Surface-Induced Dissociation of Protein Complexes in a Hybrid Fourier Transform Ion Cyclotron Resonance Mass Spectrometer
Abstract
Mass spectrometry continues to develop as a valuable tool in the analysis of proteins and protein complexes. In protein complex mass spectrometry studies, surface-induced dissociation (SID) has been successfully applied in quadrupole time-of-flight (Q-TOF) instruments. SID provides structural information on noncovalent protein complexes that is complementary to other techniques. However, the mass resolution of Q-TOF instruments can limit the information that can be obtained for protein complexes by SID. Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) provides ultrahigh resolution and ultrahigh mass accuracy measurements. Here in this study, an SID device was designed and successfully installed in a hybrid FT-ICR instrument in place of the standard gas collision cell. The SID-FT-ICR platform has been tested with several protein complex systems (homooligomers, a heterooligomer, and a protein-ligand complex, ranging from 53 to 85 kDa), and the results are consistent with data previously acquired on Q-TOF platforms, matching predictions from known protein interface information. Lastly, SID fragments with the same m/z but different charge states are well-resolved based on distinct spacing between adjacent isotope peaks, and the addition of metal cations and ligands can also be isotopically resolved with the ultrahigh mass resolution available in FT-ICR.
- Authors:
-
- The Ohio State Univ., Columbus, OH (United States). Dept. of Chemistry and Biochemistry
- Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab. (EMSL)
- Bruker Corp., Billerica, MA (United States)
- The Ohio State Univ., Columbus, OH (United States). OSU Mass Spectrometry and Proteomics Facility
- Ardara Technologies L.P., Ardara, PA (United States)
- Publication Date:
- Research Org.:
- Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
- Sponsoring Org.:
- National Science Foundation (NSF); USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH)
- OSTI Identifier:
- 1418480
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Analytical Chemistry
- Additional Journal Information:
- Journal Volume: 89; Journal Issue: 1; Journal ID: ISSN 0003-2700
- Publisher:
- American Chemical Society (ACS)
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
Citation Formats
Yan, Jing, Zhou, Mowei, Gilbert, Joshua D., Wolff, Jeremy J., Somogyi, Arpad, Pedder, Randall E., Quintyn, Royston S., Morrison, Lindsay J., Easterling, Michael L., Pasa-Tolic, Ljiljana, and Wysocki, Vicki H. Surface-Induced Dissociation of Protein Complexes in a Hybrid Fourier Transform Ion Cyclotron Resonance Mass Spectrometer. United States: N. p., 2016.
Web. doi:10.1021/acs.analchem.6b03986.
Yan, Jing, Zhou, Mowei, Gilbert, Joshua D., Wolff, Jeremy J., Somogyi, Arpad, Pedder, Randall E., Quintyn, Royston S., Morrison, Lindsay J., Easterling, Michael L., Pasa-Tolic, Ljiljana, & Wysocki, Vicki H. Surface-Induced Dissociation of Protein Complexes in a Hybrid Fourier Transform Ion Cyclotron Resonance Mass Spectrometer. United States. https://doi.org/10.1021/acs.analchem.6b03986
Yan, Jing, Zhou, Mowei, Gilbert, Joshua D., Wolff, Jeremy J., Somogyi, Arpad, Pedder, Randall E., Quintyn, Royston S., Morrison, Lindsay J., Easterling, Michael L., Pasa-Tolic, Ljiljana, and Wysocki, Vicki H. Fri .
"Surface-Induced Dissociation of Protein Complexes in a Hybrid Fourier Transform Ion Cyclotron Resonance Mass Spectrometer". United States. https://doi.org/10.1021/acs.analchem.6b03986. https://www.osti.gov/servlets/purl/1418480.
