Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer
Open accessAbstract
Mass spectrometry-based proteomics has greatly benefitted from enormous advances in high resolution instrumentation in recent years. In particular, the combination of a linear ion trap with the Orbitrap analyzer has proven to be a popular instrument configuration. Complementing this hybrid trap-trap instrument, as well as the standalone Orbitrap analyzer termed Exactive, we here present coupling of a quadrupole mass filter to an Orbitrap analyzer. This "Q Exactive" instrument features high ion currents because of an S-lens, and fast high-energy collision-induced dissociation peptide fragmentation because of parallel filling and detection modes. The image current from the detector is processed by an "enhanced Fourier Transformation" algorithm, doubling mass spectrometric resolution. Together with almost instantaneous isolation and fragmentation, the instrument achieves overall cycle times of 1 s for a top 10 higher energy collisional dissociation method. More than 2500 proteins can be identified in standard 90-min gradients of tryptic digests of mammalian cell lysate- a significant improvement over previous Orbitrap mass spectrometers. Furthermore, the quadrupole Orbitrap analyzer combination enables multiplexed operation at the MS and tandem MS levels. This is demonstrated in a multiplexed single ion monitoring mode, in which the quadrupole rapidly switches among different narrow mass ranges that are analyzed in a single composite MS spectrum. Similarly, the quadrupole allows fragmentation of different precursor masses in rapid succession, followed by joint analysis of the higher energy collisional dissociation fragment ions in the Orbitrap analyzer. High performance in a robust benchtop format together with the ability to perform complex multiplexed scan modes make the Q Exactive an exciting new instrument for the proteomics and general analytical communities.
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Recent advances in mass spectrometer hardware have provided a boost in depth of standard analyses and enabled near-complete model proteome quantification in minimal measuring time.
“Recent advances in mass spectrometer hardware (76, 77) have provided a boost in the depth of standard analyses and enabled near-complete model proteome quantification in minimal measuring time (6).”
From Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ (2014) · cites this paper as [77]
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Cites
Cox, J., & Mann, M. (2008) · Nature Biotechnology · doi:10.1038/nbt.1511 · Cited by 14,855 · see citing works
Self-citationGentleman R: R: A language for data analysis and graphics
Ihaka, R., & Gentleman, R. (1996) · Journal of Computational and Graphical Statistics · doi:10.1080/10618600.1996.10474713 · Cited by 11,747 · see citing works
Mass spectrometry-based proteomics
Aebersold, R., & Mann, M. (2003) · Nature · doi:10.1038/nature01511 · Cited by 6,955 · see citing works
Self-citationAndromeda: A Peptide Search Engine Integrated into the MaxQuant Environment
Cox, J., Neuhauser, N., Michalski, A., Scheltema, R. A., Olsen, J. V., & Mann, M. (2011) · Journal of Proteome Research · doi:10.1021/pr101065j · Cited by 5,350 · see citing works
Self-citationRappsilber, J., Ishihama, Y., & Mann, M. (2002) · Analytical Chemistry · doi:10.1021/ac026117i · Cited by 2,589 · see citing works
Self-citationMass Spectrometry and Protein Analysis
Domon, B., & Aebersold, R. H. (2006) · Science · doi:10.1126/science.1124619 · Cited by 2,188 · see citing works
Olsen, J. V., de Godoy, L. M. F., Li, G., Maček, B., Mortensen, P., Pesch, R., Makarov, A., Lange, O., Horning, S. R., & Mann, M. (2005) · Molecular & Cellular Proteomics · doi:10.1074/mcp.t500030-mcp200 · Cited by 1,513 · see citing works
Self-citationAddona, T. A., Abbatiello, S. E., Schilling, B., Skates, S. J., Mani, D. R., Bunk, D. M., Spiegelman, C. H., Zimmerman, L. J., Ham, A.-J. L., Keshishian, H., et al. (2009) · Nature Biotechnology · doi:10.1038/nbt.1546 · Cited by 1,037 · see citing works
Higher-energy C-trap dissociation for peptide modification analysis
Olsen, J., Macek, B., Lange, O., Makarov, A., Horning, S., & Mann, M. (2007) · Nature Methods · doi:10.1038/nmeth1060 · Cited by 1,007 · see citing works
Self-citationElectrostatic axially harmonic orbital trapping: a high-performance technique of mass analysis
Makarov, A. (2000) · Analytical Chemistry · doi:10.1021/ac991131p · Cited by 991 · see citing works
Self-citationPerformance evaluation of a hybrid linear ion trap/orbitrap mass spectrometer.
