Development and performance evaluation of an ultralow flow nanoliquid chromatography-tandem mass spectrometry set-up

Proteomics

Volumn 14, Issue 17-18, 2014, Pages 1999-2007

  Köcher, Thomas ^a   Pichler, Peter ^a   De Pra, Mauro ^b   Rieux, Laurent ^b   Swart, Remco ^b   Mechtler, Karl ^a,c  

^a RESEARCH INSTITUTE OF MOLECULAR PATHOLOGY   (Austria)

^b Thermo Fisher Scientific   (United States)

^c INSTITUTE OF MOLECULAR BIOTECHNOLOGY   (Austria)

Author keywords

ESI; LC MS MS; Nanoflow LC; Protein identification; Technology

Indexed keywords

NANOBEAD; PEPTIDE; PROTEIN;

ARTICLE; CELL LYSATE; FLOW RATE; HELA CELL LINE; HUMAN; HUMAN CELL; LIQUID CHROMATOGRAPHY; PARTICLE SIZE; PROTEIN ANALYSIS; PROTEOMICS; SEPARATION TECHNIQUE; TANDEM MASS SPECTROMETRY; CHEMISTRY; DEVICES; ELECTROSPRAY MASS SPECTROMETRY; EQUIPMENT DESIGN; NANOTECHNOLOGY; PROCEDURES; REPRODUCIBILITY;

CHROMATOGRAPHY, LIQUID; EQUIPMENT DESIGN; HELA CELLS; HUMANS; NANOTECHNOLOGY; PEPTIDES; PROTEINS; REPRODUCIBILITY OF RESULTS; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION; TANDEM MASS SPECTROMETRY;

EID: 84908641937     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201300418     Document Type: Article

References (43)

