General statistical modeling of data from protein relative expression isobaric tags

Journal of Proteome Research

Volumn 10, Issue 6, 2011, Pages 2758-2766

  Breitwieser, Florian P ^a   Müller, André ^a   Dayon, Loïc ^b   Köcher, Thomas ^c   Hainard, Alexandre ^b   Pichler, Peter ^d   Schmidt Erfurth, Ursula ^e   Superti Furga, Giulio ^a   Sanchez, Jean Charles ^b   Mechtler, Karl ^c   Bennett, Keiryn L ^a   Colinge, Jacques ^a  

^a ERICH SCHMID INSTITUTE OF MATERIALS SCIENCE   (Austria)

^b UNIVERSITY OF GENEVA   (Switzerland)

^c RESEARCH INSTITUTE OF MOLECULAR PATHOLOGY   (Austria)

^d UNIVERSITY OF VIENNA   (Austria)

^e MEDICAL UNIVERSITY OF VIENNA   (Austria)

Author keywords

bioinformatics; iTRAQ; quantitative proteomics; statistics; TMT

Indexed keywords

CERULOPLASMIN;

ARTICLE; COMPUTER PROGRAM; EXPERIMENTAL DESIGN; HUMAN; ISOBAR; MASS SPECTROMETRY; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEOMICS; RAT; STATISTICAL MODEL;

ALGORITHMS; ANIMALS; BLOOD PROTEINS; CERULOPLASMIN; DATA INTERPRETATION, STATISTICAL; HUMANS; MICE; MODELS, STATISTICAL; PROTEOMICS; RATS; SOFTWARE;

EID: 79958198057     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr1012784     Document Type: Article

References (44)

