Optimized fragmentation conditions for iTRAQ-labeled phosphopeptides

Journal of Proteome Research

Volumn 12, Issue 6, 2013, Pages 2755-2763

  Linke, Dennis ^a   Hung, Chien Wen ^a   Cassidy, Liam ^a   Tholey, Andreas ^a  

^a UNIVERSITY OF KIEL   (Germany)

Author keywords

isobaric labeling; LC MS; MS MS; Orbitrap; phosphorylation; posttranslational modification; quantification; tandem MS

Indexed keywords

PHOSPHOPEPTIDE;

ARTICLE; CHEMICAL LABELING; COLLISIONALLY ACTIVATED DISSOCIATION; CONTROLLED STUDY; FRAGMENTATION REACTION; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; TANDEM MASS SPECTROMETRY;

EID: 84879344463     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr400113n     Document Type: Article

References (27)

1. 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, 376-86
2. 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, 1154-69
3. Boja, E. S.; Phillips, D.; French, S. A.; Harris, R. A.; Balaban, R. S. Quantitative mitochondrial phosphoproteomics using iTRAQ on an LTQ-Orbitrap with high energy collision dissociation J. Proteome Res. 2009, 8, 4665-75
4. Zhang, Y.; Ficarro, S. B.; Li, S.; Marto, J. A. Optimized Orbitrap HCD for quantitative analysis of phosphopeptides J. Am. Soc. Mass Spectrom. 2009, 20, 1425-34
5. Wu, J.; Warren, P.; Shakey, Q.; Sousa, E.; Hill, A.; Ryan, T. E.; He, T. Integrating titania enrichment, iTRAQ labeling, and Orbitrap CID-HCD for global identification and quantitative analysis of phosphopeptides Proteomics 2010, 10, 2224-34
6. Thingholm, T. E.; Palmisano, G.; Kjeldsen, F.; Larsen, M. R. Undesirable charge-enhancement of isobaric tagged phosphopeptides leads to reduced identification efficiency J. Proteome Res. 2010, 9, 4045-52
7. Carr, S. A.; Huddleston, M. J.; Annan, R. S. Selective detection and sequencing of phosphopeptides at the femtomole level by mass spectrometry Anal. Biochem. 1996, 239, 180-92
8. Tholey, A.; Reed, J.; Lehmann, W. D. Electrospray tandem mass spectrometric studies of phosphopeptides and phosphopeptide analogues J. Mass Spectrom. 1999, 34, 117-23
9. Olsen, J. V.; Schwartz, J. C.; Griep-Raming, J.; Nielsen, M. L.; Damoc, E.; Denisov, E.; Lange, O.; Remes, P.; Taylor, D.; Splendore, M.; Wouters, E. R.; Senko, M.; Makarov, A.; Mann, M.; Horning, S. A dual pressure linear ion trap Orbitrap instrument with very high sequencing speed Mol. Cell. Proteomics 2009, 8, 2759-69
10. 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, 709-12
11. Bantscheff, M.; Boesche, M.; Eberhard, D.; Matthieson, T.; Sweetman, G.; Kuster, B. Robust and sensitive iTRAQ quantification on an LTQ Orbitrap mass spectrometer Mol. Cell. Proteomics 2008, 7, 1702-13
12. Kocher, T.; Pichler, P.; Schutzbier, M.; Stingl, C.; Kaul, A.; Teucher, N.; Hasenfuss, G.; Penninger, J. M.; Mechtler, K. High precision quantitative proteomics using iTRAQ on an LTQ Orbitrap: a new mass spectrometric method combining the benefits of all J. Proteome Res. 2009, 8, 4743-52
13. Karp, N. A.; Huber, W.; Sadowski, P. G.; Charles, P. D.; Hester, S. V.; Lilley, K. S. Addressing accuracy and precision issues in iTRAQ quantitation Mol. Cell. Proteomics 2010, 9, 1885-97
14. Jedrychowski, M. P.; Huttlin, E. L.; Haas, W.; Sowa, M. E.; Rad, R.; Gygi, S. P. Evaluation of HCD- and CID-type fragmentation within their respective detection platforms for murine phosphoproteomics Mol. Cell. Proteomics 2011, 10, M111 009910
15. Schlosser, A.; Lehmann, W. D. Five-membered ring formation in unimolecular reactions of peptides: a key structural element controlling low-energy collision-induced dissociation of peptides J. Mass Spectrom. 2000, 35, 1382-90
16. Boersema, P. J.; Mohammed, S.; Heck, A. J. Phosphopeptide fragmentation and analysis by mass spectrometry J. Mass Spectrom. 2009, 44, 861-78
17. 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, 3590-8
18. Pichler, P.; Kocher, T.; Holzmann, J.; Mazanek, M.; Taus, T.; Ammerer, G.; Mechtler, K. Peptide labeling with isobaric tags yields higher identification rates using iTRAQ 4-plex compared to TMT 6-plex and iTRAQ 8-plex on LTQ Orbitrap Anal. Chem. 2010, 82, 6549-58
19. Yates, J. R., 3rd; Eng, J. K.; McCormack, A. L.; Schieltz, D. Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database Anal. Chem. 1995, 67, 1426-36
20. Perkins, D. N.; Pappin, D. J.; Creasy, D. M.; Cottrell, J. S. Probability-based protein identification by searching sequence databases using mass spectrometry data Electrophoresis 1999, 20, 3551-67
21. Fenyo, D.; Beavis, R. C. A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes Anal. Chem. 2003, 75, 768-74
22. Geer, L. Y.; Markey, S. P.; Kowalak, J. A.; Wagner, L.; Xu, M.; Maynard, D. M.; Yang, X.; Shi, W.; Bryant, S. H. Open mass spectrometry search algorithm J. Proteome Res. 2004, 3, 958-64
23. He, Z.; Yu, W. Improving peptide identification with single-stage mass spectrum peaks Bioinformatics 2009, 25, 2969-74
24. Lemeer, S.; Kunold, E.; Klaeger, S.; Raabe, M.; Towers, M. W.; Claudes, E.; Arrey, T. N.; Strupat, K.; Urlaub, H.; Kuster, B. Phosphorylation site localization in peptides by MALDI MS/MS and the Mascot Delta Score Anal. Bioanal. Chem. 2012, 402, 249-60
25. 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, 1285-92
26. Zhang, Y.; Askenazi, M.; Jiang, J.; Luckey, C. J.; Griffin, J. D.; Marto, J. A. A robust error model for iTRAQ quantification reveals divergent signaling between oncogenic FLT3 mutants in acute myeloid leukemia Mol. Cell. Proteomics 2010, 9, 780-90
27. de Graaf, E. L.; Altelaar, A. F.; van Breukelen, B.; Mohammed, S.; Heck, A. J. Improving SRM assay development: a global comparison between triple quadrupole, ion trap, and higher energy CID peptide fragmentation spectra J. Proteome Res. 2011, 10, 4334-41