@article{osti_1418480,
title = {Surface-Induced Dissociation of Protein Complexes in a Hybrid Fourier Transform Ion Cyclotron Resonance Mass Spectrometer},
author = {Yan, Jing and Zhou, Mowei and Gilbert, Joshua D. and Wolff, Jeremy J. and Somogyi, Arpad and Pedder, Randall E. and Quintyn, Royston S. and Morrison, Lindsay J. and Easterling, Michael L. and Pasa-Tolic, Ljiljana and Wysocki, Vicki H.},
abstractNote = {Mass spectrometry continues to develop as a valuable tool in the analysis of proteins and protein complexes. In protein complex mass spectrometry studies, surface-induced dissociation (SID) has been successfully applied in quadrupole time-of-flight (Q-TOF) instruments. SID provides structural information on noncovalent protein complexes that is complementary to other techniques. However, the mass resolution of Q-TOF instruments can limit the information that can be obtained for protein complexes by SID. Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) provides ultrahigh resolution and ultrahigh mass accuracy measurements. Here in this study, an SID device was designed and successfully installed in a hybrid FT-ICR instrument in place of the standard gas collision cell. The SID-FT-ICR platform has been tested with several protein complex systems (homooligomers, a heterooligomer, and a protein-ligand complex, ranging from 53 to 85 kDa), and the results are consistent with data previously acquired on Q-TOF platforms, matching predictions from known protein interface information. Lastly, SID fragments with the same m/z but different charge states are well-resolved based on distinct spacing between adjacent isotope peaks, and the addition of metal cations and ligands can also be isotopically resolved with the ultrahigh mass resolution available in FT-ICR.},
doi = {10.1021/acs.analchem.6b03986},
journal = {Analytical Chemistry},
number = 1,
volume = 89,
place = {United States},
year = {Fri Dec 02 00:00:00 EST 2016},
month = {Fri Dec 02 00:00:00 EST 2016}
}
Web of Science
Works referenced in this record:
Protein complexes and functional modules in molecular networks
journal, September 2003
- Spirin, V.; Mirny, L. A.
- Proceedings of the National Academy of Sciences, Vol. 100, Issue 21
The molecular sociology of the cell
journal, December 2007
- Robinson, Carol V.; Sali, Andrej; Baumeister, Wolfgang
- Nature, Vol. 450, Issue 7172
How far can we go with structural mass spectrometry of protein complexes?
journal, April 2010
- Sharon, Michal
- Journal of the American Society for Mass Spectrometry, Vol. 21, Issue 4
Electrospray ionization mass spectrometry: a technology for studying noncovalent macromolecular complexes
journal, December 2000
- Loo, Joseph A.
- International Journal of Mass Spectrometry, Vol. 200, Issue 1-3
Native mass spectrometry: a bridge between interactomics and structural biology
journal, October 2008
- Heck, Albert J. R.
- Nature Methods, Vol. 5, Issue 11
Mass spectrometry of macromolecular assemblies: preservation and dissociation
journal, April 2006
- Benesch, Justin LP; Robinson, Carol V.
- Current Opinion in Structural Biology, Vol. 16, Issue 2
ETD Allows for Native Surface Mapping of a 150 kDa Noncovalent Complex on a Commercial Q-TWIMS-TOF Instrument
journal, January 2014
- Lermyte, Frederik; Konijnenberg, Albert; Williams, Jonathan P.
- Journal of The American Society for Mass Spectrometry, Vol. 25, Issue 3
Native Top-Down Electrospray Ionization-Mass Spectrometry of 158 kDa Protein Complex by High-Resolution Fourier Transform Ion Cyclotron Resonance Mass Spectrometry
journal, December 2013
- Li, Huilin; Wolff, Jeremy J.; Van Orden, Steve L.
- Analytical Chemistry, Vol. 86, Issue 1
Surface Induced Dissociation: Dissecting Noncovalent Protein Complexes in the Gas phase
journal, February 2014
- Zhou, Mowei; Wysocki, Vicki H.
- Accounts of Chemical Research, Vol. 47, Issue 4
193 nm Ultraviolet Photodissociation Mass Spectrometry of Tetrameric Protein Complexes Provides Insight into Quaternary and Secondary Protein Topology
journal, August 2016
- Morrison, Lindsay J.; Brodbelt, Jennifer S.
- Journal of the American Chemical Society, Vol. 138, Issue 34
Symmetry of Charge Partitioning in Collisional and UV Photon-Induced Dissociation of Protein Assemblies
journal, August 2016
- Tamara, Sem; Dyachenko, Andrey; Fort, Kyle L.