1. Walther, T. C., Mann, M., Mass spectrometry-based proteomics in cell biology. J. Cell Biol. 2010, 190, 491-500.
2. Bensimon, A., Heck, A. J. R., Aebersold, R., Mass spectrometry-based proteomics and network biology. Annu. Rev. Biochem. 2012, 81, 379-405.
3. Yates, J. R., The revolution and evolution of shotgun proteomics for large-scale proteome analysis. J. Am. Chem. Soc. 2013, 135, 1629-1640.
4. Steen, H., Mann, M., The ABC's (and XYZ's) of peptide sequencing. Nat. Rev. Mol. Cell Biol. 2004, 5, 699-711.
5. Nesvizhskii, A. I., Vitek, O., Aebersold, R., Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat. Methods 2007, 4, 787-797.
6. Zhang, Y. Y., Fonslow, B. R., Shan, B., Baek, M. C., Yates, J. R., Protein Analysis by Shotgun/Bottom-up Proteomics. Chem. Rev. 2013, 113, 2343-2394.
7. Kocher, T., Superti-Furga, G., Mass spectrometry-based functional proteomics: from molecular machines to protein networks. Nat. Methods 2007, 4, 807-815.
8. Rix, U., Superti-Furga, G., Target profiling of small molecules by chemical proteomics. Nat. Chem. Biol. 2009, 5, 616-624.
9. Xie, F., Liu, T., Qian, W. J., Petyuk, V. A., Smith, R. D., Liquid chromatography-mass spectrometry-based quantitative proteomics. J. Biol. Chem. 2011, 286, 25443-25449.
10. Selbach, M., Schwanhausser, B., Thierfelder, N., Fang, Z. et al., Widespread changes in protein synthesis induced by microRNAs. Nature 2008, 455, 58-63.
11. de Godoy, L. M. F., Olsen, J. V., Cox, J., Nielsen, M. L. et al., Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature 2008, 455, 1251-1260.
12. Phanstiel, D. H., Brumbaugh, J., Wenger, C. D., Tian, S. L. et al., Proteomic and phosphoproteomic comparison of human ES and iPS cells. Nat. Methods 2011, 8, 821-827.
13. Gerszten, R. E., Asnani, A., Carr, S. A., Status and prospects for discovery and verification of new biomarkers of cardiovascular disease by proteomics. Circ. Res. 2011, 109, 463-474.
14. Hood, L., Perlmutter, R. M., The impact of systems approaches on biological problems in drug discovery. Nat. Biotechnol. 2004, 22, 1215-1217.
15. Andrews, G. L., Simons, B. L., Young, J. B., Hawkridge, A. M., Muddiman, D. C., Performance characteristics of a new hybrid quadrupole time-of-flight tandem mass spectrometer (TripleTOF 5600). Anal. Chem. 2011, 83, 5442-5446.
16. Hebert, A. S., Richards, A. L., Bailey, D. J., Ulbrich, A. et al., The one hour yeast proteome. Mol. Cell. Proteomics 2014, 13, 339-347.
17. Senko, M. W., Remes, P. M., Canterbury, J. D., Mathur, R. et al., Novel parallelized quadrupole/linear ion trap/orbitrap tribrid mass spectrometer improving proteome coverage and peptide identification rates. Anal. Chem. 2013, 85, 11710-11714.
18. MacNair, J. E., Lewis, K. C., Jorgenson, J. W., Ultrahigh pressure reversed-phase liquid chromatography in packed capillary columns. Anal. Chem. 1997, 69, 983-989.
19. Jorgenson, J. W., Capillary liquid chromatography at ultrahigh pressures. Ann. Rev. Anal. Chem. 2010, 3, 129-150.
20. Shen, Y. F., Zhang, R., Moore, R. J., Kim, J. et al., Automated 20 kpsi RPLC-MS and MS/MS with chromatographic peak capacities of 1000-1500 and capabilities in proteomics and metabolomics. Anal. Chem. 2005, 77, 3090-3100.
21. Kocher, T., Swart, R., Mechtler, K., Ultra-high-pressure rplc hyphenated to an ltq-orbitrap velos reveals a linear relation between peak capacity and number of identified peptides. Anal. Chem. 2011, 83, 2699-2704.
22. Thakur, S. S., Geiger, T., Chatterjee, B., Bandilla, P. et al., Deep and Highly Sensitive Proteome Coverage by LC-MS/MS Without Prefractionation. Mol. Cell. Proteomics 2011, 10, M110.003699.
23. Shen, Y. F., Zhao, R., Berger, S. J., Anderson, G. A. et al., High-efficiency nanoscale liquid chromatography coupled on-line with mass spectrometry using nanoelectrospray ionization for proteomics. Anal. Chem. 2002, 74, 4235-4249.
24. Wilm, M., Principles of electrospray ionization. Mol. Cell. Proteomics 2011, 10, M111.009407.
25. Schmidt, A., Karas, M., Dulcks, T., Effect of different solution flow rates on analyte ion signals in nano-ESI MS, or: When does ESI turn into nano-ESI? J. Am. Soc. Mass Spectrom. 2003, 14, 492-500.
26. Juraschek, R., Dulcks, T., Karas, M., Nanoelectrospray-more than just a minimized-flow electrospray ionization source. J. Am. Soc. Mass Spectrom. 1999, 10, 300-308.
27. Heemskerk, A. A. M., Busnel, J. M., Schoenmaker, B., Derks, R. J. E. et al., Ultra-low flow electrospray ionization-mass spectrometry for improved ionization efficiency in phosphoproteomics. Anal. Chem. 2012, 84, 4552-4559.
28. Ficarro, S. B., Zhang, Y., Lu, Y., Moghimi, A. R. et al., Improved electrospray ionization efficiency compensates for diminished chromatographic resolution and enables proteomics analysis of tyrosine signaling in embryonic stem cells. Anal. Chem. 2009, 81, 3440-3447.
29. Dewit, J. S. M., Parker, C. E., Tomer, K. B., Jorgenson, J. W., Direct coupling of open-tubular liquid chromatography with mass spectrometry. Anal. Chem. 1987, 59, 2400-2404.
30. Deterding, L. J., Moseley, M. A., Tomer, K. B., Jorgensen, J. W., Nanoscale separations combined with tandem mass spectrometry. J. Chromatogr. 1991, 554, 73-82.
31. Yue, G. H., Luo, Q. Z., Zhang, J., Wu, S. L., Karger, B. L., Ultratrace LC/MS proteomic analysis using 10-mu m-i.d. Porous layer open tubular poly(styrene-divinylbenzene) capillary columns. Anal. Chem. 2007, 79, 938-946.
32. van der Heeft, E., ten Hove, G. J., Herberts, C. A., Meiring, H. D. et al., A microcapillary column switching HPLC electrospray ionization MS system for the direct identification of peptides presented by major histocompatibility complex class I molecules. Anal. Chem. 1998, 70, 3742-3751.
33. Moseley, M. A., Deterding, L. J., Tomer, K. B., Jorgenson, J. W., Coupling of capillary zone electrophoresis and capillary liquid chromatography with coaxial continuous-flow fast atom bombardment tandem sector mass spectrometry. J. Chromatogr. 1989, 480, 197-209.
34. Martin, S. E., Shabanowitz, J., Hunt, D. F., Marto, J. A., Subfemtomole MS and MS/MS peptide sequence analysis using nano-HPLC micro-ESI Fourier transform ion cyclotron resonance mass spectrometry. Anal. Chem. 2000, 72, 4266-4274.
35. Gale, D. C., Smith, R. D., Small volume and low flow-rate electrospray ionization mass spectrometry of aqueous Samples. Rapid Commun. Mass Spectrom. 1993, 7, 1017-1021.
36. Emmett, M. R., Caprioli, R. M., Micro-electrospray mass spectrometry: ultra-high-sensitivity analysis of peptides and proteins. J. Am. Soc. Mass Spectrom. 1994, 5, 605-613.
37. Wilm, M., Mann, M., Analytical properties of the nanoelectrospray ion source. Anal. Chem. 1996, 68, 1-8.
38. Kocher, T., Pichler, P., Swart, R., Mechtler, K., Analysis of protein mixtures from whole-cell extracts by single-run nanoLC-MS/MS using ultralong gradients. Nat. Protoc. 2012, 7, 882-890.
39. Licklider, L. J., Thoreen, C. C., Peng, J. M., Gygi, S. P., Automation of nanoscale microcapillary liquid chromatography-tandem mass spectromentry with a vented column. Anal. Chem. 2002, 74, 3076-3083.
40. Pichler, P., Mazanek, M., Dusberger, F., Weilnbock, L. et al., SIMPATIQCO: A Server-Based Software Suite Which Facilitates Monitoring the Time Course of LC-MS Performance Metrics on Orbitrap Instruments. J. Proteome Res. 2012, 11, 5540-5547.
41. Vizcaino, J. A., Cote, R., Reisinger, F., Barsnes, H. et al., The Proteomics Identifications database: 2010 update. Nucleic Acids Res. 2010, 38, D736-D742.
42. Kall, L., Canterbury, J. D., Weston, J., Noble, W. S., MacCoss, M. J., Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat. Methods 2007, 4, 923-925.
43. Picotti, P., Aebersold, R., Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. Nat. Methods 2012, 9, 555-566.