1. Aebersold, R.; Mann, M. Mass spectrometry-based proteomics Nature 2003, 422, 198-207 (Pubitemid 36362757)
2. Domon, B.; Aebersold, R Mass spectrometry and protein analysis Science 2006, 312, 212-7
3. Pan, S.; Aebersold, R.; Chen, R.; Rush, J.; Goodlett, D. R.; McIntosh, M. W.; Zhang, J.; Brentnall, T. A. Mass spectrometry based targeted protein quantification: methods and applications J. Proteome Res. 2009, 8, 787-97
4. Patel, V. J.; Thalassinos, K.; Slade, S. E.; Connolly, J. B.; Crombie, A.; Murrell, J. C.; Scrivens, J. H. A comparison of labeling and label-free mass spectrometry-based proteomics approaches J. Proteome Res. 2009, 8, 3752-9
5. Julka, S.; Regnier, F. Quantification in proteomics through stable isotope coding: a review J. Proteome Res. 2004, 3, 350-63 (Pubitemid 39207339)
6. Colinge, J.; Bennett, K. L. Introduction to computational proteomics PLoS Comput. Biol. 2007, 3, e114
7. Schmidt, A.; Kellermann, J.; Lottspeich, F. A novel strategy for quantitative proteomics using isotope-coded protein labels Proteomics 2005, 5, 4-15 (Pubitemid 40189632)
8. Gygi, S. P.; Rist, B.; Gerber, S. A.; Turecek, F.; Gelb, M. H.; Aebersold, R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags Nat. Biotechnol. 1999, 17, 994-9 (Pubitemid 29474856)
9. 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
10. Gevaert, K.; Goethals, M.; Martens, L.; Van Damme, J.; Staes, A.; Thomas, G. R.; Vandekerckhove, J. Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides Nat. Biotechnol. 2003, 21, 566-9 (Pubitemid 36532024)
11. Wang, Y. K.; Ma, Z.; Quinn, D. F.; Fu, E. W. Inverse 18O labeling mass spectrometry for the rapid identification of marker/target proteins Anal. Chem. 2001, 73, 3742-50 (Pubitemid 32862384)
12. Ross, P. L. Multiplexed protein quantitation in Saccharomyces cerevisiae using aminereactive isobaric tagging reagents Mol. Cell. Proteomics 2004, 3, 1154-69
13. Thompson, A.; Schafer, J.; Kuhn, K.; Kienle, S.; Schwarz, J.; Schmidt, G.; Neumann, T.; Johnstone, R.; Mohammed, A. K.; Hamon, C. Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS Anal. Chem. 2003, 75, 1895-904 (Pubitemid 36438013)
14. Keshamouni, V. G.; Michailidis, G.; Grasso, C. S.; Anthwal, S.; Strahler, J. R.; Walker, A.; Arenberg, D. A.; Reddy, R. C.; Akulapalli, S.; Thannickal, V. J.; Standiford, T. J.; Andrews, P. C.; Omenn, G. S. Differential protein expression profiling by iTRAQ-2DLCMS/ MS of lung cancer cells undergoing epithelial-mesenchymal transition reveals a migratory/ invasive phenotype J. Proteome Res. 2006, 5, 1143-54 (Pubitemid 43727792)
15. Oberg, A. L.; Mahoney, D. W.; Eckel-Passow, J. E.; Malone, C. J.; Wolfinger, R. D.; Hill, E. G.; Cooper, L. T.; Onuma, O. K.; Spiro, C.; Therneau, T. M.; Bergen, r., H. R. Statistical analysis of relative labeled mass spectrometry data from complex samples using ANOVA J. Proteome Res. 2008, 7, 225-33 (Pubitemid 351171135)
16. Wang, P.; Tang, H.; Zhang, H.; Whiteaker, J.; Paulovich, A. G.; Mcintosh, M. Normalization regarding non-random missing values in high-throughputmass spectrometry data Pac. Symp. Biocomput. 2006, 315-26
17. Hundertmark, C.; Fischer, R.; Reinl, T.; May, S.; Klawonn, F.; Jansch, L. MS-specific noise model reveals the potential of iTRAQ in quantitative proteomics Bioinformatics 2009, 25, 1004-11
18. 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, 780-790
19. 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, 1885-1897
20. Tiberti, N.; Hainard, A.; Lejon, V.; Robin, X.; Ngoyi, D. M.; Turck, N.; Matovu, E.; Enyaru, J.; Ndung'u, J. M.; Scherl, A.; Dayon, L.; Sanchez, J. C. Discovery and verification of osteopontin and Beta-2-microglobulin as promising markers for staging human African trypanosomiasis Mol. Cell Proteomics 2010, 9, 2783-2795
21. Koecher, 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, 4743-4752
22. Dost, B.; Bandeira, N.; Li, X.; Shen, Z.; Brigg, S.; Bafna, V. Shared peptides in mass spectrometry based protein quantitation. In RECOMB Conference Proceedings; Springer: New York, 2009.
23. Shevchenko, A.; Wilm, M.; Vorm, O.; Mann, M. Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels Anal. Chem. 1996, 68, 850-8
24. Wu, C. H. The Universal Protein Resource (UniProt): an expanding universe of protein information Nucleic Acids Res. 2006, 34, D187-91
25. 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, 3551-3567 (Pubitemid 30007252)
26. Colinge, J.; Masselot, A.; Giron, M.; Dessingy, T.; Magnin, J. OLAV: towards highthroughput tandem mass spectrometry data identification Proteomics 2003, 3, 1454-63 (Pubitemid 37048071)
27. Elias, J. E.; Gibbons, F. D.; King, O. D.; Roth, F. P.; Gygi, S. P. Intensity-based protein identification by machine learning from a library of tandem mass spectra Nat. Biotechnol. 2004, 22, 214-9 (Pubitemid 38160538)
28. Eisenacher, M. mzIdentML: an open community-built standard format for the results of proteomics spectrum identification algorithms Methods Mol. Biol. 2011, 696, 161-177
29. Boehm, A. M.; Putz, S.; Altenhofer, D.; Sickmann, A.; Falk, M. Precise protein quantification based on peptide quantification using iTRAQ BMC Bioinf. 2007, 8, 214
30. Ow, S. Y.; Salim, M.; Noirel, J.; Evans, C.; Rehman, I.; Wright, P. C. iTRAQ underestimation in simple and complex mixtures: "the good, the bad and the ugly J. Proteome Res. 2009, 8, 5347-55
31. Shadforth, I. P.; Dunkley, T. P.; Lilley, K. S.; Bessant, C. i-Tracker: for quantitative proteomics using iTRAQ BMC Genomics 2005, 6, 145
32. Jin, S.; Daly, D. S.; Springer, D. L.; Miller, J. H. The effects of shared peptides on protein quantitation in label-free proteomics by LC/MS/MS J. Proteome Res. 2008, 7, 164-9 (Pubitemid 351171128)
33. Usaite, R.; Wohlschlegel, J.; Venable, J. D.; Park, S. K.; Nielsen, J.; Olsson, L.; Yates Iii, J. R. Characterization of global yeast quantitative proteome data generated from the wild-type and glucose repression saccharomyces cerevisiae strains: the comparison of two quantitative methods J. Proteome Res. 2008, 7, 266-75 (Pubitemid 351171139)
34. Lin, W. T.; Hung, W. N.; Yian, Y. H.; Wu, K. P.; Han, C. L.; Chen, Y. R.; Chen, Y. J.; Sung, T. Y.; Hsu, W. L. Multi-Q: a fully automated tool for multiplexed protein quantitation J. Proteome Res. 2006, 5, 2328-38
35. 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
36. Weng, L.; Dai, H.; Zhan, Y.; He, Y.; Stepaniants, S. B.; Bassett, D. E. Rosetta error model for gene expression analysis Bioinformatics 2006, 22, 1111-1121
37. Evans, M.; Hastings, N.; Peacock, B. Statistical Distributions; Wiley-Interscience: New York, 2000.
38. Levy, P. Calcul des Probabilités; Gauthier-Villars,: Paris, 1925.
39. Rodriguez-Suarez, E.; Gubb, E.; Alzueta, I. F.; Falcon-Perez, J. M.; Amorim, A.; Elortza, F.; Matthiesen, R. Virtual expert mass spectrometrist: iTRAQ tool for database-dependent search, quantitation and result storage Proteomics 2010, 10, 1545-1556
40. Schwacke, J. H.; Hill, E. G.; Krug, E. L.; Comte-Walters, S.; Schey, K. L. iQuantitator: a tool for protein expression inference using iTRAQ BMC Bioinf. 2009, 10, 342
41. Nesvizhskii, A. I.; Aebersold, R. Interpretation of shotgun proteomic data: the protein inference problem Mol. Cell. Proteomics 2005, 4, 1419-40 (Pubitemid 41555469)
42. Choe, L.; D'Ascenzo, M.; Relkin, N. R.; Pappin, D.; Ross, P.; Williamson, B.; Guertin, S.; Pribil, P.; Lee, K. H. 8-plex quantitation of changes in cerebrospinal fluid protein expression in subjects undergoing intravenous immunoglobulin treatment for Alzheimer's disease Proteomics 2007, 7, 3651-3660 (Pubitemid 350022271)
43. Kong, Y.; Tannous, P.; Lu, G.; Berenji, K.; Rothermel, B. A.; Olson, E. N.; Hill, J. A. Suppression of class I and II histone deacetylases blunts pressure-overload cardiac hypertrophy Circulation 2006, 113, 2579-2588 (Pubitemid 43948006)
44. Goldberg, A. D. Distinct factors control histone variant H3.3 localization at specific genomic regions Cell 2010, 140, 678-691