Comparative evaluation of electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) and high-pH reversed phase (Hp-RP) chromatography in profiling of rat kidney proteome

Journal of Proteomics

Volumn 82, Issue , 2013, Pages 254-262

  Hao, Piliang ^a   Ren, Yan ^a   Dutta, Bamaprasad ^a   Sze, Siu Kwan ^a  

^a NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

Author keywords

Concatenation; ERLIC; Hp RP; Multidimensional liquid chromatography; Proteome profiling

Indexed keywords

PROTEOME;

ANIMAL EXPERIMENT; ARTICLE; CHROMATOGRAPHY; COMPARATIVE STUDY; ELECTROSTATIC REPULSION HYDROPHILIC INTERACTION CHROMATOGRAPHY; FRACTIONATION; HIGH PH REVERSED PHASE CHROMATOGRAPHY; KIDNEY; MALE; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; RAT;

ANIMALS; CHROMATOGRAPHY, REVERSE-PHASE; ISOELECTRIC POINT; KIDNEY; MALE; PROTEOME; PROTEOMICS; RATS; RATS, SPRAGUE-DAWLEY;

EID: 84877955650     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2013.02.008     Document Type: Article

References (36)

1. Domon B., Aebersold R. Mass spectrometry and protein analysis. Science 2006, 312:212-217.
2. Mann M., Kelleher N.L. Precision proteomics: the case for high resolution and high mass accuracy. Proc Natl Acad Sci U S A 2008, 105:18132-18138.
3. Thakur S.S., Geiger T., Chatterjee B., Bandilla P., Frohlich F., Cox J., et al. Deep and highly sensitive proteome coverage by LC-MS/MS without prefractionation. Mol Cell Proteomics 2011, 10:M110. [003699].
4. Yates J.R., Gilchrist A., Howell K.E., Bergeron J.J. Proteomics of organelles and large cellular structures. Nat Rev Mol Cell Biol 2005, 6:702-714.
5. Zhang H., Li X.J., Martin D.B., Aebersold R. Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry. Nat Biotechnol 2003, 21:660-666.
6. Motoyama A., Yates J.R. Multidimensional LC separations in shotgun proteomics. Anal Chem 2008, 80:7187-7193.
7. Fang X., Balgley B.M., Wang W., Park D.M., Lee C.S. Comparison of multidimensional shotgun technologies targeting tissue proteomics. Electrophoresis 2009, 30:4063-4070.
8. Fournier M.L., Gilmore J.M., Martin-Brown S.A., Washburn M.P. Multidimensional separations-based shotgun proteomics. Chem Rev 2007, 107:3654-3686.
9. 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, 2:43-50.
10. Boersema P.J., Mohammed S., Heck A.J. Hydrophilic interaction liquid chromatography (HILIC) in proteomics. Anal Bioanal Chem 2008, 391:151-159.
11. Gilar M., Olivova P., Chakraborty A.B., Jaworski A., Geromanos S.J., Gebler J.C. Comparison of 1-D and 2-D LC MS/MS methods for proteomic analysis of human serum. Electrophoresis 2009, 30:1157-1167.
12. Boersema P.J., Divecha N., Heck A.J., Mohammed S. Evaluation and optimization of ZIC-HILIC-RP as an alternative MudPIT strategy. J Proteome Res 2007, 6:937-946.
13. Cargile B.J., Sevinsky J.R., Essader A.S., Stephenson J.L., Bundy J.L. Immobilized pH gradient isoelectric focusing as a first-dimension separation in shotgun proteomics. J Biomol Tech 2005, 16:181-189.
14. 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, 28:1694-1703.
15. Wisniewski J.R., Zougman A., Mann M. Combination of FASP and StageTip-based fractionation allows in-depth analysis of the hippocampal membrane proteome. J Proteome Res 2009, 8:5674-5678.
16. Song C., Ye M., Han G., Jiang X., Wang F., Yu Z., et al. Reversed-phase-reversed-phase liquid chromatography approach with high orthogonality for multidimensional separation of phosphopeptides. Anal Chem 2010, 82:53-56.
17. Di Palma S., Hennrich M.L., Heck A.J., Mohammed S. Recent advances in peptide separation by multidimensional liquid chromatography for proteome analysis. J Proteomics 2012, 75:3791-3813.
