The impact II, a very high-resolution quadrupole time-of-flight instrument (QTOF) for deep shotgun proteomics

Molecular and Cellular Proteomics

Volumn 14, Issue 7, 2015, Pages 2014-2029

  Beck, Scarlet ^a   Michalski, Annette ^b   Raether, Oliver ^b   Lubeck, Markus ^b   Kaspar, Stephanie ^b   Goedecke, Niels ^b   Baessmann, Carsten ^b   Hornburg, Daniel ^a   Meier, Florian ^a   Paron, Igor ^a   Kulak, Nils A ^a   Cox, Juergen ^a   Mann, Matthias ^a  

^a MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

^b BRUKER DALTONIK GMBH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ANALYTIC METHOD; ANIMAL CELL; ARTICLE; CAPILLARY; CONTROLLED STUDY; DEEP SHOTGUN PROTEOMICS; DIPLOIDY; DRUG MIXTURE; ELUTION; HUMAN; HUMAN CELL; ION CURRENT; LIQUID CHROMATOGRAPHY; NONHUMAN; OPTICAL RESOLUTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; QUADRUPOLE TIME OF FLIGHT MASS SPECTROMETRY; SIMULATION; ANIMAL; CELL LINE; DEVICES; HAPLOIDY; HELA CELL LINE; MASS SPECTROMETRY; METABOLISM; MOLECULAR WEIGHT; MOUSE; PH; PROCEDURES; REPRODUCIBILITY; SACCHAROMYCES CEREVISIAE; TIME FACTOR;

ION; PEPTIDE; PROTEOME;

ANIMALS; CELL LINE; CHROMATOGRAPHY, LIQUID; DIPLOIDY; HAPLOIDY; HELA CELLS; HUMANS; HYDROGEN-ION CONCENTRATION; IONS; MASS SPECTROMETRY; MICE; MOLECULAR WEIGHT; PEPTIDES; PROTEOME; PROTEOMICS; REPRODUCIBILITY OF RESULTS; SACCHAROMYCES CEREVISIAE; TIME FACTORS;

EID: 84936804421     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.M114.047407     Document Type: Article

References (55)

