVPD leads to many fragment ions akin to the a/b/y ions commonly produced by CID, along with other sequence ions (c, x, and z) typically accessed through higher energy pathways. Extreme bias towards C-terminal fragment ions is observed upon activation of SITS-tagged peptides using multiple 266 nm laser pulses. Due to the high reaction efficiency of the isothiocyanate coupling to the N-terminus of peptides, we demonstrate the ability to adapt this strategy to a high-throughput LC-MS/MS workflow with 266 nm UVPD. Graphical Abstract ᅟ.
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Affiliation(s)
- M Montana Quick
- Department of Chemistry, University of Texas, Austin, TX, 78712, USA
| | - M Rachel Mehaffey
- Department of Chemistry, University of Texas, Austin, TX, 78712, USA
| | - Robert W Johns
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
- McKetta Department of Chemical Engineering, University of Texas, Austin, TX, 78712, USA
| | - W Ryan Parker
- Department of Chemistry, University of Texas, Austin, TX, 78712, USA
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170
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Riley NM, Westphall MS, Coon JJ. Activated Ion-Electron Transfer Dissociation Enables Comprehensive Top-Down Protein Fragmentation. J Proteome Res 2017; 16:2653-2659. [PMID: 28608681 DOI: 10.1021/acs.jproteome.7b00249] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Here we report the first demonstration of near-complete sequence coverage of intact proteins using activated ion-electron transfer dissociation (AI-ETD), a method that leverages concurrent infrared photoactivation to enhance electron-driven dissociation. AI-ETD produces mainly c/z-type product ions and provides comprehensive (77-97%) protein sequence coverage, outperforming HCD, ETD, and EThcD for all proteins investigated. AI-ETD also maintains this performance across precursor ion charge states, mitigating charge-state dependence that limits traditional approaches.
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Affiliation(s)
| | | | - Joshua J Coon
- Morgridge Institute for Research , Madison, Wisconsin 53715, United States
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171
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Baba T, Campbell JL, Le Blanc JCY, Baker PRS, Hager JW, Thomson BA. Development of a Branched Radio-Frequency Ion Trap for Electron Based Dissociation and Related Applications. Mass Spectrom (Tokyo) 2017; 6:A0058. [PMID: 28630811 PMCID: PMC5469727 DOI: 10.5702/massspectrometry.a0058] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 05/02/2017] [Indexed: 11/23/2022] Open
Abstract
Collision-induced dissociation (CID) is the most common tool for molecular analysis in mass spectrometry to date. However, there are difficulties associated with many applications because CID does not provide sufficient information to permit details of the molecular structures to be elucidated, including post-translational-modifications in proteomics, as well as isomer differentiation in metabolomics and lipidomics. To face these challenges, we are developing fast electron-based dissociation devices using a novel radio-frequency ion trap (i.e., a branched ion trap). These devices have the ability to perform electron capture dissociation (ECD) on multiply protonated peptide/proteins; in addition, the electron impact excitation of ions from organics (EIEIO) can be also performed on singly charged molecules using such a device. In this article, we review the development of this technology, in particular on how reaction speed for EIEIO analyses on singly charged ions can be improved. We also overview some unique, recently reported applications in both lipidomics and glycoproteomics.
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172
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Haverland NA, Skinner OS, Fellers RT, Tariq AA, Early BP, LeDuc RD, Fornelli L, Compton PD, Kelleher NL. Defining Gas-Phase Fragmentation Propensities of Intact Proteins During Native Top-Down Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1203-1215. [PMID: 28374312 PMCID: PMC5452613 DOI: 10.1007/s13361-017-1635-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 02/17/2017] [Accepted: 02/20/2017] [Indexed: 05/03/2023]
Abstract
Fragmentation of intact proteins in the gas phase is influenced by amino acid composition, the mass and charge of precursor ions, higher order structure, and the dissociation technique used. The likelihood of fragmentation occurring between a pair of residues is referred to as the fragmentation propensity and is calculated by dividing the total number of assigned fragmentation events by the total number of possible fragmentation events for each residue pair. Here, we describe general fragmentation propensities when performing top-down mass spectrometry (TDMS) using denaturing or native electrospray ionization. A total of 5311 matched fragmentation sites were collected for 131 proteoforms that were analyzed over 165 experiments using native top-down mass spectrometry (nTDMS). These data were used to determine the fragmentation propensities for 399 residue pairs. In comparison to denatured top-down mass spectrometry (dTDMS), the fragmentation pathways occurring either N-terminal to proline or C-terminal to aspartic acid were even more enhanced in nTDMS compared with other residues. More generally, 257/399 (64%) of the fragmentation propensities were significantly altered (P ≤ 0.05) when using nTDMS compared with dTDMS, and of these, 123 were altered by 2-fold or greater. The most notable enhancements of fragmentation propensities for TDMS in native versus denatured mode occurred (1) C-terminal to aspartic acid, (2) between phenylalanine and tryptophan (F|W), and (3) between tryptophan and alanine (W|A). The fragmentation propensities presented here will be of high value in the development of tailored scoring systems used in nTDMS of both intact proteins and protein complexes. Graphical Abstract ᅟ.
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Affiliation(s)
- Nicole A Haverland
- Department of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, 2170 Campus Drive, Evanston, IL, 60208, USA
| | - Owen S Skinner
- Department of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, 2170 Campus Drive, Evanston, IL, 60208, USA
| | - Ryan T Fellers
- Department of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, 2170 Campus Drive, Evanston, IL, 60208, USA
| | - Areeba A Tariq
- Department of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, 2170 Campus Drive, Evanston, IL, 60208, USA
| | - Bryan P Early
- Department of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, 2170 Campus Drive, Evanston, IL, 60208, USA
| | - Richard D LeDuc
- Department of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, 2170 Campus Drive, Evanston, IL, 60208, USA
| | - Luca Fornelli
- Department of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, 2170 Campus Drive, Evanston, IL, 60208, USA
| | - Philip D Compton
- Department of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, 2170 Campus Drive, Evanston, IL, 60208, USA
| | - Neil L Kelleher
- Department of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, 2170 Campus Drive, Evanston, IL, 60208, USA.