18. Slebos R.J., Brock J.W., Winters N.F., Stuart S.R., Martinez M.A., Li M., et al. Evaluation of strong cation exchange versus isoelectric focusing of peptides for multidimensional liquid chromatography-tandem mass spectrometry. J Proteome Res 2008, 7:5286-5294.
19. Manadas B., English J.A., Wynne K.J., Cotter D.R., Dunn M.J. Comparative analysis of OFFGel, strong cation exchange with pH gradient, and RP at high pH for first-dimensional separation of peptides from a membrane-enriched protein fraction. Proteomics 2009, 9:5194-5198.
20. Hao P., Guo T., Li X., Adav S.S., Yang J., Wei M., et al. Novel application of electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) in shotgun proteomics: comprehensive profiling of rat kidney proteome. J Proteome Res 2010, 9:3520-3526.
21. Wang Y., Yang F., Gritsenko M.A., Clauss T., Liu T., Shen Y., et al. Reversed-phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cells. Proteomics 2011, 11:2019-2026.
22. Hao P., Qian J., Ren Y., Sze S.K. Electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) versus strong cation exchange (SCX) for fractionation of iTRAQ-labeled peptides. J Proteome Res 2011, 10:5568-5574.
23. Alpert A.J. Electrostatic repulsion hydrophilic interaction chromatography for isocratic separation of charged solutes and selective isolation of phosphopeptides. Anal Chem 2008, 80:62-76.
24. Gokce E., Andrews G.L., Dean R.A., Muddiman D.C. Increasing proteome coverage with offline RP HPLC coupled to online RP nanoLC-MS. J Chromatogr B Analyt Technol Biomed Life Sci 2011, 879:610-614.
25. Stephanowitz H., Lange S., Lang D., Freund C., Krause E. Improved two-dimensional reversed phase-reversed phase LC-MS/MS approach for identification of peptide-protein interactions. J Proteome Res 2012, 11:1175-1183.
26. Hao P., Ren Y., Alpert A.J., Sze S.K. Detection, evaluation and minimization of nonenzymatic deamidation in proteomic sample preparation. Mol Cell Proteomics 2011, 10:O111. [009381].
27. 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.
28. Kall L., Storey J.D., MacCoss M.J., Noble W.S. Assigning significance to peptides identified by tandem mass spectrometry using decoy databases. J Proteome Res 2008, 7:29-34.
29. Rice P., Longden I., Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 2000, 16:276-277.
30. Kyte J., Doolittle R.F. A simple method for displaying the hydropathic character of a protein. J Mol Biol 1982, 157:105-132.
31. Dwivedi R.C., Spicer V., Harder M., Antonovici M., Ens W., Standing K.G., et al. Practical implementation of 2D HPLC scheme with accurate peptide retention prediction in both dimensions for high-throughput bottom-up proteomics. Anal Chem 2008, 80:7036-7042.
32. Gilar M., Olivova P., Daly A.E., Gebler J.C. Orthogonality of separation in two-dimensional liquid chromatography. Anal Chem 2005, 77:6426-6434.
33. Xie F., Smith R.D., Shen Y. Advanced proteomic liquid chromatography. J Chromatogr A 2012, 1261:78-90.
34. Hao P., Qian J., Dutta B., Cheow E.S., Sim K.H., Meng W., et al. Enhanced separation and characterization of deamidated peptides with RP-ERLIC-based multidimensional chromatography coupled with tandem mass spectrometry. J Proteome Res 2012, 11:1804-1811.
35. Delmotte N., Lasaosa M., Tholey A., Heinzle E., Huber C.G. Two-dimensional reversed-phase×ion-pair reversed-phase HPLC: an alternative approach to high-resolution peptide separation for shotgun proteome analysis. J Proteome Res 2007, 6:4363-4373.
36. de Jong E.P., Griffin T.J. Online nanoscale ERLIC-MS outperforms RPLC-MS for shotgun proteomics in complex mixtures. J Proteome Res 2012, 11:5059-5064.