1. Karas, M., and Hillenkamp, F. (1988) Laser desorption ionization of proteins with molecular masses exceeding 10, 000 daltons. Anal. Chem. 60, 2299-2301.
2. Fenn, J. B., Mann, M., Meng, C. K., Wong, S. F., and Whitehouse, C. M. (1989) Electrospray ionization for mass spectrometry of large biomolecules. Science 246, 64-71.
3. Aebersold, R., and Mann, M. (2003) Mass spectrometry-based proteomics. Nature 422, 198-207.
4. Cravatt, B. F., Simon, G. M., and Yates, J. R. 3rd (2007) The biological impact of mass-spectrometry-based proteomics. Nature 450, 991-1000.
5. Altelaar, A. F., Munoz, J., and Heck, A. J. (2013) Next-generation proteomics: Towards an integrative view of proteome dynamics. Nat. Rev. Genet. 14, 35-48.
6. Richards, A. L., Merrill, A. E., and Coon, J. J. (2014) Proteome sequencing goes deep. Curr. Opin. Chem. Biol. 24C, 11-17.
7. Domon, B., and Aebersold, R. (2006) Challenges and opportunities in proteomics data analysis. Mol. Cell. Proteomics 5, 1921-1926.
8. Mann, M., and Kelleher, N. L. (2008) Precision proteomics: The case for high-resolution and high mass-accuracy. Proc. Natl. Acad. Sci. U.S.A. 105, 18132-18138.
9. Makarov, A. (2000) Electrostatic axially harmonic orbital trapping: A highperformance technique of mass analysis. Anal. Chem. 72, 1156-1162.
10. Zubarev, R. A., and Makarov, A. (2013) Orbitrap mass spectrometry. Anal. Chem. 85, 5288-5296.
11. Michalski, A., Damoc, E., Hauschild, J. P., Lange, O., Wieghaus, A., Makarov, A., Nagaraj, N., Cox, J., Mann, M., and Horning, S. (2011) Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer. Mol. Cell. Proteomics 10, M111 011015.
12. Scheltema, R. A., Hauschild, J. P., Lange, O., Hornburg, D., Denisov, E., Damoc, E., Kuehn, A., Makarov, A., and Mann, M. (2014) The Q exactive HF, a benchtop mass spectrometer with a pre-filter, high-performance quadrupole and an ultra-high-field Orbitrap analyzer. Mol. Cell. Proteomics 13, 3698-3708.
13. Kelstrup, C. D., Jersie-Christensen, R. R., Batth, T. S., Arrey, T. N., Kuehn, A., Kellmann, M., and Olsen, J. V. (2014) Rapid and deep proteomes by faster sequencing on a benchtop quadrupole ultra-high-field Orbitrap mass spectrometer. J. Proteome Res. 13(12), 6187-6195.
14. Zhou, H., Ning, Z., Wang, F., Seebun, D., and Figeys, D. (2011) Proteomic reactors and their applications in biology. FEBS J. 278, 3796-3806.
15. Kocher, T., Swart, R., and Mechtler, K. (2011) Ultra-high-pressure RPLC hyphenated to an LTQ-Orbitrap Velos reveals a linear relation between peak capacity and number of identified peptides. Anal. Chem. 83, 2699-2704.
16. Cox, J., and Mann, M. (2011) Quantitative, high-resolution proteomics for data-driven systems biology. Annu. Rev. Biochem. 80, 273-299.
17. Nagaraj, N., Kulak, N. A., Cox, J., Neuhauser, N., Mayr, K., Hoerning, O., Vorm, O., and Mann, M. (2012) System-wide perturbation analysis with nearly complete coverage of the yeast proteome by single-shot ultra HPLC runs on a bench top Orbitrap. Mol. Cell. Proteomics 11, M111 013722.
18. Hebert, A. S., Richards, A. L., Bailey, D. J., Ulbrich, A., Coughlin, E. E., Westphall, M. S., and Coon, J. J. (2014) The one hour yeast proteome. Mol. Cell. Proteomics 13, 339-347.
19. Kulak, N. A., Pichler, G., Paron, I., Nagaraj, N., and Mann, M. (2014) Minimal, encapsulated proteomic-sample processing applied to copynumber estimation in eukaryotic cells. Nat. Methods 11, 319-324.
20. Michalski, A., Cox, J., and Mann, M. (2011) More than 100, 000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS. J. Proteome Res. 10, 1785-1793.
21. Savitski, M. M., Nielsen, M. L., and Zubarev, R. A. (2006) ModifiComb, a new proteomic tool for mapping substoichiometric post-translational modifications, finding novel types of modifications, and fingerprinting complex protein mixtures. Mol. Cell. Proteomics 5, 935-948.
