The DOI matches its Crossref record; 8 of the 8 references it cites were found in a registry or an index.
Proteomics on an Orbitrap Benchtop Mass Spectrometer Using All-ion Fragmentation
Open accessAbstract
The orbitrap mass analyzer combines high sensitivity, high resolution, and high mass accuracy in a compact format. In proteomics applications, it is used in a hybrid configuration with a linear ion trap (LTQ-Orbitrap) where the linear trap quadrupole (LTQ) accumulates, isolates, and fragments peptide ions. Alternatively, isolated ions can be fragmented by higher energy collisional dissociation. A recently introduced stand-alone orbitrap analyzer (Exactive) also features a higher energy collisional dissociation cell but cannot isolate ions. Here we report that this instrument can efficiently characterize protein mixtures by alternating MS and "all-ion fragmentation" (AIF) MS/MS scans in a manner similar to that previously described for quadrupole time-of-flight instruments. We applied the peak recognition algorithms of the MaxQuant software at both the precursor and product ion levels. Assignment of fragment ions to co-eluting precursor ions was facilitated by high resolution (100,000 at m/z 200) and high mass accuracy. For efficient fragmentation of different mass precursors, we implemented a stepped collision energy procedure with cumulative MS readout. AIF on the Exactive identified 45 of 48 proteins in an equimolar protein standard mixture and all of them when using a small database. The technique also identified proteins with more than 100-fold abundance differences in a high dynamic range standard. When applied to protein identification in gel slices, AIF unambiguously characterized an immunoprecipitated protein that was barely visible by Coomassie staining and quantified it relative to contaminating proteins. AIF on a benchtop orbitrap instrument is therefore an attractive technology for a wide range of proteomics analyses.
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Cites
Cox, J., & Mann, M. (2008) · Nature Biotechnology · doi:10.1038/nbt.1511 · Cited by 14,855
Self-citationMass spectrometry-based proteomics
Aebersold, R., & Mann, M. (2003) · Nature · doi:10.1038/nature01511 · Cited by 6,955
Self-citationOng, S.-E., Blagoev, B., Kratchmarova, I., Kristensen, D. B., Steen, H., Pandey, A., & Mann, M. (2002) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m200025-mcp200 · Cited by 5,574
Self-citationAbsolute Quantification of Proteins by LCMSE
Silva, J. C., Gorenstein, M. V., Li, G.-Z., Vissers, J. P. C., & Geromanos, S. J. (2006) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m500230-mcp200 · Cited by 1,529
Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast
de Godoy, L. M. F., Olsen, J. V., Cox, J., Nielsen, M. L., Hubner, N. C., Fröhlich, F., Walther, T. C., & Mann, M. (2008) · Nature · doi:10.1038/nature07341 · Cited by 873
Self-citationQuantitative proteomics reveals subset-specific viral recognition in dendritic cells
Luber, C. A., Cox, J., Lauterbach, H., Fancke, B., Selbach, M., Tschopp, J., Akira, S., Wiegand, M., Hochrein, H., O'Keeffe, M., et al. (2010) · Immunity · doi:10.1016/j.immuni.2010.01.013 · Cited by 576
Self-citationProteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans
Malmström, J., Beck, M., Schmidt, A., Lange, V., Deutsch, E. W., & Aebersold, R. (2009) · Nature · doi:10.1038/nature08184 · Cited by 421
A HUPO test sample study reveals common problems in mass spectrometry–based proteomics
HUPO Test Sample Working Group, Bell, A. W., Deutsch, E. W., Au, C. E., Kearney, R. E., Beavis, R., Sechi, S., Nilsson, T., & Bergeron, J. J. M. (2009) · Nature Methods · doi:10.1038/nmeth.1333 · Cited by 351
Cited by
Gillet, L. C., Navarro, P., Tate, S., Röst, H., Selevsek, N., Reiter, L., Bonner, R., & Aebersold, R. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o111.016717 · Cited by 2,877
Comet: An open‐source MS / MS sequence database search tool
Eng, J. K., Jahan, T. A., & Hoopmann, M. R. (2013) · PROTEOMICS · doi:10.1002/pmic.201200439 · Cited by 1,474
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
Michalski, A., Damoc, E., Hauschild, J.-P., Lange, O., Wieghaus, A., Makarov, A., Nagaraj, N., Cox, J., Mann, M., & Horning, S. (2011) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m111.011015 · Cited by 832
Self-citationQuantitative mass spectrometry in proteomics: critical review update from 2007 to the present
Bantscheff, M., Lemeer, S., Savitski, M. M., & Kuster, B. (2012) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-012-6203-4 · Cited by 801
Plasma Proteome Profiling to Assess Human Health and Disease
Geyer, P. E., Kulak, N. A., Pichler, G., Holdt, L. M., Teupser, D., & Mann, M. (2016) · Cell Systems · doi:10.1016/j.cels.2016.02.015 · Cited by 734
Self-citationCurrent approaches and challenges for the metabolite profiling of complex natural extracts
Wolfender, J.-L., Marti, G., Thomas, A., & Bertrand, S. (2015) · Journal of Chromatography A · doi:10.1016/j.chroma.2014.10.091 · Cited by 635
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
A multicenter study benchmarks software tools for label-free proteome quantification
Navarro, P., Kuharev, J., Gillet, L. C., Bernhardt, O. M., MacLean, B., Röst, H. L., Tate, S. A., Tsou, C.-C., Reiter, L., Distler, U., et al. (2016) · Nature Biotechnology · doi:10.1038/nbt.3685 · Cited by 346
Gillet, L. C., Leitner, A., & Aebersold, R. (2016) · Annual Review of Analytical Chemistry · doi:10.1146/annurev-anchem-071015-041535 · Cited by 323
Zeiler, M., Straube, W. L., Lundberg, E., Uhlen, M., & Mann, M. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o111.009613 · Cited by 168
Self-citation
Metadata
- Authors
- Geiger, T., Cox, J., & Mann, M.
- Venue
- Molecular & Cellular Proteomics
- Publisher
- Elsevier BV
- Published
- 2010-10
- Volume
- 9
- Issue
- 10
- Pages
- 2252-2261
- ISSN
- 1535-9476 (ISSN-L)
- OpenAlex
- W2143340505
- Cited by
- 254
- References
- 8
- FWCI
- 9.40
- Type
- journal article
- Language
- en
- Open access
- hybrid
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