Top-down mass spectrometry and assigning internal fragments for determining disulfide bond positions in proteins

Wei, Benqian; Zenaidee, Muhammad A.; Lantz, Carter; Williams, Brad J.; Totten, Sarah; Ogorzalek Loo, Rachel R.; Loo, Joseph A.

doi:10.1039/d2an01517j

Top-down mass spectrometry and assigning internal fragments for determining disulfide bond positions in proteins

Journal Article · Mon Nov 14 00:00:00 EST 2022 · Analyst

DOI:https://doi.org/10.1039/d2an01517j· OSTI ID:2418844

^[1]; Zenaidee, Muhammad A. ^[2]; Lantz, Carter ^[3]; Williams, Brad J. ^[4]; Totten, Sarah ^[4]; Ogorzalek Loo, Rachel R. ^[3]; ^[3]

Univ. of California, Los Angeles, CA (United States); OSTI
Univ. of California, Los Angeles, CA (United States); Macquarie Univ., NSW (Australia)
Univ. of California, Los Angeles, CA (United States)
Waters Corporation, Milford, MA (United States)

Disulfide bonds in proteins have a substantial impact on protein structure, stability, and biological activity. Localizing disulfide bonds is critical for understanding protein folding and higher-order structure. Conventional top-down mass spectrometry (TD-MS), where only terminal fragments are assigned for disulfide-intact proteins, can access disulfide information, but suffers from low fragmentation efficiency, thereby limiting sequence coverage. Here, we show that assigning internal fragments generated from TD-MS enhances the sequence coverage of disulfide-intact proteins by 20–60% by returning information from the interior of the protein sequence, which cannot be obtained by terminal fragments alone. Further, the inclusion of internal fragments can extend the sequence information of disulfide-intact proteins to near complete sequence coverage. Importantly, the enhanced sequence information that arise from the assignment of internal fragments can be used to determine the relative position of disulfide bonds and the exact disulfide connectivity between cysteines. The data presented here demonstrates the benefits of incorporating internal fragment analysis into the TD-MS workflow for analyzing disulfide-intact proteins, which would be valuable for characterizing biotherapeutic proteins such as monoclonal antibodies and antibody–drug conjugates.

View Accepted Manuscript (DOE)

Research Organization:: Univ. of California, Los Angeles, CA (United States)

Sponsoring Organization:: National Institutes of Health (NIH); National Science Foundation (NSF); USDOE; USDOE Office of Science (SC)

Grant/Contract Number:: FC02-02ER63421

OSTI ID:: 2418844

Alternate ID(s):: OSTI ID: 1898958

Journal Information:: Analyst, Journal Name: Analyst Journal Issue: 1 Vol. 148; ISSN 0003-2654

Publisher:: Royal Society of ChemistryCopyright Statement

Country of Publication:: United States

Language:: English

References (68)