22. Morris, H. R., Paxton, T., Dell, A., Langhorne, J., Berg, M., Bordoli, R. S., Hoyes, J., and Bateman, R. H. (1996) High sensitivity collisionally-activated decomposition tandem mass spectrometry on a novel quadrupole/orthogonal-acceleration time-of-flight mass spectrometer. Rapid Commun. Mass Spectr. 10, 889-896.
23. Silva, J. C., Denny, R., Dorschel, C., Gorenstein, M. V., Li, G. Z., Richardson, K., Wall, D., and Geromanos, S. J. (2006) Simultaneous qualitative and quantitative analysis of the Escherichia coli proteome: A sweet tale. Mol. Cell. Proteomics 5, 589-607.
24. Silva, J. C., Gorenstein, M. V., Li, G. Z., Vissers, J. P., and Geromanos, S. J. (2006) Absolute quantification of proteins by LCMSE: A virtue of parallel MS acquisition. Mol. Cell. Proteomics 5, 144-156.
25. Gillet, L. C., Navarro, P., Tate, S., Rost, H., Selevsek, N., Reiter, L., Bonner, R., and Aebersold, R. (2012) Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: A new concept for consistent and accurate proteome analysis. Mol. Cell. Proteomics 11, O111 016717.
26. Distler, U., Kuharev, J., Navarro, P., Levin, Y., Schild, H., and Tenzer, S. (2014) Drift time-specific collision energies enable deep-coverage dataindependent acquisition proteomics. Nat. Methods 11, 167-170.
27. Helm, D., Vissers, J. P., Hughes, C. J., Hahne, H., Ruprecht, B., Pachl, F., Grzyb, A., Richardson, K., Wildgoose, J., Maier, S. K., Marx, H., Wilhelm, M., Becher, I., Lemeer, S., Bantscheff, M., Langridge, J. I., and Kuster, B. (2014) Ion mobility tandem mass spectrometry enhances performance of bottom-up proteomics. Mol. Cell. Proteomics, 13, 3709-3715.
28. Hornburg, D., Drepper, C., Butter, F., Meissner, F., Sendtner, M., and Mann, M. (2014) Deep proteomic evaluation of primary and cell line motoneuron disease models delineates major differences in neuronal characteristics. Mol. Cell. Proteomics 13, 3410-3420.
29. Rappsilber, J., Mann, M., and Ishihama, Y. (2007) Protocol for micropurification, enrichment, prefractionation, and storage of peptides for proteomics using StageTips. Nature Protoc. 2, 1896-1906.
30. Wang, H., Qian, W. J., Mottaz, H. M., Clauss, T. R., Anderson, D. J., Moore, R. J., Camp, D. G. 2nd, Khan, A. H., Sforza, D. M., Pallavicini, M., Smith, D. J., and Smith, R. D. (2005) Development and evaluation of a microand nanoscale proteomic sample preparation method. J. Proteome Res. 4, 2397-2403.
31. Dwivedi, R. C., Spicer, V., Harder, M., Antonovici, M., Ens, W., Standing, K. G., Wilkins, J. A., and Krokhin, O. V. (2008) Practical implementation of 2D HPLC scheme with accurate peptide retention prediction in both dimensions for high-throughput bottom-up proteomics. Anal. Chem. 80, 7036-7042.
32. Whitehouse, C. M., Dreyer, R. N., Yamashita, M., and Fenn, J. B. (1985) Electrospray interface for liquid chromatographs and mass spectrometers. Anal. Chem. 57, 675-679.
33. Franzen, J. (1998) Method and device for transport of ions in gas through a capillary. Google Patents.
34. Ishihama, Y., Rappsilber, J., Andersen, J. S., and Mann, M. (2002) Microcolumns with self-assembled particle frits for proteomics. J. Chromatogr. A 979, 233-239.
35. Ayoub, D., Jabs, W., Resemann, A., Evers, W., Evans, C., Main, L., Baessmann, C., Wagner-Rousset, E., Suckau, D., and Beck, A. (2013) Correct primary structure assessment and extensive glyco-profiling of cetuximab by a combination of intact, middle-up, middle-down, and bottom-up ESI and MALDI mass spectrometry techniques. mAbs 5, 699-710.
36. Senko, M. W., Beu, S. C., and McLaffertycor, F. W. (1995) Determination of monoisotopic masses and ion populations for large biomolecules from resolved isotopic distributions. J. Am. Soc. Mass Spectr. 6, 229-233.
