Improved two-dimensional reversed phase-reversed phase LC-MS/MS approach for identification of peptide-protein interactions

Journal of Proteome Research

Volumn 11, Issue 2, 2012, Pages 1175-1183

  Stephanowitz, Heike ^a   Lange, Sabine ^a   Lang, Diana ^a   Freund, Christian ^a,b   Krause, Eberhard ^a  

^a LEIBNIZ INSTITUT FÜR MOLEKULARE PHARMAKOLOGIE   (Germany)

^b FREIE UNIVERSITÄT BERLIN   (Germany)

Author keywords

mass spectrometry; phosphorylation; protein interactions; quantitative proteomics; SILAC; two dimensional liquid chromatography

Indexed keywords

ACETONITRILE;

ARTICLE; FRACTIONATION; HUMAN; HUMAN CELL; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DEGRADATION; PROTEIN PHOSPHORYLATION; PROTEIN PROTEIN INTERACTION; REVERSED PHASE LIQUID CHROMATOGRAPHY; TANDEM MASS SPECTROMETRY;

ADAPTOR PROTEINS, SIGNAL TRANSDUCING; CHROMATOGRAPHY, REVERSE-PHASE; HUMANS; ISOTOPE LABELING; JURKAT CELLS; PEPTIDE FRAGMENTS; PHOSPHORYLATION; PROTEIN INTERACTION MAPPING; PROTEINS; PROTEOMICS; REPRODUCIBILITY OF RESULTS; TANDEM MASS SPECTROMETRY;

EID: 84856657286     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr200900s     Document Type: Article

References (38)