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173
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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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174
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Shen Y, Tolić N, Piehowski PD, Shukla AK, Kim S, Zhao R, Qu Y, Robinson E, Smith RD, Paša-Tolić L. High-resolution ultrahigh-pressure long column reversed-phase liquid chromatography for top-down proteomics. J Chromatogr A 2017; 1498:99-110. [DOI: 10.1016/j.chroma.2017.01.008] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 11/29/2016] [Accepted: 01/03/2017] [Indexed: 11/17/2022]
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175
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Cleland TP, DeHart CJ, Fellers RT, VanNispen AJ, Greer JB, LeDuc RD, Parker WR, Thomas PM, Kelleher NL, Brodbelt JS. High-Throughput Analysis of Intact Human Proteins Using UVPD and HCD on an Orbitrap Mass Spectrometer. J Proteome Res 2017; 16:2072-2079. [PMID: 28412815 DOI: 10.1021/acs.jproteome.7b00043] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The analysis of intact proteins (top-down strategy) by mass spectrometry has great potential to elucidate proteoform variation, including patterns of post-translational modifications (PTMs), which may not be discernible by analysis of peptides alone (bottom-up approach). To maximize sequence coverage and localization of PTMs, various fragmentation modes have been developed to produce fragment ions from deep within intact proteins. Ultraviolet photodissociation (UVPD) has recently been shown to produce high sequence coverage and PTM retention on a variety of proteins, with increasing evidence of efficacy on a chromatographic time scale. However, utilization of UVPD for high-throughput top-down analysis to date has been limited by bioinformatics. Here we detected 153 proteins and 489 proteoforms using UVPD and 271 proteins and 982 proteoforms using higher energy collisional dissociation (HCD) in a comparative analysis of HeLa whole-cell lysate by qualitative top-down proteomics. Of the total detected proteoforms, 286 overlapped between the UVPD and HCD data sets, with 68% of proteoforms having C scores greater than 40 for UVPD and 63% for HCD. The average sequence coverage (28 ± 20% for UVPD versus 17 ± 8% for HCD, p < 0.0001) was found to be higher for UVPD than HCD and with a trend toward improvement in q value for the UVPD data set. This study demonstrates the complementarity of UVPD and HCD for more extensive protein profiling and proteoform characterization.
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Affiliation(s)
- Timothy P Cleland
- Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
| | - Caroline J DeHart
- National Resource for Translational and Developmental Proteomics, Northwestern University , Evanston, Illinois 60208, United States
| | - Ryan T Fellers
- National Resource for Translational and Developmental Proteomics, Northwestern University , Evanston, Illinois 60208, United States
| | - Alexandra J VanNispen
- National Resource for Translational and Developmental Proteomics, Northwestern University , Evanston, Illinois 60208, United States
| | - Joseph B Greer
- National Resource for Translational and Developmental Proteomics, Northwestern University , Evanston, Illinois 60208, United States
| | - Richard D LeDuc
- National Resource for Translational and Developmental Proteomics, Northwestern University , Evanston, Illinois 60208, United States
| | - W Ryan Parker
- Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
| | - Paul M Thomas
- National Resource for Translational and Developmental Proteomics, Northwestern University , Evanston, Illinois 60208, United States.,Departments of Chemistry, Molecular Biosciences, and the Feinberg School of Medicine, Northwestern University , Evanston, Illinois 60208, United States
| | - Neil L Kelleher
- National Resource for Translational and Developmental Proteomics, Northwestern University , Evanston, Illinois 60208, United States.,Departments of Chemistry, Molecular Biosciences, and the Feinberg School of Medicine, Northwestern University , Evanston, Illinois 60208, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
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176
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Chen B, Hwang L, Ochowicz W, Lin Z, Guardado-Alvarez TM, Cai W, Xiu L, Dani K, Colah C, Jin S, Ge Y. Coupling functionalized cobalt ferrite nanoparticle enrichment with online LC/MS/MS for top-down phosphoproteomics. Chem Sci 2017; 8:4306-4311. [PMID: 28660060 PMCID: PMC5472028 DOI: 10.1039/c6sc05435h] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 03/30/2017] [Indexed: 01/02/2023] Open
Abstract
An integrated top-down phosphoproteomics strategy enabled by functionalized cobalt ferrite nanoparticle enrichment and online LC/MS/MS for identification, quantification, and characterization of low abundance phosphoproteins is presented.
Phosphorylation plays pivotal roles in cellular processes and dysregulated phosphorylation is considered as an underlying mechanism in many human diseases. Top-down mass spectrometry (MS) analyzes intact proteins and provides a comprehensive analysis of protein phosphorylation. However, top-down MS-based phosphoproteomics is challenging due to the difficulty in enriching low abundance intact phosphoproteins as well as separating and detecting the enriched phosphoproteins from complex mixtures. Herein, we have designed and synthesized the next generation functionalized superparamagnetic cobalt ferrite (CoFe2O4) nanoparticles (NPs), and have further developed a top-down phosphoproteomics strategy coupling phosphoprotein enrichment enabled by the functionalized CoFe2O4 NPs with online liquid chromatography (LC)/MS/MS for comprehensive characterization of phosphoproteins. We have demonstrated the highly specific enrichment of a minimal amount of spike-in β-casein from a complex tissue lysate as well as effective separation and quantification of its phosphorylated genetic variants. More importantly, this integrated top-down phosphoproteomics strategy allows for enrichment, identification, quantification, and comprehensive characterization of low abundance endogenous phosphoproteins from complex tissue extracts on a chromatographic time scale.