Makarov, A., Denisov, E. V., Kholomeev, A., Balschun, W., Lange, O., Strupat, K., & Horning, S. (2006) · Analytical Chemistry · doi:10.1021/ac0518811 · Cited by 771 · see citing works
Self-citationFull dynamic range proteome analysis of S. cerevisiae by targeted proteomics
Picotti, P., Bodenmiller, B., Mueller, L. N., Domon, B., & Aebersold, R. (2009) · Cell · doi:10.1016/j.cell.2009.05.051 · Cited by 744 · see citing works
Michalski, A., Cox, J., & Mann, M. (2011) · Journal of Proteome Research · doi:10.1021/pr101060v · Cited by 685 · see citing works
Self-citationInstrumentation, applications, and energy deposition in quadrupole ion-trap tandem mass spectrometry
Louris, J. N., Cooks, R. G., Syka, J. E. P., Kelley, P. E., Stafford, G. C., & Todd, J. F. J. (1987) · Analytical Chemistry · doi:10.1021/ac00140a021 · Cited by 500 · see citing works
Wolf‐Yadlin, A., Hautaniemi, S., Lauffenburger, D. A., & White, F. M. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0608638104 · Cited by 494 · see citing works
A dual pressure linear ion trap orbitrap instrument with very high sequencing speed
Olsen, J. V., Schwartz, J. C., Griep-Raming, J., Nielsen, M. L., Damoc, E., Denisov, E., Lange, O., Remes, P., Taylor, D., Splendore, M., et al. (2009) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m900375-mcp200 · Cited by 464 · see citing works
Self-citationPrecision proteomics: The case for high resolution and high mass accuracy
Mann, M., & Kelleher, N. L. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0800788105 · Cited by 450 · see citing works
Self-citationDynamic range of mass accuracy in LTQ orbitrap hybrid mass spectrometer
Makarov, A., Denisov, E. V., Lange, O., & Horning, S. R. (2006) · Journal of the American Society for Mass Spectrometry · doi:10.1016/j.jasms.2006.03.006 · Cited by 431 · see citing works
Self-citationMass spectrometry–based proteomics in cell biology
Walther, T. C., & Mann, M. (2010) · The Journal of Cell Biology · doi:10.1083/jcb.201004052 · Cited by 411 · see citing works
Self-citationProteomics of organelles and large cellular structures
Yates, J. R., Gilchrist, A., Howell, K. E., & Bergeron, J. J. M. (2005) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1711 · Cited by 392 · see citing works
Syka, J. E. P., Marto, J. A., Bai, D. L., Horning, S. R., Senko, M. W., Schwartz, J. C., Ueberheide, B. M., Garcia, B. A., Busby, S. A., Muratore‐Schroeder, T. L., et al. (2004) · Journal of Proteome Research · doi:10.1021/pr0499794 · Cited by 349 · see citing works
Self-citationInterfacing the Orbitrap Mass Analyzer to an Electrospray Ion Source
Hardman, M., & Makarov, A. (2003) · Analytical Chemistry · doi:10.1021/ac0258047 · Cited by 315 · see citing works
Self-citationOrbitrap Mass Analyzer – Overview and Applications in Proteomics
Ščigelová, M., & Makarov, A. (2006) · PROTEOMICS · doi:10.1002/pmic.200600528 · Cited by 288 · see citing works
Self-citationProteomics on an Orbitrap Benchtop Mass Spectrometer Using All-ion Fragmentation
Geiger, T., Cox, J., & Mann, M. (2010) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m110.001537 · Cited by 253 · see citing works
Self-citationMaček, B., Waanders, L. F., Olsen, J. V., & Mann, M. (2006) · Molecular & Cellular Proteomics · doi:10.1074/mcp.t500042-mcp200 · Cited by 198 · see citing works
Self-citationQuantitative-qualitative data acquisition using a benchtop orbitrap mass spectrometer
Bateman, K. P., Kellmann, M., Muenster, H., et al. (2009) · Journal of the American Society for Mass Spectrometry · doi:10.1016/j.jasms.2009.03.002 · Cited by 194 · see citing works
