Unambiguous phosphosite localization using electron-transfer/higher-energy collision dissociation (EThcD)

Journal of Proteome Research

Volumn 12, Issue 3, 2013, Pages 1520-1525

  Frese, Christian K ^a,b   Zhou, Houjiang ^a,b   Taus, Thomas ^c   Altelaar, A F Maarten ^a,b   Mechtler, Karl ^c,d   Heck, Albert J R ^a,b   Mohammed, Shabaz ^a,b  

^a UTRECHT UNIVERSITY   (Netherlands)

^b NETHERLANDS PROTEOMICS CENTRE   (Netherlands)

^c RESEARCH INSTITUTE OF MOLECULAR PATHOLOGY   (Austria)

^d INSTITUTE OF MOLECULAR BIOTECHNOLOGY   (Austria)

Author keywords

electron transfer dissociation; ETD; EThcD; HCD; phosphoRS; phosphorylation site localization

Indexed keywords

PHOSPHOPEPTIDE; SYNTHETIC PEPTIDE;

ARTICLE; CELL LINE; ELECTRON TRANSFER HIGHER ENEGY COLLISION DISSOCIATION; HUMAN; HUMAN CELL; INTERMETHOD COMPARISON; PRIORITY JOURNAL; PROCEDURES; PROTEIN LOCALIZATION; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; PROTEOMICS;

EID: 84874601328     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr301130k     Document Type: Article

References (41)