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Affiliation(s)
- Bifan Chen
- Department of Chemistry , University of Wisconsin-Madison , Madison , WI , USA .
| | - Leekyoung Hwang
- Department of Chemistry , University of Wisconsin-Madison , Madison , WI , USA .
| | - William Ochowicz
- Department of Chemistry , University of Wisconsin-Madison , Madison , WI , USA .
| | - Ziqing Lin
- Department of Cell and Regenerative Biology , University of Wisconsin-Madison , Madison , WI , USA
| | | | - Wenxuan Cai
- Department of Cell and Regenerative Biology , University of Wisconsin-Madison , Madison , WI , USA
| | - Lichen Xiu
- Department of Chemistry , University of Wisconsin-Madison , Madison , WI , USA .
| | - Kunal Dani
- Department of Chemistry , University of Wisconsin-Madison , Madison , WI , USA .
| | - Cyrus Colah
- Department of Cell and Regenerative Biology , University of Wisconsin-Madison , Madison , WI , USA
| | - Song Jin
- Department of Chemistry , University of Wisconsin-Madison , Madison , WI , USA .
| | - Ying Ge
- Department of Chemistry , University of Wisconsin-Madison , Madison , WI , USA . .,Department of Cell and Regenerative Biology , University of Wisconsin-Madison , Madison , WI , USA.,Human Proteomics Program , School of Medicine and Public Health , University of Wisconsin-Madison , Madison , WI , USA
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177
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Cammarata M, Thyer R, Lombardo M, Anderson A, Wright D, Ellington A, Brodbelt JS. Characterization of trimethoprim resistant E. coli dihydrofolate reductase mutants by mass spectrometry and inhibition by propargyl-linked antifolates. Chem Sci 2017; 8:4062-4072. [PMID: 29967675 PMCID: PMC6020862 DOI: 10.1039/c6sc05235e] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 03/24/2017] [Indexed: 12/12/2022] Open
Abstract
Native mass spectrometry, size exclusion chromatography, and kinetic assays were employed to study trimethoprim resistance in E. coli caused by mutations P21L and W30R of dihydrofolate reductase.
Pathogenic Escherichia coli, one of the primary causes of urinary tract infections, has shown significant resistance to the most popular antibiotic, trimethoprim (TMP), which inhibits dihydrofolate reductase (DHFR). The resistance is modulated by single point mutations of DHFR. The impact of two clinically relevant mutations, P21L and W30R, on the activity of DHFR was evaluated via measurement of Michaelis–Menten and inhibitory kinetics, and structural characterization was undertaken by native mass spectrometry with ultraviolet photodissociation (UVPD). Compared to WT-DHFR, both P21L and W30R mutants produced less stable complexes with TMP in the presence of co-factor NADPH as evidenced by the relative abundances of complexes observed in ESI mass spectra. Moreover, based on variations in the fragmentation patterns obtained by UVPD mass spectrometry of binary and ternary DHFR complexes, notable structural changes were localized to the substrate binding pocket for W30R and to the M20 loop region as well as the C-terminal portion containing the essential G–H functional loop for the P21L mutant. The results suggest that the mutations confer resistance through distinctive mechanisms. A novel propargyl-linked antifolate compound 1038 was shown to be a reasonably effective inhibitor of the P21L mutant.
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Affiliation(s)
- Michael Cammarata
- Department of Chemistry , University of Texas , Austin , TX 78712 , USA .
| | - Ross Thyer
- Center for Systems and Synthetic Biology , University of Texas , Austin , TX 78712 , USA
| | - Michael Lombardo
- Department of Pharmaceutical Sciences , University of Connecticut , Storrs , CT 06269 , USA
| | - Amy Anderson
- Department of Pharmaceutical Sciences , University of Connecticut , Storrs , CT 06269 , USA
| | - Dennis Wright
- Department of Pharmaceutical Sciences , University of Connecticut , Storrs , CT 06269 , USA
| | - Andrew Ellington
- Center for Systems and Synthetic Biology , University of Texas , Austin , TX 78712 , USA
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178
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Fornelli L, Ayoub D, Aizikov K, Liu X, Damoc E, Pevzner PA, Makarov A, Beck A, Tsybin YO. Top-down analysis of immunoglobulin G isotypes 1 and 2 with electron transfer dissociation on a high-field Orbitrap mass spectrometer. J Proteomics 2017; 159:67-76. [PMID: 28242452 DOI: 10.1016/j.jprot.2017.02.013] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 01/22/2017] [Accepted: 02/13/2017] [Indexed: 12/27/2022]
Abstract
The increasing importance of immunoglobulins G (IgGs) as biotherapeutics calls for improved structural characterization methods designed for these large (~150kDa) macromolecules. Analysis workflows have to be rapid, robust, and require minimal sample preparation. In a previous work we showed the potential of Orbitrap Fourier transform mass spectrometry (FTMS) combined with electron transfer dissociation (ETD) for the top-down investigation of an intact IgG1, resulting in ~30% sequence coverage. Here, we describe a top-down analysis of two IgGs1 (adalimumab and trastuzumab) and one IgG2 (panitumumab) performed with ETD on a mass spectrometer equipped with a high-field Orbitrap mass analyzer. For the IgGs1, sequence coverage comparable to the previous results was achieved in a two-fold reduced number of summed transients, which corresponds, taken together with the significantly increased spectra acquisition rate, to ~six-fold improvement in analysis time. Furthermore, we studied the influence of ion-ion interaction times on ETD product ions for IgGs1, and the differences in fragmentation behavior between IgGs1 and IgG2, which present structural differences. Overall, these results reinforce the hypothesis that gas phase dissociation using both energy threshold-based and radical-driven ion activations is directed to specific regions of the polypeptide chains mostly by the location of disulfide bonds. SIGNIFICANCE OF THE STUDY Compared with our previous report, the results presented herein demonstrate the power of technological advances of the next generation Orbitrap™ platform, including the use of a high-field compact (i.e., D20) Orbitrap mass analyzer, and a dedicated manipulation strategy for large protein ions (via their trapping in the HCD collision cell along with reduction of the pressure in the cell). Notably, these important developments became recently commercially available in the top-end Orbitrap platforms under the name of "Protein Mode". Furthermore, we continued exploring the advantages offered by the summation (averaging) of transients (time-domain data) for improving the signal-to-noise ratio of top-down mass spectra. Finally, for the first time we report the application of the hybrid ion activation technique that combines electron transfer dissociation and higher energy collisional dissociation, known as EThcD, on intact monoclonal antibodies. Under these specific instrumental parameters, EThcD produces a partially complementary fragmentation pattern compared to ETD, increasing the overall sequence coverage especially at the protein termini.
