Combinatorial use of electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) and strong cation exchange (SCX) chromatography for in-depth phosphoproteome analysis

Journal of Proteome Research

Volumn 11, Issue 8, 2012, Pages 4269-4276

  Zarei, Mostafa ^a   Sprenger, Adrian ^a,b   Gretzmeier, Christine ^a   Dengjel, Joern ^a  

^a UNIVERSITY OF FREIBURG   (Germany)

^b UNIVERSITY OF FREIBURG   (Germany)

Author keywords

ERLIC; mass spectrometry; MDLC; phosphoproteomics; SCX; TiO2

Indexed keywords

PROTEOME;

ARTICLE; CHROMATOGRAPHY; ELECTROSTATIC REPULSION HYDROPHILIC INTERACTION CHROMATOGRAPHY; MASS SPECTROMETRY; PHOSPHOPROTEOME ANALYSIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN LOCALIZATION; PROTEIN PHOSPHORYLATION; STRONG CATION EXCHANGE CHROMATOGRAPHY; SUPERNATANT; WORKFLOW;

CHROMATOGRAPHY, ION EXCHANGE; HELA CELLS; HUMANS; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; PEPTIDE FRAGMENTS; PHOSPHOPROTEINS; PROTEOLYSIS; PROTEOME; TANDEM MASS SPECTROMETRY; TRYPSIN;

EID: 84864616672     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr300375d     Document Type: Article

References (30)

