Fully automated multifunctional ultrahigh pressure liquid chromatography system for advanced proteome analyses

Journal of Proteome Research

Volumn 11, Issue 8, 2012, Pages 4373-4381

  Lee, Jung Hwa ^a   Hyung, Seok Won ^a   Mun, Dong Gi ^a   Jung, Hee Jung ^a   Kim, Hokeun ^a   Lee, Hangyeore ^a   Kim, Su Jin ^a   Park, Kyong Soo ^b   Moore, Ronald J ^c   Smith, Richard D ^c   Lee, Sang Won ^a  

^a Korea University   (South Korea)

^b Seoul National University College of Medicine   (South Korea)

^c PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

Author keywords

1DLC; 2DLC; Bottom Up Proteomics; Multifunctional LC; Online Phosphopeptide Enrichment; tandem mass spectrometry

Indexed keywords

PHOSPHOPEPTIDE; PROTEOME; TITANIUM DIOXIDE;

ARTICLE; AUTOMATION; CHROMATOGRAPHY; ELUTION; FLOW RATE; HUMAN; HUMAN CELL; LIQUID CHROMATOGRAPHY; MULTIFUNCTIONAL ULTRAHIGH PRESSURE LIQUID CHROMATOGRAPHY; ONLINE ANALYSIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; REVERSED PHASE LIQUID CHROMATOGRAPHY; STRONG CATION EXCHANGE CHROMATOGRAPHY;

AMINO ACID SEQUENCE; AUTOMATION, LABORATORY; CELL LINE, TUMOR; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; CHROMATOGRAPHY, ION EXCHANGE; CHROMATOGRAPHY, REVERSE-PHASE; HUMANS; MOLECULAR SEQUENCE DATA; PHOSPHOPROTEINS; PROTEOME; SOLID PHASE EXTRACTION; TANDEM MASS SPECTROMETRY;

EID: 84864580130     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr3004166     Document Type: Article

References (55)