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Affiliation(s)
- Luca Fornelli
- Biomolecular Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Daniel Ayoub
- Biomolecular Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | | | - Xiaowen Liu
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, 46202 Indianapolis, IN, USA; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 46202 Indianapolis, IN, USA
| | - Eugen Damoc
- Thermo Fisher Scientific GmbH, 28199 Bremen, Germany
| | - Pavel A Pevzner
- Department of Computer Science and Engineering, University of California in San Diego, 92093 San Diego, CA, USA
| | | | - Alain Beck
- Centre d'Immunologie Pierre Fabre, 74160 St Julien-en-Genevois, France
| | - Yury O Tsybin
- Biomolecular Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland; Spectroswiss Sàrl, EPFL Innovation Park, 1015 Lausanne, Switzerland.
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179
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Li H, Sheng Y, McGee W, Cammarata M, Holden D, Loo JA. Structural Characterization of Native Proteins and Protein Complexes by Electron Ionization Dissociation-Mass Spectrometry. Anal Chem 2017; 89:2731-2738. [PMID: 28192979 DOI: 10.1021/acs.analchem.6b02377] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mass spectrometry (MS) has played an increasingly important role in the identification and structural and functional characterization of proteins. In particular, the use of tandem mass spectrometry has afforded one of the most versatile methods to acquire structural information for proteins and protein complexes. The unique nature of electron capture dissociation (ECD) for cleaving protein backbone bonds while preserving noncovalent interactions has made it especially suitable for the study of native protein structures. However, the intra- and intermolecular interactions stabilized by hydrogen bonds and salt bridges can hinder the separation of fragments even with preactivation, which has become particularly problematic for the study of large macromolecular proteins and protein complexes. Here, we describe the capabilities of another activation method, 30 eV electron ionization dissociation (EID), for the top-down MS characterization of native protein-ligand and protein-protein complexes. Rich structural information that cannot be delivered by ECD can be generated by EID. EID allowed for the comparison of the gas-phase and the solution-phase structural stability and unfolding process of human carbonic anhydrase I (HCA-I). In addition, the EID fragmentation patterns reflect the structural similarities and differences among apo-, Zn-, and Cu,Zn-superoxide dismutase (SOD1) dimers. In particular, the structural changes due to Cu-binding and a point mutation (G41D) were revealed by EID-MS. The performance of EID was also compared to that of 193 nm ultraviolet photodissociation (UVPD), which allowed us to explore their qualitative similarities and differences as potential valuable tools for the MS study of native proteins and protein complexes.
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Affiliation(s)
- Huilin Li
- Department of Biological Chemistry, David Geffen School of Medicine, University of California , Los Angeles, California 90095, United States
| | - Yuewei Sheng
- Department of Chemistry and Biochemistry, UCLA/DOE Institute of Genomics and Proteomics, and UCLA Molecular Biology Institute, University of California , Los Angeles, California 90095, United States
| | - William McGee
- Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Michael Cammarata
- Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Dustin Holden
- Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Joseph A Loo
- Department of Biological Chemistry, David Geffen School of Medicine, University of California , Los Angeles, California 90095, United States.,Department of Chemistry and Biochemistry, UCLA/DOE Institute of Genomics and Proteomics, and UCLA Molecular Biology Institute, University of California , Los Angeles, California 90095, United States
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180
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Klein DR, Brodbelt JS. Structural Characterization of Phosphatidylcholines Using 193 nm Ultraviolet Photodissociation Mass Spectrometry. Anal Chem 2017; 89:1516-1522. [PMID: 28105803 PMCID: PMC5480246 DOI: 10.1021/acs.analchem.6b03353] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Advances in mass spectrometry have made it a preferred tool for structural characterization of glycerophospholipids. Collisional activation methods commonly implemented on commercial instruments do not provide fragmentation patterns that allow elucidation of certain structural features, including acyl chain positions on the glycerol backbone and double bond positions within acyl chains. In the present work, 193 nm ultraviolet photodissociation (UVPD) implemented on an Orbitrap mass spectrometer is used to localize double bond positions within phosphatidylcholine (PC) acyl chains. Cleavage of the carbon-carbon bonds adjacent to the double bond provides a diagnostic mass difference of 24 Da and enables differentiation of double-bond positional isomers. The UVPD method was extended to the characterization of PCs in a bovine liver extract via a shotgun strategy. Positive mode higher energy collisional dissociation (HCD) and UVPD, and negative mode HCD were undertaken in a complementary manner to identify species as PCs and to localize double bonds, respectively.
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Affiliation(s)
- Dustin R Klein
- 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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181
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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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182
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Lössl P, van de Waterbeemd M, Heck AJ. The diverse and expanding role of mass spectrometry in structural and molecular biology. EMBO J 2016; 35:2634-2657. [PMID: 27797822 PMCID: PMC5167345 DOI: 10.15252/embj.201694818] [Citation(s) in RCA: 171] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 07/25/2016] [Accepted: 10/07/2016] [Indexed: 12/20/2022] Open
Abstract
The emergence of proteomics has led to major technological advances in mass spectrometry (MS). These advancements not only benefitted MS-based high-throughput proteomics but also increased the impact of mass spectrometry on the field of structural and molecular biology. Here, we review how state-of-the-art MS methods, including native MS, top-down protein sequencing, cross-linking-MS, and hydrogen-deuterium exchange-MS, nowadays enable the characterization of biomolecular structures, functions, and interactions. In particular, we focus on the role of mass spectrometry in integrated structural and molecular biology investigations of biological macromolecular complexes and cellular machineries, highlighting work on CRISPR-Cas systems and eukaryotic transcription complexes.