- Journal of the American Chemical Society, Vol. 138, Issue 34
Tandem Mass Spectrometry Reveals the Quaternary Organization of Macromolecular Assemblies
journal, June 2006
- Benesch, Justin L. P.; Aquilina, J. Andrew; Ruotolo, Brandon T.
- Chemistry & Biology, Vol. 13, Issue 6
Ion Activation Methods for Peptides and Proteins
journal, December 2015
- Brodbelt, Jennifer S.
- Analytical Chemistry, Vol. 88, Issue 1
Surface-Induced Dissociation of Homotetramers with D2 Symmetry Yields their Assembly Pathways and Characterizes the Effect of Ligand Binding
journal, May 2015
- Quintyn, Royston S.; Yan, Jing; Wysocki, Vicki H.
- Chemistry & Biology, Vol. 22, Issue 5
Surface-Induced Dissociation Mass Spectra as a Tool for Distinguishing Different Structural Forms of Gas-Phase Multimeric Protein Complexes
journal, November 2015
- Quintyn, Royston S.; Zhou, Mowei; Yan, Jing
- Analytical Chemistry, Vol. 87, Issue 23
Surface-Induced Dissociation of Peptides and Protein Complexes in a Quadrupole/Time-of-Flight Mass Spectrometer
journal, March 2008
- Galhena, Asiri S.; Dagan, Shai; Jones, Christopher M.
- Analytical Chemistry, Vol. 80, Issue 5
Surface-Induced Dissociation of Ion Mobility-Separated Noncovalent Complexes in a Quadrupole/Time-of-Flight Mass Spectrometer
journal, June 2012
- Zhou, Mowei; Huang, Chengsi; Wysocki, Vicki H.
- Analytical Chemistry, Vol. 84, Issue 14
Boundaries of Mass Resolution in Native Mass Spectrometry
journal, April 2014
- Lössl, Philip; Snijder, Joost; Heck, Albert J. R.
- Journal of The American Society for Mass Spectrometry, Vol. 25, Issue 6
Fourier transform ion cyclotron resonance cell with dynamic harmonization of the electric field in the whole volume by shaping of the excitation and detection electrode assembly
journal, December 2010
- Boldin, Ivan A.; Nikolaev, Eugene N.
- Rapid Communications in Mass Spectrometry, Vol. 25, Issue 1
Initial Experimental Characterization of a New Ultra-High Resolution FTICR Cell with Dynamic Harmonization
journal, April 2011
- Nikolaev, Eugene N.; Boldin, Ivan A.; Jertz, Roland
- Journal of The American Society for Mass Spectrometry, Vol. 22, Issue 7
From Supercomputer Modeling to Highest Mass Resolution in FT-ICR
journal, January 2013
- N. Nikolaev, Evgene; N. Vladimirov, Gleb; Jertz, Roland
- Mass Spectrometry, Vol. 2, Issue Special_Issue
Native Electrospray Mass Spectrometry Reveals the Nature and Stoichiometry of Pigments in the FMO Photosynthetic Antenna Protein
journal, May 2011
- Wen, Jianzhong; Zhang, Hao; Gross, Michael L.
- Biochemistry, Vol. 50, Issue 17
Surface-Induced Dissociation in a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer: Instrument Design and Evaluation
journal, July 2002
- Laskin, Julia; Denisov, Eduard V.; Shukla, Anil K.
- Analytical Chemistry, Vol. 74, Issue 14
Surface-induced dissociation of peptide ions: Kinetics and dynamics
journal, December 2003
- Laskin, Julia; Futrell, Jean H.
- Journal of the American Society for Mass Spectrometry, Vol. 14, Issue 12
Protein identification via surface-induced dissociation in an FT-ICR mass spectrometer and a patchwork sequencing approach
journal, May 2006
- Fernandez, Facundo M.; Wysocki, Vicki H.; Futrell, Jean H.
- Journal of the American Society for Mass Spectrometry, Vol. 17, Issue 5
Surface-induced dissociation of peptide ions in Fourier-transform mass spectrometry
journal, September 1990
- Williams, Evan R.; Henry, Kent D.; McLafferty, Fred W.
