Genome-specific gas-phase fractionation strategy for improved shotgun proteomic profiling of proteotypic peptides

Analytical Chemistry
Alexander ScherlDavid R Goodlett

Abstract

Gas-phase fractionation (GPF) is an efficient and straightforward method to increase proteome coverage. In this report, optimal m/z ranges were calculated based on genomic complexity and experimental data. Then, theoretical precursor ion densities were calculated in silico from various organisms' genomes and found to corroborate the empirical selection of m/z ranges based on ion density mapping. According to both calculations, the choice of m/z range for most efficient GPF coverage in the lower m/z range should be very narrow and increase as m/z value increases. Next, a systematic LC-MS/MS analysis was performed to confirm this observation. The behavior of data-dependent precursor ion selection and the origin of the observed variability was investigated under three different scan modes of an LTQ-Orbitrap hybrid mass spectrometer. Finally, GPF combined with data-dependent analysis was compared to a targeted, pseudo-multiple reaction monitoring analysis of proteotypic peptides that should be, based on empirical observation of LC-ESI-MS/MS data, detectable. The result of the latter experiment supported our conclusion that data-dependent analysis using rational gas-phase fractionation was sufficient for comprehensive proteomic anal...Continue Reading

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Citations

Aug 8, 2012·Journal of the American Society for Mass Spectrometry·Didia Coelho GraçaAlexander Scherl
Sep 24, 2009·Journal of the American Society for Mass Spectrometry·Yihsuan S TsaiDavid R Goodlett
Jul 26, 2011·The Proceedings of the Nutrition Society·Sandra Sénéchal, Martin Kussmann
Feb 24, 2011·Analytical Chemistry·Alexandre PanchaudDavid R Goodlett
Jul 4, 2009·Analytical Chemistry·Alexandre PanchaudDavid R Goodlett
Sep 23, 2011·Journal of Proteome Research·Shawna Mae HengelDavid R Goodlett
Mar 5, 2010·Journal of Proteome Research·Kristian E SwearingenNorman J Dovichi
Dec 22, 2011·Molecular & Cellular Proteomics : MCP·Kristian E SwearingenRobert L Moritz
Sep 28, 2014·Journal of the American Society for Mass Spectrometry·Jesse D CanterburyScott A Shaffer
Sep 19, 2015·Data in Brief·Samantha J EmeryPaul A Haynes
Dec 1, 2009·Journal of Proteomics·Michael AffolterMartin Kussmann
Aug 8, 2008·Mass Spectrometry Reviews·Richard H PerryRobert J Noll
Nov 10, 2011·Molecular Systems Biology·Martin BeckRuedi Aebersold
Mar 13, 2014·Proteomics. Clinical Applications·Elizabeth V NguyenDavid R Goodlett
Jun 6, 2015·Molecular and Biochemical Parasitology·Samantha J EmeryPaul A Haynes
Aug 28, 2010·Journal of Proteomics·Joshua M Gilmore, Michael P Washburn
Jan 2, 2013·Journal of Proteomics·Florent GluckAlexander Scherl
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Oct 16, 2018·Experimental Eye Research·Marianne DorNatacha Turck

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