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Affiliation(s)
- Philip Lössl
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands
- Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Michiel van de Waterbeemd
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands
- Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Albert Jr Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands
- Netherlands Proteomics Center, Utrecht, The Netherlands
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183
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Anderson LC, DeHart CJ, Kaiser NK, Fellers RT, Smith DF, Greer JB, LeDuc RD, Blakney GT, Thomas PM, Kelleher NL, Hendrickson CL. Identification and Characterization of Human Proteoforms by Top-Down LC-21 Tesla FT-ICR Mass Spectrometry. J Proteome Res 2016; 16:1087-1096. [PMID: 27936753 DOI: 10.1021/acs.jproteome.6b00696] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Successful high-throughput characterization of intact proteins from complex biological samples by mass spectrometry requires instrumentation capable of high mass resolving power, mass accuracy, sensitivity, and spectral acquisition rate. These limitations often necessitate the performance of hundreds of LC-MS/MS experiments to obtain reasonable coverage of the targeted proteome, which is still typically limited to molecular weights below 30 kDa. The National High Magnetic Field Laboratory (NHMFL) recently installed a 21 T FT-ICR mass spectrometer, which is part of the NHMFL FT-ICR User Facility and available to all qualified users. Here we demonstrate top-down LC-21 T FT-ICR MS/MS of intact proteins derived from human colorectal cancer cell lysate. We identified a combined total of 684 unique protein entries observed as 3238 unique proteoforms at a 1% false discovery rate, based on rapid, data-dependent acquisition of collision-induced and electron-transfer dissociation tandem mass spectra from just 40 LC-MS/MS experiments. Our identifications included 372 proteoforms with molecular weights over 30 kDa detected at isotopic resolution, which substantially extends the accessible mass range for high-throughput top-down LC-MS/MS.
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Affiliation(s)
- Lissa C Anderson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory , Tallahassee, Florida 32310, United States
| | - Caroline J DeHart
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory , Tallahassee, Florida 32310, United States.,Proteomics Center of Excellence, Northwestern University , Evanston, Illinois 60208, United States
| | - Nathan K Kaiser
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory , Tallahassee, Florida 32310, United States
| | - Ryan T Fellers
- Proteomics Center of Excellence, Northwestern University , Evanston, Illinois 60208, United States
| | - Donald F Smith
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory , Tallahassee, Florida 32310, United States
| | - Joseph B Greer
- Proteomics Center of Excellence, Northwestern University , Evanston, Illinois 60208, United States
| | - Richard D LeDuc
- Proteomics Center of Excellence, Northwestern University , Evanston, Illinois 60208, United States
| | - Greg T Blakney
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory , Tallahassee, Florida 32310, United States
| | - Paul M Thomas
- Proteomics Center of Excellence, Northwestern University , Evanston, Illinois 60208, United States
| | - Neil L Kelleher
- Proteomics Center of Excellence, Northwestern University , Evanston, Illinois 60208, United States.,Departments of Chemistry and Molecular Biosciences and the Division of Hematology-Oncology, Northwestern University , Evanston, Illinois 60208, United States
| | - Christopher L Hendrickson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory , Tallahassee, Florida 32310, United States.,Department of Chemistry and Biochemistry, Florida State University , Tallahassee, Florida 32304, United States
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184
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Holden DD, Brodbelt JS. Ultraviolet Photodissociation of Native Proteins Following Proton Transfer Reactions in the Gas Phase. Anal Chem 2016; 88:12354-12362. [PMID: 28193062 DOI: 10.1021/acs.analchem.6b03565] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The growing use of mass spectrometry in the field of structural biology has catalyzed the development of many new strategies to examine intact proteins in the gas phase. Native mass spectrometry methods have further accelerated the need for methods that can manipulate proteins and protein complexes while minimizing disruption of noncovalent interactions critical for stabilizing conformations. Proton-transfer reactions (PTR) in the gas phase offer the ability to effectively modulate the charge states of proteins, allowing decongestion of mass spectra through separation of overlapping species. PTR was combined with ultraviolet photodissociation (UVPD) to probe the degree of structural changes that occur upon charge reduction reactions in the gas phase. For protein complexes myoglobin·heme (17.6 kDa) and dihydrofolate reductase·methotrexate (19.4 kDa), minor changes were found in the fragmentation patterns aside from some enhancement of fragmentation near the N- and C-terminal regions consistent with slight fraying. After finding little perturbation was caused by charge reduction using PTR, homodimeric superoxide dismutase/CuZn (31.4 kDa) was subjected to PTR in order to separate overlapping monomer and dimer species of the protein that were observed at identical m/z values.
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Affiliation(s)
- Dustin D Holden
- 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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185
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Fornelli L, Durbin KR, Fellers RT, Early BP, Greer JB, LeDuc RD, Compton PD, Kelleher NL. Advancing Top-down Analysis of the Human Proteome Using a Benchtop Quadrupole-Orbitrap Mass Spectrometer. J Proteome Res 2016; 16:609-618. [PMID: 28152595 DOI: 10.1021/acs.jproteome.6b00698] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Over the past decade, developments in high resolution mass spectrometry have enabled the high throughput analysis of intact proteins from complex proteomes, leading to the identification of thousands of proteoforms. Several previous reports on top-down proteomics (TDP) relied on hybrid ion trap-Fourier transform mass spectrometers combined with data-dependent acquisition strategies. To further reduce TDP to practice, we use a quadrupole-Orbitrap instrument coupled with software for proteoform-dependent data acquisition to identify and characterize nearly 2000 proteoforms at a 1% false discovery rate from human fibroblasts. By combining a 3 m/z isolation window with short transients to improve specificity and signal-to-noise for proteoforms >30 kDa, we demonstrate improving proteome coverage by capturing 439 proteoforms in the 30-60 kDa range. Three different data acquisition strategies were compared and resulted in the identification of many proteoforms not observed in replicate data-dependent experiments. Notably, the data set is reported with updated metrics and tools including a new viewer and assignment of permanent proteoform record identifiers for inclusion of highly characterized proteoforms (i.e., those with C-scores >40) in a repository curated by the Consortium for Top-Down Proteomics.
