The DOI matches its Crossref record; 10 of the 10 references it cites were found in a registry or an index.
Optimized Fast and Sensitive Acquisition Methods for Shotgun Proteomics on a Quadrupole Orbitrap Mass Spectrometer
Open accessAbstract
Advances in proteomics are continually driven by the introduction of new mass spectrometric instrumentation with improved performances. The recently introduced quadrupole Orbitrap (Q Exactive) tandem mass spectrometer allows fast acquisition of high-resolution higher-energy collisional dissociation (HCD) tandem mass spectra due to the parallel mode of operation, where the generation, filling, and storage of fragment ions can be performed while simultaneously measuring another ion packet in the Orbitrap mass analyzer. In this study, data-dependent acquisition methods for "fast" or "sensitive" scanning were optimized and assessed by comparing stable isotope labeled yeast proteome coverage. We discovered that speed was the most important parameter for sample loads above 125 ng, where a 95 ms HCD scanning method allowed for identification and quantification of more than 2000 yeast proteins from 1 h of analysis time. At sample loads below 125 ng, a 156 ms HCD acquisition method improved the sensitivity, mass accuracy, and quality of data and enabled us to identify 30% more proteins and peptides than the faster scanning method. A similar effect was observed when the LC gradient was extended to 2 or 3 h for the analysis of complex mammalian whole cell lysates. Using a 3 h LC gradient, the sensitive method enabled identification of more than 4000 proteins from 1 μg of tryptic HeLa digest, which was almost 200 more identifications compared to the faster scanning method. Our results demonstrate that peptide identification on a quadrupole Orbitrap is dependent on sample amounts, acquisition speed, and data quality, which emphasizes the need for acquisition methods tailored for different sample loads and analytical preferences.
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Cites
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Mass spectrometry-based proteomics
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Global analysis of protein expression in yeast
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A dual pressure linear ion trap orbitrap instrument with very high sequencing speed
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Self-citationPrecision proteomics: The case for high resolution and high mass accuracy
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Cited by
Protein Analysis by Shotgun/Bottom-up Proteomics
Zhang, Y., Fonslow, B. R., Shan, B., Baek, M.-C., & Yates, J. R. (2013) · Chemical Reviews · doi:10.1021/cr3003533 · Cited by 1,491
Bruderer, R., Bernhardt, O. M., Gandhi, T., Miladinović, S. M., Cheng, L.-Y., Messner, S., Ehrenberger, T., Zanotelli, V., Butscheid, Y., Escher, C., et al. (2015) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m114.044305 · Cited by 1,238
Recalibrating equus evolution using the genome sequence of an early middle pleistocene horse
Orlando, L., Ginolhac, A., Zhang, G., Froese, D., Albrechtsen, A., Stiller, M., Schubert, M., Cappellini, E., Petersen, B., Moltke, I., et al. (2013) · Nature · doi:10.1038/nature12323 · Cited by 841
Self-citationSerine ADP-ribosylation depends on HPF1
Bonfiglio, J. J., Fontana, P., Zhang, Q., Colby, T., Gibbs-Seymour, I., Atanassov, I., Bartlett, E., Zaja, R., Ahel, I., & Matic, I. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.01.003 · Cited by 352
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Metadata
- Authors
- Kelstrup, C. D., Young, C., Lavallee, R., Nielsen, M. L., & Olsen, J. V.
- Venue
- Journal of Proteome Research
- Publisher
- American Chemical Society (ACS)
- Published
- 2012-05-10
- Volume
- 11
- Issue
- 6
- Pages
- 3487-3497
- ISSN
- 1535-3893 (ISSN-L)
- 1535-3907
- OpenAlex
- W1980509906
- Cited by
- 281
- References
- 10
- FWCI
- 13.30
- Type
- journal article
- Language
- en
- Open access
- green
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