1. Mallick, P.; Kuster, B. Proteomics: A Pragmatic Perspective Nat. Biotechnol. 2010, 28, 695-709
2. Ahrens, C. H.; Brunner, E.; Qeli, E.; Basler, K.; Aebersold, R. Generating and Navigating Proteome Maps Using Mass Spectrometry Nat. Rev. Mol. Cell Biol. 2010, 11, 789-801
3. Lasonder, E.; Ishihama, Y.; Andersen, J. S.; Vermunt, A. M. W.; Pain, A.; Sauerwein, R. W.; Eling, W. M. C.; Hall, N.; Waters, A. P.; Stunnenberg, H. G.; Mann, M. Analysis of the Plasmodium falciparum Proteome by High-Accuracy Mass Spectrometry Nature 2002, 419, 537-542
4. Schirle, M.; Heurtier, M. A.; Kuster, B. Profiling Core Proteomes of Human Cell Lines by One-Dimensional PAGE and Liquid Chromatography-Tandem Mass Spectrometry Mol. Cell. Proteomics 2003, 2, 1297-1305
5. Zwang, N. A.; Hoffert, J. D.; Pisitkun, T.; Moeller, H. B.; Fenton, R. A.; Knepper, M. A. Identification of Phosphorylation-Dependent Binding Partners of Aquaporin-2 Using Protein Mass Spectrometry J. Proteome Res. 2009, 8, 1540-1554
6. Ong, S. E.; Blagoev, B.; Kratchmarova, I.; Kristensen, D. B.; Steen, H.; Pandey, A.; Mann, M. Stable Isotope Labeling by Amino Acids in Cell Culture, SILAC, As a Simple and Accurate Approach to Expression Proteomics Mol. Cell Proteomics 2002, 1, 376-386
7. Graumann, J.; Hubner, N. C.; Kim, J. B.; Ko, K.; Moser, M.; Kumar, C.; Cox, J.; Scholer, H.; Mann, M. Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) and Proteome Quantitation of Mouse Embryonic Stem Cells to a Depth of 5,111 Proteins Mol. Cell. Proteomics 2008, 7, 672-683
8. Ross, P. L.; Huang, Y. N.; Marchese, J. N.; Williamson, B.; Parker, K.; Hattan, S.; Khainovski, N.; Pillai, S.; Dey, S.; Daniels, S.; Purkayastha, S.; Juhasz, P.; Martin, S.; Bartlet-Jones, M.; He, F.; Jacobson, A.; Pappin, D. J. Multiplexed Protein Quantitation in Saccharomyces Cerevisiae Using Amine-Reactive Isobaric Tagging Reagents Mol. Cell. Proteomics 2004, 3, 1154-1169
9. Engmann, O.; Campbell, J.; Ward, M.; Giese, K. P.; Thompson, A. J. Comparison of a Protein-Level and Peptide-Level Labeling Strategy for Quantitative Proteomics of Synaptosomes Using Isobaric Tags J. Proteome Res. 2010, 9, 2725-2733
10. Mirgorodskaya, O. A.; Kozmin, Y. P.; Titov, M. I.; Korner, R.; Sonksen, C. P.; Roepstorff, P. Quantitation of Peptides and Proteins by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Using O-18-Labeled Internal Standards Rapid Commun. Mass Spectrom. 2000, 14, 1226-1232
11. Lange, S.; Sylvester, M.; Schumann, M.; Freund, C.; Krause, E. Identification of Phosphorylation-Dependent Interaction Partners of the Adapter Protein ADAP Using Quantitative Mass Spectrometry: SILAC Vs O-18-Labeling J. Proteome Res. 2010, 9, 4113-4122
12. Washburn, M. P.; Wolters, D.; Yates, J. R. Large-Scale Analysis of the Yeast Proteome by Multidimensional Protein Identification Technology Nat. Biotechnol. 2001, 19, 242-247
13. Peng, J. M.; 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
14. Motoyama, A.; Yates, J. R., III Multidimensional LC Separations in Shotgun Proteomics Anal. Chem. 2008, 80, 7187-7193
15. 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, 37-46
16. Eeltink, S.; Dolman, S.; Swart, R.; Ursem, M.; Schoenmakers, P. J. Optimizing the Peak Capacity Per Unit Time in One-Dimensional and Off-Line Two-Dimensional Liquid Chromatography for the Separation of Complex Peptide Samples J. Chromatogr. A 2009, 1216, 7368-7374
17. Gilar, M.; Olivova, P.; Daly, A. E.; Gebler, J. C. Orthogonality of Separation in Two-Dimensional Liquid Chromatography Anal. Chem. 2005, 77, 6426-6434
18. 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
19. Toll, H.; Oberacher, H.; Swart, R.; Huber, C. G. Separation, Detection, and Identification of Peptides by Ion-Pair Reversed-Phase High-Performance Liquid Chromatography-Electrospray Ionization Mass Spectrometry at High and Low pH J. Chromatogr. A 2005, 1079, 274-286
20. Nakamura, T.; Kuromitsu, J.; Oda, Y. Evaluation of Comprehensive Multidimensional Separations Using Reversed-Phase, Reversed-Phase Liquid Chromatography/Mass Spectrometry for Shotgun Proteomics J. Proteome Res. 2008, 7, 1007-1011