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Affiliation(s)
- Luca Fornelli
- Departments of Chemistry and Molecular Biosciences, Northwestern University , 2170 Campus Drive, Evanston, Illinois 60208, United States
| | - Kenneth R Durbin
- Departments of Chemistry and Molecular Biosciences, Northwestern University , 2170 Campus Drive, Evanston, Illinois 60208, United States
| | - Ryan T Fellers
- Departments of Chemistry and Molecular Biosciences, Northwestern University , 2170 Campus Drive, Evanston, Illinois 60208, United States
| | - Bryan P Early
- Departments of Chemistry and Molecular Biosciences, Northwestern University , 2170 Campus Drive, Evanston, Illinois 60208, United States
| | - Joseph B Greer
- Departments of Chemistry and Molecular Biosciences, Northwestern University , 2170 Campus Drive, Evanston, Illinois 60208, United States
| | - Richard D LeDuc
- Departments of Chemistry and Molecular Biosciences, Northwestern University , 2170 Campus Drive, Evanston, Illinois 60208, United States
| | - Philip D Compton
- Departments of Chemistry and Molecular Biosciences, Northwestern University , 2170 Campus Drive, Evanston, Illinois 60208, United States
| | - Neil L Kelleher
- Departments of Chemistry and Molecular Biosciences, Northwestern University , 2170 Campus Drive, Evanston, Illinois 60208, United States
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186
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Shaw JB, Lin TY, Leach FE, Tolmachev AV, Tolić N, Robinson EW, Koppenaal DW, Paša-Tolić L. 21 Tesla Fourier Transform Ion Cyclotron Resonance Mass Spectrometer Greatly Expands Mass Spectrometry Toolbox. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1929-1936. [PMID: 27734325 DOI: 10.1007/s13361-016-1507-9] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 09/12/2016] [Accepted: 09/13/2016] [Indexed: 06/06/2023]
Abstract
We provide the initial performance evaluation of a 21 Tesla Fourier transform ion cyclotron resonance mass spectrometer operating at the Environmental Molecular Sciences Laboratory at the Pacific Northwest National Laboratory. The spectrometer constructed for the 21T system employs a commercial dual linear ion trap mass spectrometer coupled to a FTICR spectrometer designed and built in-house. Performance gains from moving to higher magnetic field strength are exemplified by the measurement of peptide isotopic fine structure, complex natural organic matter mixtures, and large proteins. Accurate determination of isotopic fine structure was demonstrated for doubly charged Substance P with minimal spectral averaging, and 8158 molecular formulas assigned to Suwannee River Fulvic Acid standard with root-mean-square (RMS) error of 10 ppb. We also demonstrated superior performance for intact proteins; namely, broadband isotopic resolution of the entire charge state distribution of apo-transferrin (78 kDa) and facile isotopic resolution of monoclonal antibody under a variety of acquisition parameters (e.g., 6 s time-domains with absorption mode processing yielded resolution of approximately 1 M at m/z = 2700). Graphical Abstract ᅟ.
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Affiliation(s)
- Jared B Shaw
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Ave. (K8-98), P.O. Box 999, Richland, WA, 99352, USA
| | - Tzu-Yung Lin
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Ave. (K8-98), P.O. Box 999, Richland, WA, 99352, USA
| | - Franklin E Leach
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Ave. (K8-98), P.O. Box 999, Richland, WA, 99352, USA
| | - Aleksey V Tolmachev
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Ave. (K8-98), P.O. Box 999, Richland, WA, 99352, USA
| | - Nikola Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Ave. (K8-98), P.O. Box 999, Richland, WA, 99352, USA
| | - Errol W Robinson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Ave. (K8-98), P.O. Box 999, Richland, WA, 99352, USA
| | - David W Koppenaal
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Ave. (K8-98), P.O. Box 999, Richland, WA, 99352, USA
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Ave. (K8-98), P.O. Box 999, Richland, WA, 99352, USA.
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187
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Theisen A, Yan B, Brown JM, Morris M, Bellina B, Barran PE. Use of Ultraviolet Photodissociation Coupled with Ion Mobility Mass Spectrometry To Determine Structure and Sequence from Drift Time Selected Peptides and Proteins. Anal Chem 2016; 88:9964-9971. [DOI: 10.1021/acs.analchem.6b01705] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Alina Theisen
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
of Biotechnology, and Photon Science Insitute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Bin Yan
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
of Biotechnology, and Photon Science Insitute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Jeffery M. Brown
- Waters Corporation, Stamford
Avenue, Altrincham Road, Wilmslow, SK9 4AX, United Kingdom
| | - Michael Morris
- Waters Corporation, Stamford
Avenue, Altrincham Road, Wilmslow, SK9 4AX, United Kingdom
| | - Bruno Bellina
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
of Biotechnology, and Photon Science Insitute, 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 Insitute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
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188
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Cammarata MB, Schardon CL, Mehaffey MR, Rosenberg J, Singleton J, Fast W, Brodbelt JS. Impact of G12 Mutations on the Structure of K-Ras Probed by Ultraviolet Photodissociation Mass Spectrometry. J Am Chem Soc 2016; 138:13187-13196. [DOI: 10.1021/jacs.6b04474] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Michael B. Cammarata
- Department of Chemistry, ‡Graduate Program in Biochemistry, and §Division of Chemical Biology and
Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Christopher L. Schardon
- Department of Chemistry, ‡Graduate Program in Biochemistry, and §Division of Chemical Biology and
Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - M. Rachel Mehaffey
- Department of Chemistry, ‡Graduate Program in Biochemistry, and §Division of Chemical Biology and
Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Jake Rosenberg
- Department of Chemistry, ‡Graduate Program in Biochemistry, and §Division of Chemical Biology and
Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Jonathan Singleton
- Department of Chemistry, ‡Graduate Program in Biochemistry, and §Division of Chemical Biology and
Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Walter Fast
- Department of Chemistry, ‡Graduate Program in Biochemistry, and §Division of Chemical Biology and
Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Jennifer S. Brodbelt
- Department of Chemistry, ‡Graduate Program in Biochemistry, and §Division of Chemical Biology and
Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
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189
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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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190
