Online nanoscale ERLIC-MS outperforms RPLC-MS for shotgun proteomics in complex mixtures

Journal of Proteome Research

Volumn 11, Issue 10, 2012, Pages 5059-5064

  De Jong, Ebbing P ^a   Griffin, Timothy J ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

Author keywords

mass spectrometry; online ERLIC; reversed phase liquid chromatography; shotgun proteomics

Indexed keywords

PEPTIDE;

ANALYTIC METHOD; ANALYTICAL EQUIPMENT; ARTICLE; ELECTROSPRAY MASS SPECTROMETRY; ELECTROSTATIC REPULSION HYDROPHILIC INTERACTION CHROMATOGRAPHY; HELA CELL; HUMAN; HUMAN CELL; MASS SPECTROMETER; NONHUMAN; ONLINE ANALYSIS; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEOMICS; REVERSED PHASE LIQUID CHROMATOGRAPHY; SHOTGUN PROTEOMICS; SOLUBILITY; YEAST CELL;

ACETONITRILES; BUFFERS; CHROMATOGRAPHY, REVERSE-PHASE; HELA CELLS; HUMANS; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; NANOTECHNOLOGY; PROTEOME; PROTEOMICS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SOLUBILITY; SOLVENTS; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION; TANDEM MASS SPECTROMETRY;

EID: 84867479231     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr300638n     Document Type: Article

References (20)

1. Alpert, A. J. Electrostatic repulsion hydrophilic interaction chromatography for isocratic separation of charged solutes and selective isolation of phosphopeptides Anal. Chem. 2008, 80 (1) 62-76
2. Hao, P. L.; Guo, T. N.; Sze, S. K. Simultaneous analysis of proteome, phospho- and glycoproteome of rat kidney tissue with electrostatic repulsion hydrophilic interaction chromatography Plos One 2011, 6, 2
3. Chien, K. Y.; Liu, H. C.; Goshe, M. B. Development and application of a phosphoproteomic method using electrostatic repulsion-hydrophilic interaction chromatography (ERLIC), IMAC, and LC-MS/MS analysis to study Mareks disease virus infection J. Proteome Res. 2011, 10 (9) 4041-53
4. Zarei, M.; Sprenger, A.; Metzger, F.; Gretzmeier, C.; Dengjel, J. Comparison of ERLIC-TiO2, HILIC-TiO2, and SCX-TiO2 for global phosphoproteomics approaches J. Proteome Res. 2011, 10 (8) 3474-83
5. Hao, P. L.; Guo, T. N.; Li, X.; Adav, S. S.; Yang, J.; Wei, M.; Sze, S. K. Novel application of electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) in shotgun proteomics: comprehensive profiling of rat kidney proteome J. Proteome Res. 2010, 9 (7) 3520-26
6. Hao, P.; Qian, J.; Dutta, B.; Cheow, E. S.; Sim, K. H.; Meng, W.; Adav, S. S.; Alpert, A.; Sze, S. K. Enhanced separation and characterization of deamidated peptides with RP-ERLIC-based multidimensional chromatography coupled with tandem mass spectrometry J. Proteome Res. 2012, 11 (3) 1804-11
7. Wisniewski, J. R.; Zougman, A.; Nagaraj, N.; Mann, M. Universal sample preparation method for proteome analysis Nat. Methods 2009, 6 (5) 359-62
8. Griffin, T. J.; Xie, H. W.; Bandhakavi, S.; Popko, J.; Mohan, A.; Carlis, J. V.; Higgins, L. iTRAQ reagent-based quantitative proteomic analysis on a linear ion trap mass spectrometer J. Proteome Res. 2007, 6 (11) 4200-09
9. Hao, P. L.; Ren, Y.; Alpert, A. J.; Sze, S. K. Detection, evaluation and minimization of nonenzymatic deamidation in proteomic sample preparation Mol. Cell. Proteomics 2011, 10 (10) 1-11
10. Di Palma, S.; Boersema, P. J.; Heck, A. J. R.; Mohammed, S. Zwitterionic hydrophilic interaction liquid chromatography (ZIC-HILIC and ZIC-cHILIC) provide high resolution separation and increase sensitivity in proteome analysis Anal. Chem. 2011, 83 (9) 3440-7
11. Di Palma, S.; Stange, D.; van de Wetering, M.; Clevers, H.; Heck, A. J. R.; Mohammed, S. Highly sensitive proteome analysis of FACS-sorted adult colon stem cells J. Proteome Res. 2011, 10 (8) 3814-9
12. Gilar, M.; Olivova, P.; Daly, A. E.; Gebler, J. C. Orthogonality of separation in two-dimensional liquid chromatography Anal. Chem. 2005, 77 (19) 6426-34
13. Zhang, H. M.; Guo, T. N.; Li, X.; Datta, A.; Park, J. E.; Yang, J.; Lim, S. K.; Tam, J. P.; Sze, S. K. Simultaneous characterization of glyco- and phosphoproteomes of mouse brain membrane proteome with electrostatic repulsion hydrophilic interaction chromatography Mol. Cell. Proteomics 2010, 9 (4) 635-47
14. Zarei, M.; Sprenger, A.; Metzger, F.; Gretzmeier, C.; Dengjel, J. Comparison of ERLIC-TiO(2), HILIC-TiO(2), and SCX-TiO(2) for global phosphoproteomics approaches J. Proteome Res. 2011, 10 (8) 3474-83
15. Boersema, P. J.; Divecha, N.; Heck, A. J. R.; Mohammed, S. Evaluation and optimization of ZIC-HILIC-RP as an alternative MudPIT strategy J. Proteome Res. 2007, 6 (3) 937-46
16. Kyte, J.; Doolittle, R. F. A simple method for displaying the hydropathic character of a protein J. Mol. Biol. 1982, 157 (1) 105-32
17. Weng, N. D.; Eerkes, A. Development and validation of a hydrophilic interaction liquid chromatography-tandem mass spectrometric method for the analysis of paroxetine in human plasma Biomedical Chromatography 2004, 18 (1) 28-36
18. Nguyen, H. P.; Schug, K. A. The advantages of ESI-MS detection in conjunction with HILIC mode separations: Fundamentals and applications J. Sep. Sci. 2008, 31 (9) 1465-80
19. Keller, A.; Nesvizhskii, A. I.; Kolker, E.; Aebersold, R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search Anal. Chem. 2002, 74 (20) 5383-92
20. Nesvizhskii, A. I., Protein identification by tandem mass spectrometry and sequence database searching. In Mass Spectrometry Data Analysis in Proteomics; Matthiesen, R., Ed.; Humana Press Inc.: Totowa, NJ, 2007; Vol. 367, pp 87-119.