Journal
ANALYTICAL CHEMISTRY
Volume 82, Issue 1, Pages 316-322Publisher
AMER CHEMICAL SOC
DOI: 10.1021/ac902005s
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Funding
- Beckman Foundation
- National Science Foundation (NSF) [0701846, 0747990]
- National Institutes of Health (NIH) [R01GM080148, PO1GM081629, 5T32GM08349, 5T32HG002760]
- NATIONAL HUMAN GENOME RESEARCH INSTITUTE [T32HG002760] Funding Source: NIH RePORTER
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [R01GM080148, T32GM008349, P01GM081629] Funding Source: NIH RePORTER
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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 (similar to 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 (similar to 30% improvement for CAD and similar to 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 using isobaric tags.
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