Facile Disulfide Bond Cleavage in Gaseous Peptide and Protein Cations by Ultraviolet Photodissociation at 157 nm Fung, Y. M. Eva; Kjeldsen, Frank; Silivra, Oleg A. Angewandte Chemie International Edition, Vol. 44, Issue 39 https://doi.org/10.1002/anie.200501533	journal	October 2005
Top‐down mass spectrometry of intact phosphorylated β‐casein: Correlation between the precursor charge state and internal fragments Chen, Jianzhong; Shiyanov, Pavel; Green, Kari B. Journal of Mass Spectrometry, Vol. 54, Issue 6 https://doi.org/10.1002/jms.4364	journal	May 2019
Protein disulfide bond determination by mass spectrometry Gorman, Jeffrey J.; Wallis, Tristan P.; Pitt, James J. Mass Spectrometry Reviews, Vol. 21, Issue 3 https://doi.org/10.1002/mas.10025	journal	May 2002
Does Electron Capture Dissociation Cleave Protein Disulfide Bonds? Ganisl, Barbara; Breuker, Kathrin ChemistryOpen, Vol. 1, Issue 6 https://doi.org/10.1002/open.201200038	journal	November 2012
High throughput screening of disulfide-containing proteins in a complex mixture Zhao, Dong S.; Gregorich, Zachery R.; Ge, Ying PROTEOMICS, Vol. 13, Issue 22 https://doi.org/10.1002/pmic.201300242	journal	October 2013
Electron Transfer Dissociation (ETD) of Peptides Containing Intrachain Disulfide Bonds Cole, Scott R.; Ma, Xiaoxiao; Zhang, Xinrong Journal of The American Society for Mass Spectrometry, Vol. 23, Issue 2 https://doi.org/10.1007/s13361-011-0300-z	journal	December 2011
On-Line Electrochemical Reduction of Disulfide Bonds: Improved FTICR-CID and -ETD Coverage of Oxytocin and Hepcidin Nicolardi, Simone; Giera, Martin; Kooijman, Pieter Journal of the American Society for Mass Spectrometry, Vol. 24, Issue 12 https://doi.org/10.1007/s13361-013-0725-7	journal	September 2013
Analyzing Internal Fragmentation of Electrosprayed Ubiquitin Ions During Beam-Type Collisional Dissociation Durbin, Kenneth R.; Skinner, Owen S.; Fellers, Ryan T. Journal of The American Society for Mass Spectrometry, Vol. 26, Issue 5 https://doi.org/10.1007/s13361-015-1078-1	journal	February 2015
The Ups and Downs of Repeated Cleavage and Internal Fragment Production in Top-Down Proteomics Lyon, Yana A.; Riggs, Dylan; Fornelli, Luca Journal of The American Society for Mass Spectrometry, Vol. 29, Issue 1 https://doi.org/10.1007/s13361-017-1823-8	journal	October 2017
Directed-Backbone Dissociation Following Bond-Specific Carbon-Sulfur UVPD at 213 nm Talbert, Lance E.; Julian, Ryan R. Journal of the American Society for Mass Spectrometry, Vol. 29, Issue 9 https://doi.org/10.1007/s13361-018-1934-x	journal	April 2018
Top or Middle? Up or Down? Toward a Standard Lexicon for Protein Top-Down and Allied Mass Spectrometry Approaches Lermyte, Frederik; Tsybin, Yury O.; O’Connor, Peter B. Journal of The American Society for Mass Spectrometry, Vol. 30, Issue 7 https://doi.org/10.1007/s13361-019-02201-x	journal	May 2019
Sequential mass spectrometry applied to the study of the formation of “internal” fragment ions of protonated peptides Ballard, Kevin D.; Gaskell, Simon J. International Journal of Mass Spectrometry and Ion Processes, Vol. 111 https://doi.org/10.1016/0168-1176(91)85054-P	journal	December 1991
Characterization of disulfide linkages and disulfide bond scrambling in recombinant human macrophage colony stimulating factor by fast-atom bombardment mass spectrometry of enzymatic digests Glocker, M. O.; Arbogast, B.; Deinzer, M. L. Journal of the American Society for Mass Spectrometry, Vol. 6, Issue 8 https://doi.org/10.1016/1044-0305(95)00250-H	journal	August 1995
