In-house construction of a UHPLC system enabling the identification of over 4000 protein groups in a single analysis

Analyst

Volumn 137, Issue 15, 2012, Pages 3541-3548

  Cristobal, Alba ^a,b   Hennrich, Marco L ^a,b   Giansanti, Piero ^a,b   Goerdayal, Soenita S ^a,b   Heck, Albert J R ^a,b   Mohammed, Shabaz ^a,b  

^a UTRECHT UNIVERSITY   (Netherlands)

^b NETHERLANDS PROTEOMICS CENTRE   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84863700845     PISSN: 00032654     EISSN: 13645528     Source Type: Journal    
DOI: 10.1039/c2an35445d     Document Type: Article

References (45)

1. J. R. Yates 3rd Mass spectrometry as an emerging tool for systems biology BioTechniques 2004 36 6 917 919
2. R. Aebersold M. Mann Mass spectrometry-based proteomics Nature 2003 422 6928 198 207 (Pubitemid 36362757)
3. N. Bisson D. A. James G. Ivosev S. A. Tate R. Bonner L. Taylor T. Pawson Selected reaction monitoring mass spectrometry reveals the dynamics of signaling through the GRB2 adaptor Nat. Biotechnol. 2011 29 7 653 658
4. J. V. Olsen J. C. Schwartz J. Griep-Raming M. L. Nielsen E. Damoc E. Denisov O. Lange P. Remes D. Taylor M. Splendore E. R. Wouters M. Senko A. Makarov M. Mann S. Horning A dual pressure linear ion trap Orbitrap instrument with very high sequencing speed Mol. Cell. Proteomics 2009 8 12 2759 2769
5. T. P. Second J. D. Blethrow J. C. Schwartz G. E. Merrihew M. J. MacCoss D. L. Swaney J. D. Russell J. J. Coon V. Zabrouskov Dual-pressure linear ion trap mass spectrometer improving the analysis of complex protein mixtures Anal. Chem. 2009 81 18 7757 7765
6. G. L. Andrews B. L. Simons J. B. Young A. M. Hawkridge D. C. Muddiman Performance characteristics of a new hybrid quadrupole time-of-flight tandem mass spectrometer (TripleTOF 5600) Anal. Chem. 2011 83 13 5442 5446
7. J. V. Olsen B. Macek O. Lange A. Makarov S. Horning M. Mann Higher-energy C-trap dissociation for peptide modification analysis Nat. Methods 2007 4 9 709 712 (Pubitemid 47338163)
8. J. E. P. Syka J. J. Coon M. J. Schroeder J. Shabanowitz D. F. Hunt Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry Proc. Natl. Acad. Sci. U. S. A. 2004 101 26 9528 9533 (Pubitemid 38869270)
9. J. C. Giddings Two-dimensional separations: concept and promise Anal. Chem. 1984 56 12 1258A 1270A
10. M. P. Washburn D. Wolters J. R. Yates Large-scale analysis of the yeast proteome by multidimensional protein identification technology Nat. Biotechnol. 2001 19 3 242 247 (Pubitemid 32220565)
11. J. Peng J. E. Elias C. C. Thoreen L. J. Licklider S. P. Gygi Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome J. Proteome Res. 2003 2 1 43 50 (Pubitemid 36207189)
12. J. Chen C. S. Lee Y. Shen R. D. Smith E. H. Baehrecke Integration of capillary isoelectric focusing with capillary reversed-phase liquid chromatography for two-dimensional proteomics separation Electrophoresis 2002 23 18 3143 3148 (Pubitemid 35154165)
13. M. R. Emmett R. M. Caprioli Micro-electrospray mass spectrometry: ultra-high-sensitivity analysis of peptides and proteins J. Am. Soc. Mass Spectrom. 1994 5 7 605 613
14. J. P. Chervet M. Ursem J. P. Salzmann Instrumental requirements for nanoscale liquid chromatography Anal. Chem. 1996 68 9 1507 1512
