Analysis of tandem mass spectra by FTMS for improved large-scale proteomics with superior protein quantification.

Analytical Chemistry
Graeme C McAlisterJoshua J Coon

Abstract

Using a newly developed dual-cell quadrupole linear ion trap-orbitrap hybrid mass spectrometer (dcQLT-orbitrap), we demonstrate the utility of collecting high-resolution tandem mass spectral data for large-scale shotgun proteomics. Multiple nanoLC-MS/MS experiments on both an older generation quadrupole linear ion trap-orbitrap hybrid (QLT-orbitrap) and the dcQLT-orbitrap, using both resonant-excitation CAD and beam-type CAD (HCD), were performed. Resulting from various technological advances (e.g., a stacked ring ion guide AP inlet, a dual cell QLT), the dcQLT-orbitrap exhibited increased duty cycle (approximately 1.5-2 times) and sensitivity for both CAD (ion trap detection) and HCD (orbitrap detection) methods. As compared to the older system, the dcQLT-orbitrap produced significantly more unique peptide identifications for both methods (approximately 30% improvement for CAD and approximately 115% improvement for HCD). The sizable improvement of the HCD method on the dcQLT-orbitrap system outperforms the current standard method of CAD with ion trap detection for large-scale analysis. Finally, we demonstrate that the increased HCD performance translates to a direct and substantial improvement in protein quantitation precision...Continue Reading

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Citations

Jul 8, 2010·Clinical & Experimental Metastasis·Petra HudlerRadovan Komel
May 17, 2013·Journal of the American Society for Mass Spectrometry·Aaron R LedvinaJoshua J Coon
Feb 18, 2012·Analytical Chemistry·Graeme C McAlisterJoshua J Coon
Apr 7, 2012·Analytical Chemistry·Aaron R LedvinaJoshua J Coon
Feb 27, 2013·Chemical Reviews·Yaoyang ZhangJohn R Yates
Jan 18, 2013·Journal of Proteome Research·Craig D Wenger, Joshua J Coon
Oct 11, 2011·Nature Methods·Douglas H PhanstielJoshua J Coon
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Mar 12, 2011·Molecular & Cellular Proteomics : MCP·Graeme C McAlisterJoshua J Coon
Apr 3, 2010·Molecular & Cellular Proteomics : MCP·Alexander LeitnerRuedi Aebersold
Nov 30, 2011·Bioanalysis·W Bart Emary, Nanyan Rena Zhang
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Feb 18, 2016·Analytical Chemistry·Gregory K PottsJoshua J Coon
Jul 25, 2013·Molecular & Cellular Proteomics : MCP·Alexander S HebertJoshua J Coon
Jan 26, 2018·Rapid Communications in Mass Spectrometry : RCM·Stefanie IckertMichael W Linscheid
Mar 19, 2011·Journal of Proteome Research·Christian K FreseShabaz Mohammed
Nov 3, 2011·Analytical Chemistry·Carol L Nilsson

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