Complete disulfide bond assignment of a recombinant immunoglobulin G4 monoclonal antibody Zhang, Wei; Marzilli, Lisa A.; Rouse, Jason C. Analytical Biochemistry, Vol. 311, Issue 1 https://doi.org/10.1016/S0003-2697(02)00394-9	journal	December 2002
Disulfide bonds as switches for protein function Hogg, Philip J. Trends in Biochemical Sciences, Vol. 28, Issue 4 https://doi.org/10.1016/S0968-0004(03)00057-4	journal	April 2003
Picomole-level mapping of protein disulfides by mass spectrometry following partial reduction and alkylation Foley, Susan F.; Sun, Yaping; Zheng, Timothy S. Analytical Biochemistry, Vol. 377, Issue 1 https://doi.org/10.1016/j.ab.2008.02.025	journal	June 2008
Towards understanding the formation of internal fragments generated by collisionally activated dissociation for top-down mass spectrometry Wei, Benqian; Zenaidee, Muhammad A.; Lantz, Carter Analytica Chimica Acta, Vol. 1194 https://doi.org/10.1016/j.aca.2021.339400	journal	February 2022
Top Down proteomics: Facts and perspectives Catherman, Adam D.; Skinner, Owen S.; Kelleher, Neil L. Biochemical and Biophysical Research Communications, Vol. 445, Issue 4 https://doi.org/10.1016/j.bbrc.2014.02.041	journal	March 2014
Disulfide bond formation and its impact on the biological activity and stability of recombinant therapeutic proteins produced by Escherichia coli expression system Zhang, Lin; Chou, C. Perry; Moo-Young, Murray Biotechnology Advances, Vol. 29, Issue 6 https://doi.org/10.1016/j.biotechadv.2011.07.013	journal	November 2011
Is it biologically relevant to measure the structures of small peptides in the gas-phase? Barran, Perdita E.; Polfer, Nick C.; Campopiano, Dominic J. International Journal of Mass Spectrometry, Vol. 240, Issue 3 https://doi.org/10.1016/j.ijms.2004.09.013	journal	February 2005
Increasing fragmentation of disulfide-bonded proteins for top–down mass spectrometry by supercharging Zhang, Jiang; Loo, Rachel R. Ogorzalek; Loo, Joseph A. International Journal of Mass Spectrometry, Vol. 377 https://doi.org/10.1016/j.ijms.2014.07.047	journal	February 2015
Enhancing protein disulfide bond cleavage by UV excitation and electron capture dissociation for top-down mass spectrometry Wongkongkathep, Piriya; Li, Huilin; Zhang, Xing International Journal of Mass Spectrometry, Vol. 390 https://doi.org/10.1016/j.ijms.2015.07.008	journal	November 2015
Towards understanding the tandem mass spectra of protonated oligopeptides. 1: Mechanism of amide bond cleavage Paizs, Béla.; Suhai, Sándor Journal of the American Society for Mass Spectrometry, Vol. 15, Issue 1 https://doi.org/10.1016/j.jasms.2003.09.010	journal	January 2004
A novel salt bridge mechanism highlights the need for nonmobile proton conditions to promote disulfide bond cleavage in protonated peptides under low-energy collisional activation Lioe, Hadi; OrsHair, Richard A. J. Journal of the American Society for Mass Spectrometry, Vol. 18, Issue 6 https://doi.org/10.1016/j.jasms.2007.03.003	journal	June 2007
Structural characterization of intact proteins is enhanced by prevalent fragmentation pathways rarely observed for peptides Cobb, Jennifer S.; Easterling, Michael L.; Agar, Jeffrey N. Journal of the American Society for Mass Spectrometry, Vol. 21, Issue 6 https://doi.org/10.1016/j.jasms.2010.02.009	journal	June 2010
Tracking internal and external ions for constrained peptides leads to enhanced sequence coverage and disulfide bond deciphering Chin, Steven; Chen, Tao; Hannoush, Rami N. Journal of Pharmaceutical and Biomedical Analysis, Vol. 195 https://doi.org/10.1016/j.jpba.2021.113893	journal	February 2021