15. T. Masuda N. Sugiyama M. Tomita Y. Ishihama Microscale phosphoproteome analysis of 10,000 cells from human cancer cell lines Anal. Chem. 2011 83 20 7698 7703
16. S. S. Thakur, T. Geiger, B. Chatterjee, P. Bandilla, F. Fröhlich, J. Cox and M. Mann, Deep and highly sensitive proteome coverage by LC-MS/MS without prefractionation, Mol. Cell. Proteomics, 2011, 10 (8), M110.003699
17. A. Michalski J. Cox M. Mann 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. 2011 10 4 1785 1793
18. G. L. Andrews C. M. Shuford J. C. Burnett Jr A. M. Hawkridge D. C. Muddiman Coupling of a vented column with splitless nanoRPLC-ESI-MS for the improved separation and detection of brain natriuretic peptide-32 and its proteolytic peptides J. Chromatogr., B: Anal. Technol. Biomed. Life Sci. 2009 877 10 948 954
19. B. Devreese F. Vanrobaeys J. Van Beeumen Automated nanoflow liquid chromatography/tandem mass spectrometric identification of proteins from Shewanella putrefaciens separated by two-dimensional polyacrylamide gel electrophoresis Rapid Commun. Mass Spectrom. 2001 15 1 50 56 (Pubitemid 32094791)
20. L. J. Licklider C. C. Thoreen J. Peng S. P. Gygi Automation of nanoscale microcapillary liquid chromatography-tandem mass spectrometry with a vented column Anal. Chem. 2002 74 13 3076 3083 (Pubitemid 34755220)
21. Y. Ishihama, J. Rappsilber, J. S. Andersen and M. Mann, in Proceedings of the 50th Annual Conference on Mass Spectrometry and Allied Topics, Orlando, FL, USA, June, 2002
22. H. Yin K. Killeen R. Brennen D. Sobek M. Werlich T. van de Goor Microfluidic chip for peptide analysis with an integrated HPLC column, sample enrichment column, and nanoelectrospray tip Anal. Chem. 2004 77 2 527 533 (Pubitemid 40116832)
23. R. Gallagher, R. Peter, K. Pickup, K. Samuelsson, I. Wilson, L. Dillon and D. Douce, in Proceedings of the 59th Annual Conference on Mass Spectrometry and Allied Topics, Denver, CO, USA, June, 2011
24. J. W. Jorgenson Capillary liquid chromatography at ultrahigh pressures Annu. Rev. Anal. Chem. 2010 3 129 150
25. J. E. MacNair K. D. Patel J. W. Jorgenson Ultrahigh-pressure reversed-phase capillary liquid chromatography: isocratic and gradient elution using columns packed with 1.0 μm particles Anal. Chem. 1999 71 3 700 708
26. J. E. MacNair K. C. Lewis J. W. Jorgenson Ultrahigh-pressure reversed-phase liquid chromatography in packed capillary columns Anal. Chem. 1997 69 6 983 989
27. M. E. Swartz UPLCTM: an introduction and review J. Liq. Chromatogr. Relat. Technol. 2005 28 7-8 1253 1263
28. T. Köcher R. Swart K. Mechtler 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 7 2699 2704
29. M. Iwasaki S. Miwa T. Ikegami M. Tomita N. Tanaka Y. Ishihama One-dimensional capillary liquid chromatographic separation coupled with tandem mass spectrometry unveils the Escherichia coli proteome on a microarray scale Anal. Chem. 2010 82 7 2616 2620
30. Y. Shen R. Zhang R. J. Moore J. Kim T. O. Metz K. K. Hixson R. Zhao E. A. Livesay H. R. Udseth R. D. Smith 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 10 3090 3100 (Pubitemid 40695464)
31. Q. Luo Y. Shen K. K. Hixson R. Zhao F. Yang R. J. Moore H. M. Mottaz R. D. Smith Preparation of 20 μm-i.d. Silica-based monolithic columns and their performance for proteomics analyses Anal. Chem. 2005 77 15 5028 5035 (Pubitemid 41076696)