21. Delmotte, N.; Lasaosa, M.; Tholey, A.; Heinzle, E.; Huber, C. G. Two-Dimensional Reversed-Phase x Ion-Pair Reversed-Phase HPLC: An Alternative Approach to High-Resolution Peptide Separation for Shotgun Proteome Analysis J. Proteome Res. 2007, 6, 4363-4373
22. Zhou, F.; Cardoza, J. D.; Ficarro, S. B.; Adelmant, G. O.; Lazaro, J. B.; Marto, J. A. Online Nanoflow RP-RP-MS Reveals Dynamics of Multicomponent Ku Complex in Response to DNA Damage J. Proteome Res. 2010, 9, 6242-6255
23. Lasaosa, M.; Delmotte, N.; Huber, C. G.; Melchior, K.; Heinzle, E.; Tholey, A. A 2D Reversed-Phase x Ion-Pair Reversed-Phase HPLC-MALDI TOF/TOF-MS Approach for Shotgun Proteome Analysis Anal. Bioanal. Chem. 2009, 393, 1245-1256
24. Song, C. X.; Ye, M. L.; Han, G. H.; Jiang, X. N.; Wang, F. J.; Yu, Z. Y.; Chen, R.; Zou, H. F. Reversed-Phase-Reversed-Phase Liquid Chromatography Approach With High Orthogonality for Multidimensional Separation of Phosphopeptides Anal. Chem. 2010, 82, 53-56
25. 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: Anal. Technol. Biomed. Life Sci. 2011, 879, 610-614
26. Ong, S. E.; Mann, M. A Practical Recipe for Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) Nat. Protoc. 2006, 1, 2650-2660
27. Klemm, C.; Schroder, S.; Gluckmann, M.; Beyermann, M.; Krause, E. Derivatization of Phosphorylated Peptides With S- and N-Nucleophiles for Enhanced Ionization Efficiency in Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Rapid Commun. Mass Spectrom. 2004, 18, 2697-2705
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, 1367-1372
29. McCalley, D. V. Effect of Buffer on Peak Shape of Peptides in Reversed-Phase High Performance Liquid Chromatography J. Chromatogr. A 2004, 1038, 77-84
30. Spicer, V.; Yamchuk, A.; Cortens, J.; Sousa, S.; Ens, W.; Standing, K. G.; Wilkins, J. A.; Krokhin, O. V. Sequence-Specific Retention Calculator. A Family of Peptide Retention Time Prediction Algorithms in Reversed-Phase HPLC: Applicability to Various Chromatographic Conditions and Columns Anal. Chem. 2007, 79, 8762-8768
31. Apffel, A.; Fischer, S.; Goldberg, G.; Goodley, P. C.; Kuhlmann, F. E. Enhanced Sensitivity for Peptide-Mapping With Electrospray Liquid-Chromatography Mass-Spectrometry in the Presence of Signal Suppression Due to Trifluoroacetic Acid-Containing Mobile Phases J. Chromatogr. A 1995, 712, 177-190
32. Huber, C. G.; Premstaller, A. Evaluation of Volatile Eluents and Electrolytes for High-Performance Liquid Chromatography-Electrospray Ionization Mass Spectrometry and Capillary Electrophoresis-Electrospray Ionization Mass Spectrometry of Proteins-I. Liquid Chromatography J. Chromatogr. A 1999, 849, 161-173
33. Gropengiesser, J.; Varadarajan, B. T.; Stephanowitz, H.; Krause, E. The Relative Influence of Phosphorylation and Methylation on Responsiveness of Peptides to MALDI and ESI Mass Spectrometry J. Mass Spectrom. 2009, 44, 821-831
34. McCalley, D. V. Comparison of an Organic Polymeric Column and a Silica-Based Reversed-Phase for the Analysis of Basic Peptides by High-Performance Liquid Chromatography J. Chromatogr. A 2005, 1073, 137-145
35. Geng, L.; Raab, M.; Rudd, C. E. Cutting Edge: SLP-76 Cooperativity With FYB/FYN-T in the Up-Regulation of TCR-Driven IL-2 Transcription Requires SLP-76 Binding to FYB at Tyr595 and Tyr651 J. Immunol. 1999, 163, 5753-5757
36. Raab, M.; Kang, H.; da, S. A.; Zhu, X.; Rudd, C. E. FYN-T-FYB-SLP-76 Interactions Define a T-Cell Receptor Zeta/CD3-Mediated Tyrosine Phosphorylation Pathway That Up-Regulates Interleukin 2 Transcription in T-Cells J. Biol. Chem. 1999, 274, 21170-21179
37. Lettau, M.; Pieper, J.; Gerneth, A.; Lengl-Janssen, B.; Voss, M.; Linkermann, A.; Schmidt, H.; Gelhaus, C.; Leippe, M.; Kabelitz, D.; Janssen, O. The Adapter Protein Nck: Role of Individual SH3 and SH2 Binding Modules for Protein Interactions in T Lymphocytes Protein Sci. 2010, 19, 658-669
38. Sylvester, M.; Kliche, S.; Lange, S.; Geithner, S.; Klemm, C.; Schlosser, A.; Grossmann, A.; Stelzl, U.; Schraven, B.; Krause, E.; Freund, C. Adhesion and Degranulation Promoting Adapter Protein (ADAP) Is a Central Hub for Phosphotyrosine-Mediated Interactions in T Cells PLoS One 2010, 5, e11708