Mass spectrometry of peptides and proteins Wysocki, Vicki H.; Resing, Katheryn A.; Zhang, Qingfen Methods, Vol. 35, Issue 3 https://doi.org/10.1016/j.ymeth.2004.08.013	journal	March 2005
Localization of Intramolecular Monosulfide Bridges in Lantibiotics Determined with Electron Capture Induced Dissociation Kleinnijenhuis, Anne J.; Duursma, Marc C.; Breukink, Eefjan Analytical Chemistry, Vol. 75, Issue 13 https://doi.org/10.1021/ac0263770	journal	May 2003
Top-Down Characterization of a Native Highly Intralinked Protein: Concurrent Cleavages of Disulfide and Protein Backbone Bonds Chen, Jianzhong; Shiyanov, Pavel; Zhang, Liwen Analytical Chemistry, Vol. 82, Issue 14 https://doi.org/10.1021/ac1006766	journal	June 2010
Resolving Disulfide Structural Isoforms of IgG2 Monoclonal Antibodies by Ion Mobility Mass Spectrometry Bagal, Dhanashri; Valliere-Douglass, John F.; Balland, Alain Analytical Chemistry, Vol. 82, Issue 16 https://doi.org/10.1021/ac1013139	journal	August 2010
Direct Elucidation of Disulfide Bond Partners Using Ultraviolet Photodissociation Mass Spectrometry Agarwal, Arun; Diedrich, Jolene K.; Julian, Ryan R. Analytical Chemistry, Vol. 83, Issue 17 https://doi.org/10.1021/ac201650v	journal	August 2011
PADLOC: A Powerful Tool to Assign Disulfide Bond Connectivities in Peptides and Proteins by NMR Spectroscopy Poppe, Leszek; Hui, John O.; Ligutti, Joseph Analytical Chemistry, Vol. 84, Issue 1 https://doi.org/10.1021/ac203078x	journal	December 2011
Electrochemistry-Assisted Top-Down Characterization of Disulfide-Containing Proteins Zhang, Yun; Cui, Weidong; Zhang, Hao Analytical Chemistry, Vol. 84, Issue 8, p. 3838-3842 https://doi.org/10.1021/ac300106y	journal	April 2012
Mass Spectrometric Determination of Disulfide Linkages in Recombinant Therapeutic Proteins Using Online LC−MS with Electron-Transfer Dissociation Wu, Shiaw-Lin; Jiang, Haitao; Lu, Qiaozhen Analytical Chemistry, Vol. 81, Issue 1 https://doi.org/10.1021/ac801560k	journal	January 2009
Mass Spectrometric Sequencing of Proteins from Silver-Stained Polyacrylamide Gels Shevchenko, Andrej; Wilm, Matthias; Vorm, Ole Analytical Chemistry, Vol. 68, Issue 5 https://doi.org/10.1021/ac950914h	journal	January 1996
Increasing Top-Down Mass Spectrometry Sequence Coverage by an Order of Magnitude through Optimized Internal Fragment Generation and Assignment Schmitt, Nicholas D.; Berger, Joshua M.; Conway, Jeremy B. Analytical Chemistry, Vol. 93, Issue 16 https://doi.org/10.1021/acs.analchem.0c04670	journal	April 2021
Disulfide Linkage Characterization of Disulfide Bond-Containing Proteins and Peptides by Reducing Electrochemistry and Mass Spectrometry Cramer, Christian N.; Haselmann, Kim F.; Olsen, Jesper V. Analytical Chemistry, Vol. 88, Issue 3 https://doi.org/10.1021/acs.analchem.5b03148	journal	January 2016
Structural Characterization of Native Proteins and Protein Complexes by Electron Ionization Dissociation-Mass Spectrometry Li, Huilin; Sheng, Yuewei; McGee, William Analytical Chemistry, Vol. 89, Issue 5 https://doi.org/10.1021/acs.analchem.6b02377	journal	February 2017
Determination of the Disulfide Structure of Murine Meteorin, a Neurotrophic Factor, by LC–MS and Electron Transfer Dissociation-High-Energy Collisional Dissociation Analysis of Proteolytic Fragments Wen, Dingyi; Xiao, Yongsheng; Vecchi, Malgorzata M. Analytical Chemistry, Vol. 89, Issue 7 https://doi.org/10.1021/acs.analchem.6b04600	journal	March 2017
Complete Mapping of Complex Disulfide Patterns with Closely-Spaced Cysteines by In-Source Reduction and Data-Dependent Mass Spectrometry Cramer, Christian N.; Kelstrup, Christian D.; Olsen, Jesper V. Analytical Chemistry, Vol. 89, Issue 11 https://doi.org/10.1021/acs.analchem.7b00424	journal	May 2017
