High-performance hybrid Orbitrap mass spectrometers for quantitative proteome analysis: Observations and implications

Proteomics
James C WilliamsonMartin R Larsen

Abstract

We present basic workups and quantitative comparisons for two current generation Orbitrap mass spectrometers, the Q Exactive Plus and Orbitrap Fusion Tribrid, which are widely considered two of the highest performing instruments on the market. We assessed the performance of two quantitative methods on both instruments, namely label-free quantitation and stable isotope labeling using isobaric tags, for studying the heat shock response in Escherichia coli. We investigated the recently reported MS3 method on the Fusion instrument and the potential of MS3-based reporter ion isolation Synchronous Precursor Selection (SPS) and its impact on quantitative accuracy. We confirm that the label-free approach offers a more linear response with a wider dynamic range than MS/MS-based isobaric tag quantitation and that the MS3/SPS approach alleviates but does not eliminate dynamic range compression. We observed, however, that the choice of quantitative approach had little impact on the ability to statistically evaluate the E. coli heat shock response. We conclude that in the experimental conditions tested, MS/MS-based reporter ion quantitation provides reliable biological insight despite the issue of compressed dynamic range, an observation th...Continue Reading

References

May 2, 2006·Statistical Applications in Genetics and Molecular Biology·Gordon K Smyth
May 23, 2006·Nature Reviews. Microbiology·Gary RowleyMark Roberts
Apr 3, 2009·Journal of Proteome Research·Markus BroschJyoti Choudhary
Jun 7, 2011·Molecular & Cellular Proteomics : MCP·Annette MichalskiStevan Horning
Apr 28, 2012·Journal of Proteome Research·Christian D KelstrupJesper V Olsen
Jul 21, 2012·Bioinformatics·Tom TavernerRichard D Smith
Oct 23, 2012·Journal of Proteomics·A F Maarten AltelaarShabaz Mohammed
Nov 13, 2012·Nucleic Acids Research·Ingrid M KeselerPeter D Karp
Jun 19, 2013·Journal of Proteome Research·Mikhail M SavitskiMarcus Bantscheff
Jun 25, 2013·Molecular & Cellular Proteomics : MCP·Ileana R LeónRichard R Sprenger
Oct 22, 2013·Molecular & Cellular Proteomics : MCP·Alexander S HebertJoshua J Coon
Mar 13, 2014·Journal of Proteome Research·Hendrik NolteMarcus Krüger
Oct 29, 2014·Nucleic Acids Research·UNKNOWN UniProt Consortium

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Citations

Sep 21, 2016·Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences·Stephen W HolmanRobert J Beynon
Feb 7, 2017·Molecular & Cellular Proteomics : MCP·Todd M Greco, Ileana M Cristea
Oct 4, 2017·The Journal of Biological Chemistry·Stephen R ThomDavid J Margolis
May 29, 2018·Developmental Dynamics : an Official Publication of the American Association of Anatomists·Suya WangAlexander R Moise
Mar 15, 2018·Nature Communications·Alexander HogrebeJesper V Olsen
Jul 4, 2019·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Amy E DefnetDeepak A Deshpande
Apr 3, 2020·International Journal of Molecular Sciences·Line Aas MortensenHans Christian Beck
Mar 2, 2017·Proteomes·Stanislav Naryzhny
Aug 20, 2017·Scientific Reports·Michelle D GlewEric C Reynolds
Jan 30, 2018·Expert Review of Proteomics·Camilla ThygesenMartin R Larsen
Aug 10, 2019·Archives of Biochemistry and Biophysics·Bennett J GiardinaAngela Wilks
Nov 1, 2020·Journal of Mass Spectrometry : JMS·Domenico Taverna, Marco Gaspari
Apr 6, 2021·Journal of Cerebral Blood Flow and Metabolism : Official Journal of the International Society of Cerebral Blood Flow and Metabolism·Jesse A StokumJ Marc Simard
Jul 28, 2016·Journal of Proteome Research·Ana Martinez-ValJavier Munoz
May 24, 2019·Journal of Proteome Research·Thualfeqar Al-MohannaSorina C Popescu
Jan 23, 2019·Journal of Proteome Research·Katie J LeeElizabeth G Canty-Laird
Mar 7, 2020·Journal of Proteome Research·Abla TannousPeter Lobel

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