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Snyder DT, Fedick PW, Cooks RG. Multigenerational Collision-Induced Dissociation for Characterization of Organic Compounds. Anal Chem 2016; 88:9572-9581. [PMID: 27622856 DOI: 10.1021/acs.analchem.6b02209] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Dalton T. Snyder
- Department
of Chemistry and
Center for Analytical Instrumentation Development, Purdue University, West Lafayette, Indiana 47907, United States
| | - Patrick W. Fedick
- Department
of Chemistry and
Center for Analytical Instrumentation Development, Purdue University, West Lafayette, Indiana 47907, United States
| | - R. Graham Cooks
- Department
of Chemistry and
Center for Analytical Instrumentation Development, Purdue University, West Lafayette, Indiana 47907, United States
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191
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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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192
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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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193
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Morrison LJ, Rosenberg JA, Singleton JP, Brodbelt JS. Statistical Examination of the a and a + 1 Fragment Ions from 193 nm Ultraviolet Photodissociation Reveals Local Hydrogen Bonding Interactions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1443-53. [PMID: 27206509 PMCID: PMC4974117 DOI: 10.1007/s13361-016-1418-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 05/01/2016] [Accepted: 05/06/2016] [Indexed: 05/11/2023]
Abstract
Dissociation of proteins and peptides by 193 nm ultraviolet photodissociation (UVPD) has gained momentum in proteomic studies because of the diversity of backbone fragments that are produced and subsequent unrivaled sequence coverage obtained by the approach. The pathways that form the basis for the production of particular ion types are not completely understood. In this study, a statistical approach is used to probe hydrogen atom elimination from a + 1 radical ions, and different extents of elimination are found to vary as a function of the identity of the C-terminal residue of the a product ions and the presence or absence of hydrogen bonds to the cleaved residue. Graphical Abstract ᅟ.
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Affiliation(s)
| | - Jake A Rosenberg
- Department of Chemistry, University of Texas, Austin, TX, 78712, USA
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194
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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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195
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Gabant G, Boyer A, Cadene M. SSPaQ: A Subtractive Segmentation Approach for the Exhaustive Parallel Quantification of the Extent of Protein Modification at Every Possible Site. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1328-1343. [PMID: 27245456 DOI: 10.1007/s13361-016-1416-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 04/19/2016] [Accepted: 04/24/2016] [Indexed: 06/05/2023]
Abstract
Protein modifications, whether chemically induced or post-translational (PTMs), play an essential role for the biological activity of proteins. Understanding biological processes and alterations thereof will rely on the quantification of these modifications on individual residues. Here we present SSPaQ, a subtractive method for the parallel quantification of the extent of modification at each possible site of a protein. The method combines uniform isotopic labeling and proteolysis with MS, followed by a segmentation approach, a powerful tool to refine the quantification of the degree of modification of a peptide to a segment containing a single modifiable amino acid. The strength of this strategy resides in: (1) quantification of all modifiable sites in a protein without prior knowledge of the type(s) of modified residues; (2) insensitivity to changes in the solubility and ionization efficiency of peptides upon modification; and (3) detection of missed cleavages caused by the modification for mitigation. The SSPaQ method was applied to quantify modifications resulting from the interaction of human phosphatidyl ethanolamine binding protein 1 (hPEBP1), a metastasis suppressor gene product, with locostatin, a covalent ligand and antimigratory compound with demonstrated activity towards hPEBP1. Locostatin is shown to react with several residues of the protein. SSPaQ can more generally be applied to induced modification in the context of drugs that covalently bind their target protein. With an alternate front-end protocol, it could also be applied to the quantification of protein PTMs, provided a removal tool is available for that PTM. Graphical Abstract ᅟ.
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Affiliation(s)
- Guillaume Gabant
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique, UPR 4301, rue Charles Sadron, 45071, Orléans cedex 2, France
- University of Orléans, Orléans, France
| | - Alain Boyer
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique, UPR 4301, rue Charles Sadron, 45071, Orléans cedex 2, France
| | - Martine Cadene
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique, UPR 4301, rue Charles Sadron, 45071, Orléans cedex 2, France.
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196
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Cai W, Tucholski TM, Gregorich ZR, Ge Y. Top-down Proteomics: Technology Advancements and Applications to Heart Diseases. Expert Rev Proteomics 2016; 13:717-30. [PMID: 27448560 DOI: 10.1080/14789450.2016.1209414] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Heart diseases are a leading cause of morbidity and mortality for both men and women worldwide, and impose significant economic burdens on the healthcare systems. Despite substantial effort over the last several decades, the molecular mechanisms underlying diseases of the heart remain poorly understood. AREAS COVERED Altered protein post-translational modifications (PTMs) and protein isoform switching are increasingly recognized as important disease mechanisms. Top-down high-resolution mass spectrometry (MS)-based proteomics has emerged as the most powerful method for the comprehensive analysis of PTMs and protein isoforms. Here, we will review recent technology developments in the field of top-down proteomics, as well as highlight recent studies utilizing top-down proteomics to decipher the cardiac proteome for the understanding of the molecular mechanisms underlying diseases of the heart. Expert commentary: Top-down proteomics is a premier method for the global and comprehensive study of protein isoforms and their PTMs, enabling the identification of novel protein isoforms and PTMs, characterization of sequence variations, and quantification of disease-associated alterations. Despite significant challenges, continuous development of top-down proteomics technology will greatly aid the dissection of the molecular mechanisms underlying diseases of the hearts for the identification of novel biomarkers and therapeutic targets.