McAlister, G. C., Berggren, W. T., Griep‐Raming, J., Horning, S. R., Makarov, A., Phanstiel, D., Stafford, G. C., Swaney, D. L., Syka, J. E. P., Zabrouskov, V., et al. (2008) · Journal of Proteome Research · doi:10.1021/pr800264t · Cited by 145 · see citing works
Self-citationKöcher, T., Swart, R., & Mechtler, K. (2011) · Analytical Chemistry · doi:10.1021/ac103243t · Cited by 140 · see citing works
Broadband Phase Correction of FT-ICR Mass Spectra via Simultaneous Excitation and Detection
Beu, S. C., Blakney, G. T., Quinn, J. P., et al. (2004) · Analytical Chemistry · doi:10.1021/ac049733i · Cited by 60 · see citing works
Higher-energy Collision-activated Dissociation Without a Dedicated Collision Cell
McAlister, G. C., Phanstiel, D. H., Brumbaugh, J., Westphall, M. S., & Coon, J. J. (2011) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o111.009456 · Cited by 43 · see citing works
Vining, B. A., Bossio, R. E., & Marshall, A. G. (1998) · Analytical Chemistry · doi:10.1021/ac9808019 · Cited by 34 · see citing works
Dryhurst, G. (1977) · Elsevier eBooks · doi:10.1016/b978-0-12-222650-2.50006-9 · Cited by 11 · see citing works
Flagged first, then by citations
Research works printed but not linked: 1
- [24]Lange O. Makarov A. Denisov E. Balschun W. (2010) Accelerating spectral acquisition rate of Orbitrap mass spectrometry. Proc. 58th Conf. Amer. Soc. Mass Spectrom
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Cox, J., Hein, M. Y., Luber, C. A., Paron, I., Nagaraj, N., & Mann, M. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m113.031591 · Cited by 5,180 · see citing works
Self-citationL-Arginine Modulates T Cell Metabolism and Enhances Survival and Anti-tumor Activity
Geiger, R., Rieckmann, J. C., Wolf, T., Basso, C., Feng, Y., Fuhrer, T., Kogadeeva, M., Picotti, P., Meissner, F., Mann, M., et al. (2016) · Cell · doi:10.1016/j.cell.2016.09.031 · Cited by 1,775 · see citing works
Self-citationKulak, N. A., Pichler, G., Paron, I., Nagaraj, N., & Mann, M. (2014) · Nature Methods · doi:10.1038/nmeth.2834 · Cited by 1,719 · see citing works
Self-citationProtein 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 · see citing works
Peterson, A. C., Russell, J. D., Bailey, D. J., Westphall, M. S., & Coon, J. J. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o112.020131 · Cited by 1,288 · see citing works
Budnik, B., Levy, E., Harmange, G., & Slavov, N. (2018) · Genome Biology · doi:10.1186/s13059-018-1547-5 · Cited by 832 · see citing works
Richter, B., Sliter, D. A., Herhaus, L., Stolz, A., Wang, C., Beli, P., Zaffagnini, G., Wild, P., Martens, S., Wagner, S. A., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1523926113 · Cited by 755 · see citing works
An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics
Angelidis, I., Simon, L. M., Fernandez, I. E., Strunz, M., Mayr, C. H., Greiffo, F. R., Tsitsiridis, G., Ansari, M., Graf, E., Strom, T.-M., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-08831-9 · Cited by 637 · see citing works
Self-citationProgress in Top-Down Proteomics and the Analysis of Proteoforms
Toby, T. K., Fornelli, L., & Kelleher, N. L. (2016) · Annual Review of Analytical Chemistry · doi:10.1146/annurev-anchem-071015-041550 · Cited by 576 · see citing works
Targeted Proteomic Quantification on Quadrupole-Orbitrap Mass Spectrometer
Gallien, S., Duriez, E., Crone, C., Kellmann, M., Moehring, T., & Domon, B. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o112.019802 · Cited by 510 · see citing works
Liu, X., & Locasale, J. W. (2017) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2017.01.004 · Cited by 453 · see citing works