37. Tsybin, Y. O., Fornelli, L., Stoermer, C., Luebeck, M., Parra, J., Nallet, S., Wurm, F. M., and Hartmer, R. (2011) Structural analysis of intact monoclonal antibodies by electron transfer dissociation mass spectrometry. Anal. Chem. 83, 8919-8927.
38. Cox, J., Neuhauser, N., Michalski, A., Scheltema, R. A., Olsen, J. V., and Mann, M. (2011) Andromeda: A peptide search engine integrated into the MaxQuant environment. J. Proteome Res. 10, 1794-1805.
39. Cox, J., Hein, M. Y., Luber, C. A., Paron, I., Nagaraj, N., and Mann, M. (2014) Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ. Mol. Cell. Proteomics 13, 2513-2526.
40. R Core Team (2014) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL http://www.R-project.org/.
41. Cox, J., and Mann, M. (2012) 1D and 2D annotation enrichment: A statistical method integrating quantitative proteomics with complementary highthroughput data. BMC Bioinformatics 13, S12.
42. Shaffer, S. A., Prior, D. C., Anderson, G. A., Udseth, H. R., and Smith, R. D. (1998) An ion funnel interface for improved ion focusing and sensitivity using electrospray ionization mass spectrometry. Anal. Chem. 70, 4111-4119.
43. Gerlich, D. (1992) Inhomogeneous RF fields a versatile tool for the study of processes with slow ions., John Wiley & Sons, Inc, Hoboken, NJ, U.S.A.
44. Steen, H., Kuster, B., Fernandez, M., Pandey, A., and Mann, M. (2001) Detection of tyrosine phosphorylated peptides by precursor ion scanning quadrupole TOF mass spectrometry in positive ion mode. Anal. Chem. 73, 1440-1448.
45. Räther, O. (2005) High resolution detection for time-of-flight mass spectrometers. US6870156 B2 patent.
46. Cox, J., and Mann, M. (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nature Biotechnol. 26, 1367-1372.
47. Cox, J., Hubner, N. C., and Mann, M. (2008) How much peptide sequence information is contained in ion trap tandem mass spectra? J. Am. Soc. Mass Spectr. 19, 1813-1820.
48. Cox, J., Michalski, A., and Mann, M. (2011) Software lock mass by twodimensional minimization of peptide mass errors. J. Am. Soc. Mass Spectr. 22, 1373-1380.
49. Wang, Y., Yang, F., Gritsenko, M. A., Wang, Y., Clauss, T., Liu, T., Shen, Y., Monroe, M. E., LopezFerrer, D., Reno, T., Moore, R. J., Klemke, R. L., Camp, D. G. 2nd, and Smith, R. D. (2011) Reversed-phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cells. Proteomics 11, 2019-2026.
50. de Godoy, L. M., Olsen, J. V., Cox, J., Nielsen, M. L., Hubner, N. C., Frohlich, F., Walther, T. C., and Mann, M. (2008) Comprehensive massspectrometry- based proteome quantification of haploid versus diploid yeast. Nature 455, 1251-1254.
51. Apanovitch, D. M., Slep, K. C., Sigler, P. B., and Dohlman, H. G. (1998) Sst2 is a GTPase-activating protein for Gpa1: purification and characterization of a cognate RGS-Galpha protein pair in yeast. Biochemistry 37, 4815-4822.
52. Pan, C., Kumar, C., Bohl, S., Klingmueller, U., and Mann, M. (2009) Comparative proteomic phenotyping of cell lines and primary cells to assess preservation of cell type-specific functions. Mol. Cell. Proteomics 8, 443-450.
53. Suzuki, H., Okunishi, R., Hashizume, W., Katayama, S., Ninomiya, N., Osato, N., Sato, K., Nakamura, M., Iida, J., Kanamori, M., and Hayashizaki, Y. (2004) Identification of region-specific transcription factor genes in the adult mouse brain by medium-scale real-time RT-PCR. FEBS Letters 573, 214-218.
54. Geiger, T., Wehner, A., Schaab, C., Cox, J., and Mann, M. (2012) Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins. Mol. Cell. Proteomics 11, M111 014050.
55. Schwanhausser, B., Busse, D., Li, N., Dittmar, G., Schuchhardt, J., Wolf, J., Chen, W., and Selbach, M. (2011) Global quantification of mammalian gene expression control. Nature 473, 337-342.