1. Cohen, P. The regulation of protein function by multisite phosphorylation - a 25 year update Trends Biochem. Sci. 2000, 25 (12) 596-601
2. Hunter, T. Signaling - 2000 and beyond Cell 2000, 100 (1) 113-27
3. Olsen, J. V.; Blagoev, B.; Gnad, F.; Macek, B.; Kumar, C.; Mortensen, P.; Mann, M. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks Cell 2006, 127 (3) 635-48
4. Eyrich, B.; Sickmann, A.; Zahedi, R. P. Catch me if you can: mass spectrometry-based phosphoproteomics and quantification strategies Proteomics 2011, 11 (4) 554-70
5. Mann, M.; Jensen, O. N. Proteomic analysis of post-translational modifications Nat. Biotechnol. 2003, 21 (3) 255-61
6. 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 (13) 3791-813
7. Rush, J.; Moritz, A.; Lee, K. A.; Guo, A.; Goss, V. L.; Spek, E. J.; Zhang, H.; Zha, X. M.; Polakiewicz, R. D.; Comb, M. J. Immunoaffinity profiling of tyrosine phosphorylation in cancer cells Nat. Biotechnol. 2005, 23 (1) 94-101
8. 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
9. Zhou, H.; Low, T. Y.; Hennrich, M. L.; van der Toorn, H.; Schwend, T.; Zou, H.; Mohammed, S.; Heck, A. J. Enhancing the identification of phosphopeptides from putative basophilic kinase substrates using Ti (IV) based IMAC enrichment Mol. Cell. Proteomics 2011, 10 (10) M110 006452
10. Boersema, P. J.; Mohammed, S.; Heck, A. J. Phosphopeptide fragmentation and analysis by mass spectrometry J. Mass Spectrom. 2009, 44 (6) 861-78
11. 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
12. Schroeder, M. J.; Shabanowitz, J.; Schwartz, J. C.; Hunt, D. F.; Coon, J. J. A neutral loss activation method for improved phosphopeptide sequence analysis by quadrupole ion trap mass spectrometry Anal. Chem. 2004, 76 (13) 3590-8
13. Olsen, J. V.; Macek, B.; Lange, O.; Makarov, A.; Horning, S.; Mann, M. Higher-energy C-trap dissociation for peptide modification analysis Nat. Methods 2007, 4 (9) 709-12
14. Chi, A.; Huttenhower, C.; Geer, L. Y.; Coon, J. J.; Syka, J. E.; Bai, D. L.; Shabanowitz, J.; Burke, D. J.; Troyanskaya, O. G.; Hunt, D. F. Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry Proc. Natl. Acad. Sci. U.S.A. 2007, 104 (7) 2193-8
15. Molina, H.; Matthiesen, R.; Kandasamy, K.; Pandey, A. Comprehensive comparison of collision induced dissociation and electron transfer dissociation Anal. Chem. 2008, 80 (13) 4825-35
16. Beausoleil, S. A.; Villen, J.; Gerber, S. A.; Rush, J.; Gygi, S. P. A probability-based approach for high-throughput protein phosphorylation analysis and site localization Nat. Biotechnol. 2006, 24 (10) 1285-92
17. Stensballe, A.; Jensen, O. N.; Olsen, J. V.; Haselmann, K. F.; Zubarev, R. A. Electron capture dissociation of singly and multiply phosphorylated peptides Rapid Commun. Mass Spectrom. 2000, 14 (19) 1793-800
18. Kelstrup, C. D.; Hekmat, O.; Francavilla, C.; Olsen, J. V. Pinpointing phosphorylation sites: Quantitative filtering and a novel site-specific x-ion fragment J. Proteome Res. 2011, 10 (7) 2937-48
19. Shin, Y. S.; Moon, J. H.; Kim, M. S. Observation of phosphorylation site-specific dissociation of singly protonated phosphopeptides J. Am. Soc. Mass Spectrom. 2010, 21 (1) 53-9
20. Gehrig, P. M.; Roschitzki, B.; Rutishauser, D.; Reiland, S.; Schlapbach, R. Phosphorylated serine and threonine residues promote site-specific fragmentation of singly charged, arginine-containing peptide ions Rapid Commun. Mass Spectrom. 2009, 23 (10) 1435-45
21. Lu, B.; Ruse, C.; Xu, T.; Park, S. K.; Yates, J. R., 3rd Automatic validation of phosphopeptide identifications from tandem mass spectra Anal. Chem. 2007, 79 (4) 1301-10
22. Bailey, C. M.; Sweet, S. M.; Cunningham, D. L.; Zeller, M.; Heath, J. K.; Cooper, H. J. SLoMo: automated site localization of modifications from ETD/ECD mass spectra J. Proteome Res. 2009, 8 (4) 1965-71
23. Savitski, M. M.; Mathieson, T.; Becher, I.; Bantscheff, M. H-score, a mass accuracy driven rescoring approach for improved peptide identification in modification rich samples J. Proteome Res. 2010, 9 (11) 5511-6
24. Ruttenberg, B. E.; Pisitkun, T.; Knepper, M. A.; Hoffert, J. D. PhosphoScore: an open-source phosphorylation site assignment tool for MSn data Journal of Proteome Research 2008, 7 (7) 3054-9
25. Hansen, T. A.; Sylvester, M.; Jensen, O. N.; Kjeldsen, F. Automated and high confidence protein phosphorylation site localization using complementary collision-activated dissociation and electron transfer dissociation tandem mass spectrometry Anal. Chem. 2012, 84 (22) 9694-9
26. Vandenbogaert, M.; Hourdel, V.; Jardin-Mathe, O.; Bigeard, J.; Bonhomme, L.; Legros, V.; Hirt, H.; Schwikowski, B.; Pflieger, D. Automated phosphopeptide identification using multiple MS/MS fragmentation modes J. Proteome Res. 2012, 11 (12) 5695-703
27. Taus, T.; Kocher, T.; Pichler, P.; Paschke, C.; Schmidt, A.; Henrich, C.; Mechtler, K. Universal and confident phosphorylation site localization using phosphoRS J. Proteome Res. 2011, 10 (12) 5354-62
28. Frese, C. K.; Altelaar, M.; van den Toorn, H. W.; Nolting, D.; Griep-Raming, J.; Heck, A. J.; Mohammed, S. Toward full peptide sequence coverage by dual fragmentation combining electron-transfer and higher-energy collision dissociation tandem mass spectrometry Anal. Chem. 2012, 84 (22) 9668-73
29. Altelaar, A. F.; Frese, C. K.; Preisinger, C.; Hennrich, M. L.; Schram, A. W.; Timmers, H. T.; Heck, A. J.; Mohammed, S. Benchmarking stable isotope labeling based quantitative proteomics J. Proteomics 2012, 10.1016/j.jprot.2012. 10.009
30. Zhou, H.; Ye, M.; Dong, J.; Han, G.; Jiang, X.; Wu, R.; Zou, H. Specific phosphopeptide enrichment with immobilized titanium ion affinity chromatography adsorbent for phosphoproteome analysis J. Proteome Res. 2008, 7 (9) 3957-67
31. Yu, Z.; Han, G.; Sun, S.; Jiang, X.; Chen, R.; Wang, F.; Wu, R.; Ye, M.; Zou, H. Preparation of monodisperse immobilized Ti(4+) affinity chromatography microspheres for specific enrichment of phosphopeptides Anal. Chim. Acta 2009, 636 (1) 34-41
32. Zhou, H.; Ye, M.; Dong, J.; Corradini, E.; Cristobal, A.; Heck, A. J. R.; Zou, H.; Mohammed, S. Robust phosphoproteome enrichment using monodisperse microspheres-based immobilized titanium (IV) ion affinity chromatography. Nat. Protoc. 2012, in press.
33. 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 (11) 923-5
34. Mertins, P.; Udeshi, N. D.; Clauser, K. R.; Mani, D. R.; Patel, J.; Ong, S. E.; Jaffe, J. D.; Carr, S. A. iTRAQ labeling is superior to mTRAQ for quantitative global proteomics and phosphoproteomics Mol. Cell. Proteomics 2012, 11 (6) M111 014423
35. Kandasamy, K.; Pandey, A.; Molina, H. Evaluation of Several MS/MS Search Algorithms for Analysis of Spectra Derived from Electron Transfer Dissociation Experiments Anal. Chem. 2009, 81 (17) 7170-80
36. Elias, J. E.; Gygi, S. P. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry Nat. Methods 2007, 4 (3) 207-14
37. Horn, D. M.; Zubarev, R. A.; McLafferty, F. W. Automated de novo sequencing of proteins by tandem high-resolution mass spectrometry Proc. Natl. Acad. Sci. U.S.A. 2000, 97 (19) 10313-7
38. Cooper, H. J.; Hudgins, R. R.; Hakansson, K.; Marshall, A. G. Secondary fragmentation of linear peptides in electron capture dissociation Int. J. Mass Spectrom. 2003, 228 (2-3) 723-8
39. Li, W.; Song, C.; Bailey, D. J.; Tseng, G. C.; Coon, J. J.; Wysocki, V. H. Statistical analysis of electron transfer dissociation pairwise fragmentation patterns Anal. Chem. 2011, 83 (24) 9540-5
40. Kim, M. S.; Zhong, J.; Kandasamy, K.; Delanghe, B.; Pandey, A. Systematic evaluation of alternating CID and ETD fragmentation for phosphorylated peptides Proteomics 2011, 11 (12) 2568-72
41. Nielsen, M. L.; Savitski, M. M.; Zubarev, R. A. Improving protein identification using complementary fragmentation techniques in fourier transform mass spectrometry Mol. Cell. Proteomics 2005, 4 (6) 835-45