Nagaraj, N., Alexander Kulak, N., Cox, J., Neuhauser, N., Mayr, K., Hoerning, O., Vorm, O., & Mann, M. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m111.013722 · Cited by 392 · see citing works
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Rose, R. J., Damoc, E., Denisov, E., Makarov, A., & Heck, A. J. R. (2012) · Nature Methods · doi:10.1038/nmeth.2208 · Cited by 392 · see citing works
Self-citationMichalski, A., Damoc, E., Lange, O., Denisov, E., Nolting, D., Müller, M., Viner, R., Schwartz, J., Remes, P., Belford, M., et al. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o111.013698 · Cited by 373 · see citing works
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Mann, M., Kulak, N. A., Nagaraj, N., & Cox, J. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.01.029 · Cited by 350 · see citing works
Self-citationSchiller, H. B., Fernandez, I. E., Burgstaller, G., Schaab, C., Scheltema, R. A., Schwarzmayr, T., Strom, T. M., Eickelberg, O., & Mann, M. (2015) · Molecular Systems Biology · doi:10.15252/msb.20156123 · Cited by 261 · see citing works
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Geiger, T., Velic, A., Macek, B., Lundberg, E., Kampf, C., Nagaraj, N., Uhlen, M., Cox, J., & Mann, M. (2013) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m112.024919 · Cited by 235 · see citing works
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Satpathy, S., Wagner, S. A., Beli, P., Gupta, R., Kristiansen, T. A., Malinova, D., Francavilla, C., Tolar, P., Bishop, G. A., Hostager, B. S., et al. (2015) · Molecular Systems Biology · doi:10.15252/msb.20145880 · Cited by 124 · see citing works
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Johnsen, E., Leknes, S., Wilson, S. R., & Lundanes, E. (2015) · Scientific Reports · doi:10.1038/srep09308 · Cited by 65 · see citing works
Xie, J. L., Qin, L., Miao, Z., Grys, B. T., Diaz, J. D. L. C., Ting, K., Krieger, J. R., Tong, J., Tan, K., Leach, M. D., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-00547-y · Cited by 60 · see citing works
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- Authors
- Michalski, A., Damoc, E., Hauschild, J.-P., Lange, O., Wieghaus, A., Makarov, A., Nagaraj, N., Cox, J., Mann, M., & Horning, S.
- Affiliations
- Max Planck Institute of Biochemistry (DE)
- Thermo Fisher Scientific (Germany) (DE)
- Max Planck Society (DE)
- Corresponding author
- Mann, Matthias
- Horning, Stevan
- Venue
- Molecular & Cellular Proteomics
- Publisher
- Elsevier BV
- Published
- 2011-09
- Volume
- 10
- Issue
- 9
- Pages
- M111.011015
- ISSN
- 1535-9476 (ISSN-L)
- PMC
- PMC3284220
- OpenAlex
- W2124081847
- Cited by
- 832
- References
- 32
- Citations by year
- 2026: 24 · 2025: 26 · 2024: 26 · 2023: 23 · 2022: 38 · 2021: 42 · 2020: 63 · 2019: 63 · 2018: 66 · 2017: 73 · 2016: 71 · 2015: 84 · 2014: 87 · 2013: 82 · 2012: 54
- FWCI
- 33.34
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Molecular & Cellular Proteomics (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
- Max Planck Institute for Plasma Physics (submittedVersion)
- Funders
- European Commission
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
- Keywords
- high-energy collision-induced dissociation, tandem mass spectrometry, protein identification, tryptic digest, high-resolution mass spectrometry
- MeSH terms
- Algorithms, Amino Acid Sequence, Female, HeLa Cells, Humans, Ions, Molecular Sequence Data, Peptide Fragments, Proteins, Mass Spectrometry, Proteomics
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