Top-Down Characterization of Proteins with Intact Disulfide Bonds Using Activated-Ion Electron Transfer Dissociation Rush, Matthew J. P.; Riley, Nicholas M.; Westphall, Michael S. Analytical Chemistry, Vol. 90, Issue 15 https://doi.org/10.1021/acs.analchem.8b01113	journal	June 2018
Characterization of Disulfide Linkages in Proteins by 193 nm Ultraviolet Photodissociation (UVPD) Mass Spectrometry Quick, M. Montana; Crittenden, Christopher M.; Rosenberg, Jake A. Analytical Chemistry, Vol. 90, Issue 14 https://doi.org/10.1021/acs.analchem.8b01556	journal	June 2018
All Ion Differential Analysis Refines the Detection of Terminal and Internal Diagnostic Fragment Ions for the Characterization of Biologics Product-Related Variants and Impurities by Middle-down Mass Spectrometry Griaud, François; Denefeld, Blandine; Kao-Scharf, Chi-Ya Analytical Chemistry, Vol. 91, Issue 14 https://doi.org/10.1021/acs.analchem.8b05886	journal	June 2019
Direct Determination of Antibody Chain Pairing by Top-down and Middle-down Mass Spectrometry Using Electron Capture Dissociation and Ultraviolet Photodissociation Shaw, Jared B.; Liu, Weijing; Vasil′ev, Yury V. Analytical Chemistry, Vol. 92, Issue 1 https://doi.org/10.1021/acs.analchem.9b03129	journal	November 2019
ClipsMS: An Algorithm for Analyzing Internal Fragments Resulting from Top-Down Mass Spectrometry Lantz, Carter; Zenaidee, Muhammad A.; Wei, Benqian Journal of Proteome Research, Vol. 20, Issue 4 https://doi.org/10.1021/acs.jproteome.0c00952	journal	March 2021
Internal Fragment Ions Disambiguate and Increase Identifications in Top-Down Proteomics Rolfs, Zach; Smith, Lloyd M. Journal of Proteome Research, Vol. 20, Issue 12 https://doi.org/10.1021/acs.jproteome.1c00599	journal	November 2021
Direct Ultraviolet Laser-Induced Reduction of Disulfide Bonds in Insulin and Vasopressin Gammelgaard, Simon K.; Petersen, Steffen B.; Haselmann, Kim F. ACS Omega, Vol. 5, Issue 14 https://doi.org/10.1021/acsomega.9b04375	journal	April 2020
Bridging Disulfides for Stable and Defined Antibody Drug Conjugates Badescu, George; Bryant, Penny; Bird, Matthew Bioconjugate Chemistry, Vol. 25, Issue 6 https://doi.org/10.1021/bc500148x	journal	May 2014
Disulfide Bonds and Protein Folding ^† Wedemeyer, William J.; Welker, Ervin; Narayan, Mahesh Biochemistry, Vol. 39, Issue 15 https://doi.org/10.1021/bi992922o	journal	April 2000
Multifaceted Roles of Disulfide Bonds. Peptides as Therapeutics Góngora-Benítez, Miriam; Tulla-Puche, Judit; Albericio, Fernando Chemical Reviews, Vol. 114, Issue 2 https://doi.org/10.1021/cr400031z	journal	October 2013
NMR-Based Mapping of Disulfide Bridges in Cysteine-Rich Peptides: Application to the μ-Conotoxin SxIIIA Walewska, Aleksandra; Skalicky, Jack J.; Davis, Darrell R. Journal of the American Chemical Society, Vol. 130, Issue 43 https://doi.org/10.1021/ja804303p	journal	October 2008
Electron Capture Dissociation of Gaseous Multiply-Charged Proteins Is Favored at Disulfide Bonds and Other Sites of High Hydrogen Atom Affinity Zubarev, Roman A.; Kruger, Nathan A.; Fridriksson, Einar K. Journal of the American Chemical Society, Vol. 121, Issue 12 https://doi.org/10.1021/ja981948k	journal	March 1999
Internal Fragments Generated by Electron Ionization Dissociation Enhance Protein Top-Down Mass Spectrometry Zenaidee, Muhammad A.; Lantz, Carter; Perkins, Taylor Journal of the American Society for Mass Spectrometry, Vol. 31, Issue 9 https://doi.org/10.1021/jasms.0c00160	journal	August 2020