1. Fournier, M. L.; Gilmore, J. M.; Martin-Brown, S. A.; Washburn, M. P. Multidimensional separations-based shotgun proteomics Chem. Rev. 2007, 107 (8) 3654-86 (Pubitemid 47322747)
2. Motoyama, A.; Yates, J. R., 3rd Multidimensional LC separations in shotgun proteomics Anal. Chem. 2008, 80 (19) 7187-93
3. Motoyama, A.; Venable, J. D.; Ruse, C. I.; Yates, J. R., 3rd Automated ultra-high-pressure multidimensional protein identification technology (UHP-MudPIT) for improved peptide identification of proteomic samples Anal. Chem. 2006, 78 (14) 5109-18 (Pubitemid 44100648)
4. Link, A. J.; Eng, J.; Schieltz, D. M.; Carmack, E.; Mize, G. J.; Morris, D. R.; Garvik, B. M.; Yates, J. R., 3rd Direct analysis of protein complexes using mass spectrometry Nat. Biotechnol. 1999, 17 (7) 676-82 (Pubitemid 29316146)
5. Mann, M.; Kelleher, N. L. Precision proteomics: the case for high resolution and high mass accuracy Proc. Natl. Acad. Sci. U.S.A. 2008, 105 (47) 18132-8
6. Shen, Y.; Zhang, R.; Moore, R. J.; Kim, J.; Metz, T. O.; Hixson, K. K.; Zhao, R.; Livesay, E. A.; Udseth, H. R.; Smith, R. D. 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) 3090-100 (Pubitemid 40695464)
7. Liu, H.; Lin, D.; Yates, J. R., 3rd Multidimensional separations for protein/peptide analysis in the post-genomic era. Biotechniques 2002, 32 (4), 898, 900, 902 passim.
8. Ivanov, A. R.; Zang, L.; Karger, B. L. Low-attomole electrospray ionization MS and MS/MS analysis of protein tryptic digests using 20-microm-i.d. polystyrene-divinylbenzene monolithic capillary columns Anal. Chem. 2003, 75 (20) 5306-16 (Pubitemid 37280554)
9. Shen, Y.; Tolic, N.; Zhao, R.; Pasa-Tolic, L.; Li, L.; Berger, S. J.; Harkewicz, R.; Anderson, G. A.; Belov, M. E.; Smith, R. D. High-throughput proteomics using high-efficiency multiple-capillary liquid chromatography with on-line high-performance ESI FTICR mass spectrometry Anal. Chem. 2001, 73 (13) 3011-21 (Pubitemid 32868160)
10. Opiteck, G. J.; Jorgenson, J. W. Two-dimensional SEC/RPLC coupled to mass spectrometry for the analysis of peptides Anal. Chem. 1997, 69 (13) 2283-91
11. Nagele, E.; Vollmer, M.; Horth, P. Two-dimensional nano-liquid chromatography-mass spectrometry system for applications in proteomics J. Chromatogr., A 2003, 1009 (1-2) 197-205 (Pubitemid 36966684)
12. Davis, M. T.; Beierle, J.; Bures, E. T.; McGinley, M. D.; Mort, J.; Robinson, J. H.; Spahr, C. S.; Yu, W.; Luethy, R.; Patterson, S. D. Automated LC-LC-MS-MS platform using binary ion-exchange and gradient reversed-phase chromatography for improved proteomic analyses J. Chromatogr., B: Biomed. Sci. Appl. 2001, 752 (2) 281-91 (Pubitemid 32168162)
13. Wolters, D. A.; Washburn, M. P.; Yates, J. R., 3rd An automated multidimensional protein identification technology for shotgun proteomics Anal. Chem. 2001, 73 (23) 5683-90 (Pubitemid 33126725)
14. Vollmer, M.; Nagele, E.; Horth, P. Differential proteome analysis: two-dimensional nano-LC/MS of E. coli proteome grown on different carbon sources J. Biomol. Tech. 2003, 14 (2) 128-35
15. Gilar, M.; Olivova, P.; Daly, A. E.; Gebler, J. C. Two-dimensional separation of peptides using RP-RP-HPLC system with different pH in first and second separation dimensions J. Sep. Sci. 2005, 28 (14) 1694-703 (Pubitemid 43055013)
16. Shen, Y.; Jacobs, J. M.; Camp, D. G., 2nd; Fang, R.; Moore, R. J.; Smith, R. D.; Xiao, W.; Davis, R. W.; Tompkins, R. G. Ultra-high-efficiency strong cation exchange LC/RPLC/MS/MS for high dynamic range characterization of the human plasma proteome Anal. Chem. 2004, 76 (4) 1134-44 (Pubitemid 38235564)
17. Dai, J.; Shieh, C. H.; Sheng, Q. H.; Zhou, H.; Zeng, R. Proteomic analysis with integrated multiple dimensional liquid chromatography/mass spectrometry based on elution of ion exchange column using pH steps Anal. Chem. 2005, 77 (18) 5793-9 (Pubitemid 41324277)
18. Evans, C. R.; Jorgenson, J. W. Multidimensional LC-LC and LC-CE for high-resolution separations of biological molecules Anal. Bioanal. Chem. 2004, 378 (8) 1952-61 (Pubitemid 40871547)
19. Masuda, J.; Maynard, D. M.; Nishimura, M.; Ueda, T.; Kowalak, J. A.; Markey, S. P. Fully automated micro- and nanoscale one- or two-dimensional high-performance liquid chromatography system for liquid chromatography-mass spectrometry compatible with non-volatile salts for ion exchange chromatography J. Chromatogr., A 2005, 1063 (1-2) 57-69 (Pubitemid 40075533)