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Affiliation(s)
- Wenxuan Cai
- a Department of Cell and Regenerative Biology , University of Wisconsin-Madison , Madison , WI , USA.,b Molecular and Cellular Pharmacology Training Program , University of Wisconsin-Madison , Madison , WI , USA
| | - Trisha M Tucholski
- c Department of Chemistry , University of Wisconsin-Madison , Madison , WI , USA
| | - Zachery R Gregorich
- a Department of Cell and Regenerative Biology , University of Wisconsin-Madison , Madison , WI , USA.,b Molecular and Cellular Pharmacology Training Program , University of Wisconsin-Madison , Madison , WI , USA
| | - Ying Ge
- a Department of Cell and Regenerative Biology , University of Wisconsin-Madison , Madison , WI , USA.,c Department of Chemistry , University of Wisconsin-Madison , Madison , WI , USA.,d Human Proteomics Program , University of Wisconsin-Madison , Madison , WI , USA
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197
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Bartman CE, Metwally H, Konermann L. Effects of Multidentate Metal Interactions on the Structure of Collisionally Activated Proteins: Insights from Ion Mobility Spectrometry and Molecular Dynamics Simulations. Anal Chem 2016; 88:6905-13. [DOI: 10.1021/acs.analchem.6b01627] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Claire E. Bartman
- Department
of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Haidy Metwally
- Department
of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department
of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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198
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Toby TK, Fornelli L, Kelleher NL. Progress in Top-Down Proteomics and the Analysis of Proteoforms. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2016; 9:499-519. [PMID: 27306313 PMCID: PMC5373801 DOI: 10.1146/annurev-anchem-071015-041550] [Citation(s) in RCA: 382] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
From a molecular perspective, enactors of function in biology are intact proteins that can be variably modified at the genetic, transcriptional, or post-translational level. Over the past 30 years, mass spectrometry (MS) has become a powerful method for the analysis of proteomes. Prevailing bottom-up proteomics operates at the level of the peptide, leading to issues with protein inference, connectivity, and incomplete sequence/modification information. Top-down proteomics (TDP), alternatively, applies MS at the proteoform level to analyze intact proteins with diverse sources of intramolecular complexity preserved during analysis. Fortunately, advances in prefractionation workflows, MS instrumentation, and dissociation methods for whole-protein ions have helped TDP emerge as an accessible and potentially disruptive modality with increasingly translational value. In this review, we discuss technical and conceptual advances in TDP, along with the growing power of proteoform-resolved measurements in clinical and translational research.
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Affiliation(s)
- Timothy K Toby
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208;
| | - Luca Fornelli
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Neil L Kelleher
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208;
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208
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199
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Weisz DA, Gross ML, Pakrasi HB. The Use of Advanced Mass Spectrometry to Dissect the Life-Cycle of Photosystem II. FRONTIERS IN PLANT SCIENCE 2016; 7:617. [PMID: 27242823 PMCID: PMC4862242 DOI: 10.3389/fpls.2016.00617] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 04/22/2016] [Indexed: 05/23/2023]
Abstract
Photosystem II (PSII) is a photosynthetic membrane-protein complex that undergoes an intricate, tightly regulated cycle of assembly, damage, and repair. The available crystal structures of cyanobacterial PSII are an essential foundation for understanding PSII function, but nonetheless provide a snapshot only of the active complex. To study aspects of the entire PSII life-cycle, mass spectrometry (MS) has emerged as a powerful tool that can be used in conjunction with biochemical techniques. In this article, we present the MS-based approaches that are used to study PSII composition, dynamics, and structure, and review the information about the PSII life-cycle that has been gained by these methods. This information includes the composition of PSII subcomplexes, discovery of accessory PSII proteins, identification of post-translational modifications and quantification of their changes under various conditions, determination of the binding site of proteins not observed in PSII crystal structures, conformational changes that underlie PSII functions, and identification of water and oxygen channels within PSII. We conclude with an outlook for the opportunity of future MS contributions to PSII research.
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Affiliation(s)
- Daniel A. Weisz
- Department of Biology, Washington University in St. LouisSt. Louis, MO, USA
- Department of Chemistry, Washington University in St. LouisSt. Louis, MO, USA
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. LouisSt. Louis, MO, USA
| | - Himadri B. Pakrasi
- Department of Biology, Washington University in St. LouisSt. Louis, MO, USA
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200
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Crittenden CM, Parker WR, Jenner ZB, Bruns KA, Akin LD, McGee WM, Ciccimaro E, Brodbelt JS. Exploitation of the Ornithine Effect Enhances Characterization of Stapled and Cyclic Peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:856-863. [PMID: 26864791 DOI: 10.1007/s13361-016-1355-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 01/13/2016] [Accepted: 01/22/2016] [Indexed: 06/05/2023]
Abstract
A method to facilitate the characterization of stapled or cyclic peptides is reported via an arginine-selective derivatization strategy coupled with MS/MS analysis. Arginine residues are converted to ornithine residues through a deguanidination reaction that installs a highly selectively cleavable site in peptides. Upon activation by CID or UVPD, the ornithine residue cyclizes to promote cleavage of the adjacent amide bond. This Arg-specific process offers a unique strategy for site-selective ring opening of stapled and cyclic peptides. Upon activation of each derivatized peptide, site-specific backbone cleavage at the ornithine residue results in two complementary products: the lactam ring-containing portion of the peptide and the amine-containing portion. The deguanidination process not only provides a specific marker site that initiates fragmentation of the peptide but also offers a means to unlock the staple and differentiate isobaric stapled peptides.
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Affiliation(s)
| | - W Ryan Parker
- Department of Chemistry, University of Texas, Austin, TX, 78712, USA
| | - Zachary B Jenner
- Department of Chemistry and Biochemistry, Southwestern University, Georgetown, TX, 78626, USA
| | - Kerry A Bruns
- Department of Chemistry and Biochemistry, Southwestern University, Georgetown, TX, 78626, USA
| | - Lucas D Akin
- Department of Chemistry, University of Texas, Austin, TX, 78712, USA
| | - William M McGee
- Department of Chemistry, University of Texas, Austin, TX, 78712, USA
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