Improved Peak Detection and Deconvolution of Native Electrospray Mass Spectra from Large Protein Complexes

Journal of the American Society for Mass Spectrometry
Jonathan LuShenheng Guan

Abstract

Native electrospray-ionization mass spectrometry (native MS) measures biomolecules under conditions that preserve most aspects of protein tertiary and quaternary structure, enabling direct characterization of large intact protein assemblies. However, native spectra derived from these assemblies are often partially obscured by low signal-to-noise as well as broad peak shapes because of residual solvation and adduction after the electrospray process. The wide peak widths together with the fact that sequential charge state series from highly charged ions are closely spaced means that native spectra containing multiple species often suffer from high degrees of peak overlap or else contain highly interleaved charge envelopes. This situation presents a challenge for peak detection, correct charge state and charge envelope assignment, and ultimately extraction of the relevant underlying mass values of the noncovalent assemblages being investigated. In this report, we describe a comprehensive algorithm developed for addressing peak detection, peak overlap, and charge state assignment in native mass spectra, called PeakSeeker. Overlapped peaks are detected by examination of the second derivative of the raw mass spectrum. Charge state di...Continue Reading

References

Jan 8, 1999·Journal of the American Society for Mass Spectrometry·Z Zhang, A G Marshall
May 17, 2001·Analytical Chemistry·J R Engen, D L Smith
Jan 24, 2002·Proceedings of the National Academy of Sciences of the United States of America·David A BushnellRoger D Kornberg
Nov 26, 2003·Molecular Cell·Douglas E FeldmanJudith Frydman
Apr 1, 1951·Proceedings of the National Academy of Sciences of the United States of America·L PAULINGH R BRANSON
Jul 21, 2004·Mass Spectrometry Reviews·Albert J R Heck, Robert H H Van Den Heuvel
Oct 14, 2004·Journal of Mass Spectrometry : JMS·Lekha Sleno, Dietrich A Volmer
Dec 14, 2004·The Journal of Biological Chemistry·Karim-Jean ArmachePatrick Cramer
Jul 25, 2006·Rapid Communications in Mass Spectrometry : RCM·Bas van BreukelenRobert H H van den Heuvel
Aug 31, 2006·Journal of the American Chemical Society·Adam R McKayCarol V Robinson
Mar 3, 2007·Annual Review of Biochemistry·Michal Sharon, Carol V Robinson
Jun 13, 2008·Nature Protocols·Swapan S Jain, Thomas D Tullius
Dec 27, 2008·Journal of the American Society for Mass Spectrometry·Justin L P Benesch
Mar 3, 2011·Analytical Chemistry·Yao-Hsin TsengWen-Ping Peng
Mar 15, 2011·Physical Chemistry Chemical Physics : PCCP·Harry J SterlingEvan R Williams
Apr 19, 2011·International Journal of Mass Spectrometry·Sheng Yin, Joseph A Loo
Sep 29, 2011·Journal of the American Society for Mass Spectrometry·Harry J SterlingEvan R Williams
Dec 14, 2011·Journal of the American Society for Mass Spectrometry·Harry J SterlingEvan R Williams
May 29, 2012·Chemistry & Biology·Florian StengelJustin L P Benesch
Sep 27, 2012·Cell Stress & Chaperones·Kelly M KneeJonathan A King
Oct 16, 2012·Nature Methods·Rebecca J RoseAlbert J R Heck
Oct 17, 2012·Proceedings of the National Academy of Sciences of the United States of America·Philip J J RobinsonRoger D Kornberg
Mar 2, 2013·Angewandte Chemie·Joost SnijderAlbert J R Heck
Mar 26, 2013·Current Opinion in Structural Biology·Thomas WalzthoeniRuedi Aebersold
Apr 17, 2013·Proceedings of the National Academy of Sciences of the United States of America·Andrey DyachenkoMichal Sharon
Apr 23, 2013·Chemistry & Biology·Carrie ShiauDanica Galonić Fujimori
Jul 12, 2014·Annual Review of Analytical Chemistry·Joost Snijder, Albert J R Heck
Jul 1, 2013·International Journal of Mass Spectrometry·Ganesh N SivalingamKonstantinos Thalassinos

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Citations

Dec 8, 2015·Analytical Chemistry·Rian L Griffiths, Helen Jill Cooper
Nov 1, 2016·Journal of the American Society for Mass Spectrometry·Shengsheng Xu, Igor A Kaltashov
Mar 10, 2018·Rapid Communications in Mass Spectrometry : RCM·Guang XuJianjun Li
Apr 27, 2019·Journal of the American Society for Mass Spectrometry·Pavel I KitovJohn S Klassen
Jan 21, 2020·Essays in Biochemistry·Lauren Elizabeth Smith, Adelina Rogowska-Wrzesinska
Jul 15, 2020·Journal of Mass Spectrometry : JMS·Marie Barth, Carla Schmidt
Feb 26, 2020·Journal of Separation Science·Tijmen S BosBob W J Pirok
Aug 17, 2016·Proceedings of the National Academy of Sciences of the United States of America·Sisi LiSteven E Jacobsen
Nov 20, 2020·European Journal of Pharmaceutics and Biopharmaceutics : Official Journal of Arbeitsgemeinschaft Für Pharmazeutische Verfahrenstechnik E.V·Silvia Millán-MartínJonathan Bones
Mar 25, 2019·Methods : a Companion to Methods in Enzymology·Katlyn Hughes Burriss, Amber L Mosley
Apr 23, 2021·Journal of the American Society for Mass Spectrometry·Iain D G Campuzano, Wendy Sandoval
Jan 17, 2017·Journal of the American Society for Mass Spectrometry·Pengfei Li, Glen P Jackson
Apr 19, 2018·Journal of the American Society for Mass Spectrometry·Deseree J ReidMichael T Marty
Jul 14, 2018·Journal of the American Society for Mass Spectrometry·Sean P ClearyJames S Prell
Jul 22, 2021·Food & Function·Wenhua YangIgor A Kaltashov
Jan 30, 2018·Journal of Proteome Research·Marshall BernAlbert J R Heck
Sep 15, 2020·Journal of Proteome Research·Manuel David Peris-DíazArtur Krężel
Aug 21, 2021·Chemical Reviews·Sem TamaraAlbert J R Heck
Jul 11, 2020·Analytical Chemistry·Timothy M AllisonKonstantinos Thalassinos
Sep 3, 2021·Chemical Reviews·Amber D Rolland, James S Prell

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