Highly multiplexed targeted proteomics using precise control of peptide retention time

Proteomics
Sebastien GallienBruno Domon

Abstract

Large-scale proteomics applications using SRM analysis on triple quadrupole mass spectrometers present new challenges to LC-MS/MS experimental design. Despite the automation of building large-scale LC-SRM methods, the increased numbers of targeted peptides can compromise the balance between sensitivity and selectivity. To facilitate large target numbers, time-scheduled SRM transition acquisition is performed. Previously published results have demonstrated incorporation of a well-characterized set of synthetic peptides enabled chromatographic characterization of the elution profile for most endogenous peptides. We have extended this application of peptide trainer kits to not only build SRM methods but to facilitate real-time elution profile characterization that enables automated adjustment of the scheduled detection windows. Incorporation of dynamic retention time adjustments better facilitate targeted assays lasting several days without the need for constant supervision. This paper provides an overview of how the dynamic retention correction approach identifies and corrects for commonly observed LC variations. This adjustment dramatically improves robustness in targeted discovery experiments as well as routine quantification e...Continue Reading

References

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Jan 2, 2007·Nature Biotechnology·Parag MallickRuedi Aebersold
Jul 24, 2007·Molecular & Cellular Proteomics : MCP·Jianru Stahl-ZengBruno Domon
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Jul 29, 2010·Molecular & Cellular Proteomics : MCP·Reiko KiyonamiBruno Domon
Mar 12, 2011·Journal of Mass Spectrometry : JMS·Sebastien GallienBruno Domon

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Citations

Sep 11, 2012·Molecular & Cellular Proteomics : MCP·Sebastien GallienBruno Domon
Aug 19, 2014·Journal of Proteome Research·Petra MajovskyWolfgang Hoehenwarter
Jul 21, 2015·Expert Review of Proteomics·Sebastien Gallien, Bruno Domon
Jan 19, 2016·Journal of Proteome Research·Stephen W HolmanClaire E Eyers
Jan 23, 2016·Mass Spectrometry Reviews·Luminita Moruz, Lukas Käll
Oct 31, 2015·Journal of Proteome Research·Nina A KhristenkoBruno Domon
Dec 17, 2014·Proteomics. Clinical Applications·Bruno Domon, Sebastien Gallien
Dec 1, 2012·Proteomics·Zon W LaiOliver Schilling
Oct 15, 2013·Proteomics. Clinical Applications·Yeoun Jin KimBruno Domon
Sep 12, 2015·Analytical Chemistry·James L SowersKangling Zhang
Apr 7, 2015·Methods : a Companion to Methods in Enzymology·Sebastien Gallien, Bruno Domon
Nov 10, 2013·Journal of Proteomics·Sebastien GallienBruno Domon
Nov 20, 2012·Journal of Proteomics·Sebastien GallienBruno Domon
May 29, 2016·Clinica Chimica Acta; International Journal of Clinical Chemistry·Kazuo YamadaKen-Ichi Matsumoto
Jan 7, 2015·Molecular & Cellular Proteomics : MCP·Nathalie SelevsekRuedi Aebersold
Mar 11, 2015·Molecular & Cellular Proteomics : MCP·Sebastien GallienBruno Domon
Dec 30, 2017·Expert Review of Proteomics·Merry L LindseyKristine Y DeLeon-Pennell
Jun 27, 2019·Proteomics·Sara SalehKris Gevaert
Aug 2, 2017·Mass Spectrometry Reviews·Francisco Calderón-CelisAlfredo Sanz-Medel
Oct 5, 2017·Proteomics. Clinical Applications·Coşkun GüzelTheo M Luider
Apr 14, 2018·Journal of Proteomics·David Gomez-VarelaManuela Schmidt

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