Comprehensive label-free method for the relative quantification of proteins from biological samples

Journal of Proteome Research

Volumn 4, Issue 4, 2005, Pages 1442-1450

  Higgs, Richard E ^a   Knierman, Michael D ^a   Gelfanova, Valentina ^a   Butler, Jon P ^a   Hale, John E ^a  

^a ELI LILLY AND COMPANY   (United States)

Author keywords

Biomarkers; Differential expression; LC MS MS; Proteomics; Relative quantification

Indexed keywords

BIOLOGICAL MARKER;

ANIMAL CELL; ANIMAL TISSUE; ARTICLE; BIOLOGICAL MONITORING; CONTROLLED STUDY; DRUG RESEARCH; ION PAIR CHROMATOGRAPHY; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; NONHUMAN; PRIORITY JOURNAL; PRODUCTIVITY; PROTEIN ANALYSIS; PROTEIN BLOOD LEVEL; PROTEIN CEREBROSPINAL FLUID LEVEL; PROTEIN DEGRADATION; QUANTITATIVE ANALYSIS; RAT;

AMINO ACID SEQUENCE; ANIMALS; BIOLOGICAL MARKERS; CHROMATOGRAPHY, LIQUID; MALE; MASS SPECTROMETRY; MOLECULAR SEQUENCE DATA; PROTEINS; RATS; REPRODUCIBILITY OF RESULTS; SERUM; TRYPSIN INHIBITOR, KUNITZ SOYBEAN;

EID: 23944472666     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr050109b     Document Type: Article

References (34)

1. FDA Critical Path Initiative, http://www.fda.gov/oc/initiatives/ criticalpath.
2. NIH Road map for Medical Research, http://www.nihroad map.nih.gov/index.asp.
3. Aebersold, R.; Mann, M. Nature 2003, 422, 198-207.
4. Patterson, S. D.; Aebersold, R. H. Nat. Genet. 2003, 33, 311-323.
5. Domon, B.; Alving, K.; He, T.; Ryan, T. E.; Patterson, S. D. Curr. Opin. Mol. Ther. 2002, 4, 577-586.
6. Kaiser, R. E.; Higgs, R. E.; Julian, R. K. System and Methods for Quantitatively Comparing Complex Mixtures Using Single Ion Chromatograms Derived From Spectroscopic Analysis of Such Admixtures. United States Patent #5,885,841, granted 23 Mar 1999.
7. Gygi, S.; Rist, B.; Gerber, S. A.; Turecek, F.; Gelb, M. H.; Aebersold, R. Nat. Biotechnol. 1999, 19, 994-999.
8. Ji, J.; Chakraborty, A.; Geng, M.; Zhang, X.; Amini, A.; Bina, M.; Regnier, F. J. Chromatogr., B 2000, 745, 197-210.
9. Cagney, G.; Emili, A. Nat. Biotechnol. 2002, 20, 163-170.
10. Bondarenko, P. V.; Chelius, D.; Shaler, T. A. Anal. Chem. 2002, 74, 4741-4749.
11. Chelius, D.; Bondarenko, P. V. J. Proteome Res. 2002, 1, 317-323.
12. Wang, W.; Zhou, H.; Lin, H.; Roy, S.; Shaler, T. A.; Hill, L. R.; Norton, S.; Kumar, P.; Anderle, M.; Becker, C. H. Anal. Chem. 2003, 75, 4818-4826.
13. Petricoin, E. F., III; Ardekani, A. M.; Hitt, B. A.; et al. Lancet 2002, 359, 572-577.
14. Radulovic, D.; Jelveh, S.; Ryu, S.; Hamilton, T. G.; Foss, E.; Mao, Y.; Emili, A. Mol. Cell. Proteomics 2004, 3, 984-997.
15. Wiener, M. C.; Sachs, J. R.; Deyanova, E. G.; Yates N. A. Anal. Chem. 2004, 76, 6085-6096.
16. Gao, J.; Opiteck, G. J.; Friedrichs, M. S.; Dongre, A. R.; Hefta, S. A. J. Proteome Res. 2003, 2, 643-649.
17. Colinge, J.; Chiappe, D.; Lagache, S.; Moniatte, M.; Bougueleret, L. Anal. Chem. 2005, 77, 596-606.
18. Hale, J. E.; Butler, J. P.; Gelfanova, V.; You, J.-S.; Knierman, M. D. Anal. Biochem. 2004, 333, 174-181.
19. Proakis, J. G.; Manolakis, D. G. Digital Signal Processing-Principles, Algorithms and Applications, 2nd ed.; Prentice Hall: New York, 1992.
20. Eng, J. K.; McCormack, A. L.; Yates, R. R. J. Am. Soc. Mass Spectrom. 1994, 5, 976-989.
21. Craig, R.; Beavis, R. C. Rapid Commun. Mass Spectrom. 2003, 17, 2310-2316.
22. Craig, R.; Beavis, R. C. Bioinformatics 2004, 20, 1466-1467.
23. Perkins, D. N.; Pappin, D. J.; Creasy, D. M.; Cottrell, J. S. Electrophoresis 1999, 20, 3551-3567.
24. Nesvizhskii, A. I.; Keller, A.; Kolker, E.; Aebersold, R. Anal. Chem. 2004, 75, 4646-4658.
25. International Protein Index, European Bioinformatics Institute 2005. http://www.ebi.ac.uk/IPI/IPIhelp.html.
26. National Center for Biotechnology Information 2005, http:// www.ncbi.nlm.nih.gov.
27. Peng, J.; Elias, J. E.; Thoreen, C. C.; Licklider, J. J.; Gygi, S. P. J. Proteome Res. 2003, 2, 43-50.
28. Cleveland, W. S.; Grosse, E.; Shyu, W. M. Local regression models. Chapter 8 of Statistical Models in S; Chambers, J. M., Hastie, T. J., Eds.; Wadsworth & Brooks/Cole: 1992.
29. Bolstad, B. M.; Irizarry, R. A.; Astrand, M.; Speed, T. P. Bioinformatics 2003, 19, 185-193.
30. R Development Core Team, R: A language and environment for statistical computing, R Foundation for Statistical Computing 2004, http://www.R-project. org.
31. Sun Grid Engine Project 2004, http://gridengine.sunsource.net.
32. SAS Institute. 2000. The SAS system: SAS Online Doc, version 8, HTML format [CD-ROM]. Cary, NC.
33. JMP Statistical Discovery Software, version 5.1.1, SAS Institute, Cary NC.
34. Anderle, M.; Roy, S.; Lin, H.; Becker, C.; Joho, K. Bioinformatics 2004, 20, 3575-3582.