Characterization of Insulin Dimers by Top-Down Mass Spectrometry Gammelgaard, Simon K.; Petersen, Steffen B.; Haselmann, Kim F. Journal of the American Society for Mass Spectrometry, Vol. 32, Issue 8 https://doi.org/10.1021/jasms.0c00257	journal	October 2020
Internal Fragments Generated from Different Top-Down Mass Spectrometry Fragmentation Methods Extend Protein Sequence Coverage Zenaidee, Muhammad A.; Wei, Benqian; Lantz, Carter Journal of the American Society for Mass Spectrometry, Vol. 32, Issue 7 https://doi.org/10.1021/jasms.1c00113	journal	June 2021
High-Resolution IMS–MS to Assign Additional Disulfide Bridge Pairing in Complementarity-Determining Regions of an IgG4 Monoclonal Antibody Deslignière, Evolène; Botzanowski, Thomas; Diemer, Hélène Journal of the American Society for Mass Spectrometry, Vol. 32, Issue 10 https://doi.org/10.1021/jasms.1c00151	journal	August 2021
Online Mass Spectrometric Analysis of Proteins/Peptides Following Electrolytic Cleavage of Disulfide Bonds Zhang, Yun; Dewald, Howard D.; Chen, Hao Journal of Proteome Research, Vol. 10, Issue 3 https://doi.org/10.1021/pr101053q	journal	February 2011
A Systematic Investigation into the Nature of Tryptic HCD Spectra Michalski, Annette; Neuhauser, Nadin; Cox, Jürgen Journal of Proteome Research, Vol. 11, Issue 11 https://doi.org/10.1021/pr3007045	journal	October 2012
Substantial increase of protein stability by multiple disulphide bonds Matsumura, Masazumi; Signor, Giovanni; Matthews, Brian W. Nature, Vol. 342, Issue 6247 https://doi.org/10.1038/342291a0	journal	November 1989
An integrated native mass spectrometry and top-down proteomics method that connects sequence to structure and function of macromolecular complexes Li, Huilin; Nguyen, Hong Hanh; Ogorzalek Loo, Rachel R. Nature Chemistry, Vol. 10, Issue 2 https://doi.org/10.1038/nchem.2908	journal	January 2018
Mass spectrometry–based proteomics turns quantitative Ong, Shao-En; Mann, Matthias Nature Chemical Biology, Vol. 1, Issue 5 https://doi.org/10.1038/nchembio736	journal	September 2005
Decoding protein modifications using top-down mass spectrometry Siuti, Nertila; Kelleher, Neil L. Nature Methods, Vol. 4, Issue 10 https://doi.org/10.1038/nmeth1097	journal	September 2007
Simplified identification of disulfide, trisulfide, and thioether pairs with 213 nm UVPD Bonner, James; Talbert, Lance E.; Akkawi, Nicholas The Analyst, Vol. 143, Issue 21 https://doi.org/10.1039/C8AN01582A	journal	January 2018
Human IgG2 Antibodies Display Disulfide-mediated Structural Isoforms Wypych, Jette; Li, Ming; Guo, Amy Journal of Biological Chemistry, Vol. 283, Issue 23 https://doi.org/10.1074/jbc.M709987200	journal	March 2008
Progress in Top-Down Proteomics and the Analysis of Proteoforms Toby, Timothy K.; Fornelli, Luca; Kelleher, Neil L. Annual Review of Analytical Chemistry, Vol. 9, Issue 1 https://doi.org/10.1146/annurev-anchem-071015-041550	journal	June 2016
Mass spectrometry-based strategies for protein disulfide bond identification Tsai, Pei Lun; Chen, Sung-Fang; Huang, Sheng Yu Reviews in Analytical Chemistry, Vol. 32, Issue 4 https://doi.org/10.1515/revac-2013-0011	journal	January 2013
Advanced mass spectrometry workflows for analyzing disulfide bonds in biologics Wiesner, Jan; Resemann, Anja; Evans, Catherine Expert Review of Proteomics, Vol. 12, Issue 2 https://doi.org/10.1586/14789450.2015.1018896	journal	February 2015
The Role of Thiols and Disulfides on Protein Stability Trivedi, Maulik; Laurence, Jennifer; Siahaan, Teruna Current Protein & Peptide Science, Vol. 10, Issue 6 https://doi.org/10.2174/138920309789630534	journal	December 2009

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