- Journal of the American Society for Mass Spectrometry, Vol. 1, Issue 5
Peptide amino acid sequence analysis using matrix-assisted laser desorption/ionization and fourier transform mass spectrometry
journal, January 1995
- Castoro, John A.; Wilkins, Charles L.; Woods, Amina S.
- Journal of Mass Spectrometry, Vol. 30, Issue 1
Influence of Secondary Structure on the Fragmentation of Protonated Peptides
journal, June 1999
- Tsaprailis, George; Nair, Hari; Somogyi, Árpád
- Journal of the American Chemical Society, Vol. 121, Issue 22
Improved ion extraction from a linear octopole ion trap: SIMION analysis and experimental demonstration
journal, November 2002
- Wilcox, Bruce E.; Hendrickson, Christopher L.; Marshall, Alan G.
- Journal of the American Society for Mass Spectrometry, Vol. 13, Issue 11
Novel Linac II Electrode Geometry for Creating An Axial Field in a Multipole Ion Guide
journal, December 2000
- Loboda, Alexander; Krutchinsky, Andrew; Loboda, Olga
- European Journal of Mass Spectrometry, Vol. 6, Issue 6
Analytical performance of a high-pressure radio frequency-only quadrupole collision cell with an axial field applied by using conical rods
journal, August 1998
- Mansoori, Bashir A.; Dyer, Edward W.; Lock, Christopher M.
- Journal of the American Society for Mass Spectrometry, Vol. 9, Issue 8
The Alpha Subunit of Nitrile Hydratase Is Sufficient for Catalytic Activity and Post-Translational Modification
journal, June 2014
- Nelp, Micah T.; Astashkin, Andrei V.; Breci, Linda A.
- Biochemistry, Vol. 53, Issue 24
Refining the Structural Model of a Heterohexameric Protein Complex: Surface Induced Dissociation and Ion Mobility Provide Key Connectivity and Topology Information
journal, November 2015
- Song, Yang; Nelp, Micah T.; Bandarian, Vahe
- ACS Central Science, Vol. 1, Issue 9
Inference of Macromolecular Assemblies from Crystalline State
journal, September 2007
- Krissinel, Evgeny; Henrick, Kim
- Journal of Molecular Biology, Vol. 372, Issue 3
Dissociation of tetrameric ions of noncovalent streptavidin complexes formed by electrospray ionization
journal, June 1995
- Schwartz, Brenda L.; Bruce, James E.; Anderson, Gordon A.
- Journal of the American Society for Mass Spectrometry, Vol. 6, Issue 6
The Role of Salt Bridges, Charge Density, and Subunit Flexibility in Determining Disassembly Routes of Protein Complexes
journal, August 2013
- Hall, Zoe; Hernández, Helena; Marsh, Joseph A.
- Structure, Vol. 21, Issue 8
Collision-Induced Dissociation of Electrosprayed Protein Complexes: An All-Atom Molecular Dynamics Model with Mobile Protons
journal, May 2016
- Popa, Vlad; Trecroce, Danielle A.; McAllister, Robert G.
- The Journal of Physical Chemistry B, Vol. 120, Issue 23
Works referencing / citing this record:
Radical solutions: Principles and application of electron-based dissociation in mass spectrometry-based analysis of protein structure
journal, February 2018
- Lermyte, Frederik; Valkenborg, Dirk; Loo, Joseph A.
- Mass Spectrometry Reviews, Vol. 37, Issue 6
Surface Induced Dissociation Coupled with High Resolution Mass Spectrometry Unveils Heterogeneity of a 211 kDa Multicopper Oxidase Protein Complex
journal, January 2018
- Zhou, Mowei; Yan, Jing; Romano, Christine A.
- Journal of The American Society for Mass Spectrometry, Vol. 29, Issue 4
Experimental and theoretical investigation of overall energy deposition in surface-induced unfolding of protein ions
journal, January 2019
- Donor, Micah T.; Mroz, Austin M.; Prell, James S.
- Chemical Science, Vol. 10, Issue 14
Experimental and theoretical investigation of overall energy deposition in surface-induced unfolding of protein ions
journal, January 2019
- Donor, Micah T.; Mroz, Austin M.; Prell, James S.
- Chemical Science, Vol. 10, Issue 14