1. Hunter, T. The age of crosstalk: Phosphorylation, ubiquitination, and beyond Mol. Cell 2007, 28 (5) 730-8 (Pubitemid 350217067)
2. Kalume, D. E.; Molina, H.; Pandey, A. Tackling the phosphoproteome: Tools and strategies Curr. Opin. Chem. Biol. 2003, 7 (1) 64-9 (Pubitemid 36126494)
3. Hammond, D. E.; Hyde, R.; Kratchmarova, I.; Beynon, R. J.; Blagoev, B.; Clague, M. J. Quantitative analysis of HGF and EGF-dependent phosphotyrosine signaling networks J. Proteome Res. 2010, 9 (5) 2734-42
4. Dengjel, J.; Kratchmarova, I.; Blagoev, B. Receptor tyrosine kinase signaling: a view from quantitative proteomics Mol. BioSyst. 2009, 5 (10) 1112-21
5. Dengjel, J.; Akimov, V.; Olsen, J. V.; Bunkenborg, J.; Mann, M.; Blagoev, B.; Andersen, J. S. Quantitative proteomic assessment of very early cellular signaling events Nat. Biotechnol. 2007, 25 (5) 566-8 (Pubitemid 46834842)
6. Rigbolt, K. T.; Prokhorova, T. A.; Akimov, V.; Henningsen, J.; Johansen, P. T.; Kratchmarova, I.; Kassem, M.; Mann, M.; Olsen, J. V.; Blagoev, B. System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation Sci. Signal. 2011, 4 (164) rs3
7. Bantscheff, M.; Schirle, M.; Sweetman, G.; Rick, J.; Kuster, B. Quantitative mass spectrometry in proteomics: A critical review Anal. Bioanal. Chem. 2007, 389 (4) 1017-31 (Pubitemid 47482251)
8. Nilsson, C. L. Advances in quantitative phosphoproteomics Anal. Chem. 2012, 84 (2) 735-46
9. Gan, C. S.; Guo, T.; Zhang, H.; Lim, S. K.; Sze, S. K. A comparative study of electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) versus SCX-IMAC-based methods for phosphopeptide isolation/enrichment J. Proteome Res. 2008, 7 (11) 4869-77
10. Link, A. J. Multidimensional peptide separations in proteomics Trends Biotechnol. 2002, 20 (12 Suppl.) S8-13
11. McNulty, D. E.; Annan, R. S. Hydrophilic interaction chromatography reduces the complexity of the phosphoproteome and improves global phosphopeptide isolation and detection Mol. Cell. Proteomics 2008, 7 (5) 971-80 (Pubitemid 351737096)
12. Macek, B.; Mann, M.; Olsen, J. V. Global and site-specific quantitative phosphoproteomics: principles and applications Annu. Rev. Pharmacol. Toxicol. 2009, 49, 199-221
13. Villen, J.; Beausoleil, S. A.; Gerber, S. A.; Gygi, S. P. Large-scale phosphorylation analysis of mouse liver Proc. Natl. Acad. Sci. U.S.A. 2007, 104 (5) 1488-93 (Pubitemid 46214617)
14. Zhang, H.; Guo, T.; 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
15. Gruhler, A.; Olsen, J. V.; Mohammed, S.; Mortensen, P.; Faergeman, N. J.; Mann, M.; Jensen, O. N. Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway Mol. Cell. Proteomics 2005, 4 (3) 310-27 (Pubitemid 40439774)
16. Hennrich, M. L.; Groenewold, V.; Kops, G. J.; Heck, A. J. Mohammed, S., Improving depth in phosphoproteomics by using a strong cation exchange-weak anion exchange-reversed phase multidimensional separation approach Anal. Chem. 2011, 83 (18) 7137-43
17. 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)
18. 2 for global phosphoproteomics approaches J. Proteome Res. 2011, 10 (8) 3474-83
19. 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 (Pubitemid 351448406)
20. Nagaraj, N.; D'Souza, R. C.; Cox, J.; Olsen, J. V.; Mann, M. Feasibility of large-scale phosphoproteomics with higher energy collisional dissociation fragmentation J. Proteome Res. 2010, 9 (12) 6786-94
21. Nie, S.; Dai, J.; Ning, Z. B.; Cao, X. J.; Sheng, Q. H.; Zeng, R. Comprehensive profiling of phosphopeptides based on anion exchange followed by flow-through enrichment with titanium dioxide (AFET) J. Proteome Res. 2010, 9 (9) 4585-94
22. Thingholm, T. E.; Jensen, O. N.; Robinson, P. J.; Larsen, M. R. SIMAC (sequential elution from IMAC), a phosphoproteomics strategy for the rapid separation of monophosphorylated from multiply phosphorylated peptides Mol. Cell. Proteomics 2008, 7 (4) 661-71 (Pubitemid 351597478)
23. Zhang, X.; Fang, A.; Riley, C. P.; Wang, M.; Regnier, F. E.; Buck, C. Multi-dimensional liquid chromatography in proteomics-a review Anal. Chim. Acta 2010, 664 (2) 101-13
24. Kong, R. P.; Siu, S. O.; Lee, S. S.; Lo, C.; Chu, I. K. Development of online high-/low-pH reversed-phase-reversed-phase two-dimensional liquid chromatography for shotgun proteomics: A reversed-phase-strong cation exchange-reversed-phase approach J. Chromatogr., A 2011, 1218 (23) 3681-8
25. Lau, E.; Lam, M. P.; Siu, S. O.; Kong, R. P.; Chan, W. L.; Zhou, Z.; Huang, J.; Lo, C.; Chu, I. K. Combinatorial use of offline SCX and online RP-RP liquid chromatography for iTRAQ-based quantitative proteomics applications Mol. BioSyst. 2011, 7 (5) 1399-408
26. Larsen, M. R.; Thingholm, T. E.; Jensen, O. N.; Roepstorff, P.; Jorgensen, T. J. Highly selective enrichment of phosphorylated peptides from peptide mixtures using titanium dioxide microcolumns Mol. Cell. Proteomics 2005, 4 (7) 873-86 (Pubitemid 41309146)
27. Sprenger, A.; Kuttner, V.; Biniossek, M. L.; Gretzmeier, C.; Boerries, M.; Mack, C.; Has, C.; Bruckner-Tuderman, L.; Dengjel, J. Comparative quantitation of proteome alterations induced by aging or immortalization in primary human fibroblasts and keratinocytes for clinical applications Mol. BioSyst. 2010, 6 (9) 1579-82
28. Cox, J.; Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification Nat. Biotechnol. 2008, 26 (12) 1367-72
29. Cox, J.; Neuhauser, N.; Michalski, A.; Scheltema, R. A.; Olsen, J. V.; Mann, M. Andromeda: a peptide search engine integrated into the MaxQuant environment J. Proteome Res. 2011, 10 (4) 1794-805
30. Kyono, Y.; Sugiyama, N.; Imami, K.; Tomita, M.; Ishihama, Y. Successive and selective release of phosphorylated peptides captured by hydroxy acid-modified metal oxide chromatography J. Proteome Res. 2008, 7 (10) 4585-93