20. Nagele, E.; Vollmer, M.; Horth, P.; Vad, C. 2D-LC/MS techniques for the identification of proteins in highly complex mixtures Expert Rev. Proteomics 2004, 1 (1) 37-46 (Pubitemid 43826427)
21. Peng, J.; Elias, J. E.; Thoreen, C. C.; Licklider, L. J.; Gygi, S. P. 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)
22. Gygi, S. P.; Rist, B.; Gerber, S. A.; Turecek, F.; Gelb, M. H.; Aebersold, R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags Nat. Biotechnol. 1999, 17 (10) 994-9 (Pubitemid 29474856)
23. Winnik, W. M. Continuous pH/salt gradient and peptide score for strong cation exchange chromatography in 2D-nano-LC/MS/MS peptide identification for proteomics Anal. Chem. 2005, 77 (15) 4991-8 (Pubitemid 41076692)
24. Nagele, E.; Vollmer, M.; Horth, P. Improved 2D nano-LC/MS for proteomics applications: a comparative analysis using yeast proteome J. Biomol. Tech. 2004, 15 (2) 134-43
25. Min, H. K.; Hyung, S. W.; Shin, J. W.; Nam, H. S.; Ahn, S. H.; Jung, H. J.; Lee, S. W. Ultrahigh-pressure dual online solid phase extraction/capillary reverse-phase liquid chromatography/tandem mass spectrometry (DO-SPE/cRPLC/MS/MS): a versatile separation platform for high-throughput and highly sensitive proteomic analyses Electrophoresis 2007, 28 (6) 1012-21 (Pubitemid 46554605)
26. Wang, N.; Xie, C.; Young, J. B.; Li, L. Off-line two-dimensional liquid chromatography with maximized sample loading to reversed-phase liquid chromatography-electrospray ionization tandem mass spectrometry for shotgun proteome analysis Anal. Chem. 2009, 81 (3) 1049-60
27. Yan, J. X.; Packer, N. H.; Gooley, A. A.; Williams, K. L. Protein phosphorylation: technologies for the identification of phosphoamino acids J. Chromatogr., A 1998, 808 (1-2) 23-41 (Pubitemid 28273216)
28. Mann, M.; Ong, S. E.; Gronborg, M.; Steen, H.; Jensen, O. N.; Pandey, A. Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome Trends Biotechnol. 2002, 20 (6) 261-8 (Pubitemid 34451062)
29. Beausoleil, S. A.; Jedrychowski, M.; Schwartz, D.; Elias, J. E.; Villen, J.; Li, J.; Cohn, M. A.; Cantley, L. C.; Gygi, S. P. Large-scale characterization of HeLa cell nuclear phosphoproteins Proc. Natl. Acad. Sci. U.S.A. 2004, 101 (33) 12130-5 (Pubitemid 39145408)
30. Schlosser, A.; Bodem, J.; Bossemeyer, D.; Grummt, I.; Lehmann, W. D. Identification of protein phosphorylation sites by combination of elastase digestion, immobilized metal affinity chromatography, and quadrupole-time of flight tandem mass spectrometry Proteomics 2002, 2 (7) 911-8 (Pubitemid 34803974)
31. Aebersold, R.; Goodlett, D. R. Mass spectrometry in proteomics Chem. Rev. 2001, 101 (2) 269-95 (Pubitemid 32325797)
32. Ficarro, S. B.; McCleland, M. L.; Stukenberg, P. T.; Burke, D. J.; Ross, M. M.; Shabanowitz, J.; Hunt, D. F.; White, F. M. Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae Nat. Biotechnol. 2002, 20 (3) 301-5 (Pubitemid 34205425)
33. Dunn, J. D.; Reid, G. E.; Bruening, M. L. Techniques for phosphopeptide enrichment prior to analysis by mass spectrometry Mass Spectrom. Rev. 2010, 29 (1) 29-54
34. McLachlin, D. T.; Chait, B. T. Analysis of phosphorylated proteins and peptides by mass spectrometry Curr. Opin. Chem. Biol. 2001, 5 (5) 591-602 (Pubitemid 32907613)
35. Wang, J.; Zhang, Y.; Jiang, H.; Cai, Y.; Qian, X. Phosphopeptide detection using automated online IMAC-capillary LC-ESI-MS/MS Proteomics 2006, 6 (2) 404-11 (Pubitemid 43208019)
36. Dai, J.; Wang, L. S.; Wu, Y. B.; Sheng, Q. H.; Wu, J. R.; Shieh, C. H.; Zeng, R. Fully automatic separation and identification of phosphopeptides by continuous pH-gradient anion exchange online coupled with reversed-phase liquid chromatography mass spectrometry J. Proteome Res. 2009, 8 (1) 133-41
37. Pinkse, M. W.; Mohammed, S.; Gouw, J. W.; van Breukelen, B.; Vos, H. R.; Heck, A. J. Highly robust, automated, and sensitive online TiO2-based phosphoproteomics applied to study endogenous phosphorylation in Drosophila melanogaster J. Proteome Res. 2008, 7 (2) 687-97 (Pubitemid 351294031)
38. Chomyn, A. Platelet-mediated transformation of human mitochondrial DNA-less cells Methods Enzymol. 1996, 264, 334-9 (Pubitemid 26089321)
39. Wisniewski, J. R.; Zougman, A.; Nagaraj, N.; Mann, M. Universal sample preparation method for proteome analysis Nat. Methods 2009, 6 (5) 359-62