32. A. O. Helbig S. Gauci R. Raijmajers B. van Breukelen M. Slijper S. Mohammed A. J. R. Heck Profiling of N-acetylated protein termini provides in-depth insights into the N-terminal nature of the proteome Mol. Cell. Proteomics 2010 9 5 928 939
33. J. J. Kirkland J. J. Destefano The art and science of forming packed analytical high-performance liquid chromatography columns J. Chromatogr., A 2006 1126 1-2 50 57 (Pubitemid 44403914)
34. H. J. Cortes C. D. Pfeiffer B. E. Richter T. S. Stevens Porous ceramic bed supports for fused silica packed capillary columns used in liquid chromatography J. High Resolut. Chromatogr. 1987 10 8 446 448 (Pubitemid 17652169)
35. M. M. Savitski T. Mathieson I. Becher M. Bantscheff H-score, a mass accuracy driven rescoring approach for improved peptide identification in modification rich samples J. Proteome Res. 2010 9 11 5511 5516
36. L. Kall J. D. Canterbury J. Weston W. S. Noble M. J. MacCoss Semi-supervised learning for peptide identification from shotgun proteomics datasets Nat. Methods 2007 4 11 923 925 (Pubitemid 350042380)
37. W. P. van den Toorn Henk J. Muñoz S. Mohammed R. Raijmakers A. J. Heck B. van Breukelen RockerBox: analysis and filtering of massive proteomics search results J. Proteome Res. 2011 10 3 1420 1424
38. J. E. Elias S. P. Gygi Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry Nat. Methods 2007 4 3 207 214 (Pubitemid 46358868)
39. M. Gilar A. E. Daly M. Kele U. D. Neue J. C. Gebler Implications of column peak capacity on the separation of complex peptide mixtures in single- and two-dimensional high-performance liquid chromatography J Chromatogr., A 2004 1061 2 183 192 (Pubitemid 39586746)
40. H. D. Meiring E. Van Der Heeft G. J. Ten Hove A. P. J. M. De Jong Nanoscale LC-MS(n): technical design and applications to peptide and protein analysis J. Sep. Sci. 2002 25 9 557 568 (Pubitemid 34790383)
41. J. J. van Deemter F. J. Zuiderweg A. Klinkenberg Longitudinal diffusion and resistance to mass transfer as causes of nonideality in chromatography Chem. Eng. Sci. 1956 5 6 271 289
42. M. L. Hennrich V. Groenewold G. J. P. L. Kops A. J. R. Heck S. Mohammed Improving depth in phosphoproteomics by using a strong cation exchange-weak anion exchange-reversed phase multidimensional separation approach Anal. Chem. 2011 83 18 7137 7143
43. A. Michalski E. Damoc J. P. Hauschild O. Lange A. Wieghaus A. Makarov N. Nagaraj J. Cox M. Mann S. Horning Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer Mol. Cell. Proteomics 2011 10 9
44. A. Michalski E. Damoc O. Lange E. Denisov D. Nolting M. Müller R. Viner J. Schwartz P. Remes M. Belford J. J. Dunyach J. Cox S. Horning M. Mann A. Makarov Ultra high resolution linear ion trap Orbitrap mass spectrometer (Orbitrap Elite) facilitates top down LC MS/MS and versatile peptide fragmentation modes Mol. Cell. Proteomics 2011
45. M. Iwasaki, N. Sugiyama, N. Tanaka, Y. Ishihama. Human proteome analysis by using reversed phase monolithic silica capillary columns with enhanced sensitivity. J Chromatogr., A, http://www.sciencedirect.com/science/article/pii/ S0021967311016013, accessed 20 December 2011