40. Zhao, R.; Ding, S. J.; Shen, Y.; Camp, D. G., 2nd; Livesay, E. A.; Udseth, H.; Smith, R. D. Automated metal-free multiple-column nanoLC for improved phosphopeptide analysis sensitivity and throughput J. Chromatogr., B: Anal. Technol. Biomed. Life Sci. 2009, 877 (8-9) 663-70
41. Shen, Y.; Zhao, R.; Berger, S. J.; Anderson, G. A.; Rodriguez, N.; Smith, R. D. High-efficiency nanoscale liquid chromatography coupled on-line with mass spectrometry using nanoelectrospray ionization for proteomics Anal. Chem. 2002, 74 (16) 4235-49 (Pubitemid 34912927)
42. Shen, Y.; Moore, R. J.; Zhao, R.; Blonder, J.; Auberry, D. L.; Masselon, C.; Pasa-Tolic, L.; Hixson, K. K.; Auberry, K. J.; Smith, R. D. High-efficiency on-line solid-phase extraction coupling to 15-150-microm-i.d. column liquid chromatography for proteomic analysis Anal. Chem. 2003, 75 (14) 3596-3605 (Pubitemid 36871253)
43. Shen, Y.; Tolic, N.; Masselon, C.; Pasa-Tolic, L.; Camp, D. G., 2nd; Hixson, K. K.; Zhao, R.; Anderson, G. A.; Smith, R. D. Ultrasensitive proteomics using high-efficiency on-line micro-SPE-nanoLC-nanoESI MS and MS/MS Anal. Chem. 2004, 76 (1) 144-54 (Pubitemid 38040644)
44. Hyung, S. W.; Kim, M. S.; Mun, D. G.; Lee, H.; Lee, S. W. The effect and potential of using a temperature controlled separation column with ultra-high pressure microcapillary liquid chromatography/tandem mass spectrometry on proteomic analysis Analyst 2011, 136 (10) 2100-5
45. Jung, H. J.; Purvine, S. O.; Kim, H.; Petyuk, V. A.; Hyung, S. W.; Monroe, M. E.; Mun, D. G.; Kim, K. C.; Park, J. M.; Kim, S. J.; Tolic, N.; Slysz, G. W.; Moore, R. J.; Zhao, R.; Adkins, J. N.; Anderson, G. A.; Lee, H.; Camp, D. G., 2nd; Yu, M. H.; Smith, R. D.; Lee, S. W. Integrated post-experiment monoisotopic mass refinement: an integrated approach to accurately assign monoisotopic precursor masses to tandem mass spectrometric data Anal. Chem. 2010, 82 (20) 8510-8
46. Mayampurath, A. M.; Jaitly, N.; Purvine, S. O.; Monroe, M. E.; Auberry, K. J.; Adkins, J. N.; Smith, R. D. DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra Bioinformatics 2008, 24 (7) 1021-3 (Pubitemid 351448041)
47. Shin, B.; Jung, H. J.; Hyung, S. W.; Kim, H.; Lee, D.; Lee, C.; Yu, M. H.; Lee, S. W. Postexperiment monoisotopic mass filtering and refinement (PE-MMR) of tandem mass spectrometric data increases accuracy of peptide identification in LC/MS/MS Mol. Cell. Proteomics 2008, 7 (6) 1124-34 (Pubitemid 351943959)
48. Petyuk, V. A.; Jaitly, N.; Moore, R. J.; Ding, J.; Metz, T. O.; Tang, K.; Monroe, M. E.; Tolmachev, A. V.; Adkins, J. N.; Belov, M. E.; Dabney, A. R.; Qian, W. J.; Camp, D. G., 2nd; Smith, R. D. Elimination of systematic mass measurement errors in liquid chromatography-mass spectrometry based proteomics using regression models and a priori partial knowledge of the sample content Anal. Chem. 2008, 80 (3) 693-706 (Pubitemid 351206857)
49. Petyuk, V. A.; Mayampurath, A. M.; Monroe, M. E.; Polpitiya, A. D.; Purvine, S. O.; Anderson, G. A.; Camp, D. G., 2nd; Smith, R. D. DtaRefinery, a software tool for elimination of systematic errors from parent ion mass measurements in tandem mass spectra data sets Mol. Cell. Proteomics 2010, 9 (3) 486-96
50. Wren, S. A. Peak capacity in gradient ultra performance liquid chromatography (UPLC) J. Pharm. Biomed. Anal. 2005, 38 (2) 337-43 (Pubitemid 40733163)
51. Neue, U. D. Theory of peak capacity in gradient elution J. Chromatogr., A 2005, 1079 (1-2) 153-61 (Pubitemid 40813197)
52. Shen, Y.; Smith, R. D.; Unger, K. K.; Kumar, D.; Lubda, D. Ultrahigh-throughput proteomics using fast RPLC separations with ESI-MS/MS Anal. Chem. 2005, 77 (20) 6692-701 (Pubitemid 41504454)
53. Zimmer, J. S.; Monroe, M. E.; Qian, W. J.; Smith, R. D. Advances in proteomics data analysis and display using an accurate mass and time tag approach Mass Spectrom. Rev. 2006, 25 (3) 450-82
54. Neilson, K. A.; Ali, N. A.; Muralidharan, S.; Mirzaei, M.; Mariani, M.; Assadourian, G.; Lee, A.; van Sluyter, S. C.; Haynes, P. A. Less label, more free: approaches in label-free quantitative mass spectrometry Proteomics 2011, 11 (4) 535-53
55. Lopez-Ferrer, D.; Petritis, K.; Robinson, E. W.; Hixson, K. K.; Tian, Z.; Lee, J. H.; Lee, S. W.; Tolic, N.; Weitz, K. K.; Belov, M. E.; Smith, R. D.; Pasa-Tolic, L. Pressurized pepsin digestion in proteomics: an automatable alternative to trypsin for integrated top-down bottom-up proteomics Mol. Cell. Proteomics 2011, 10 (2) M110 001479