iQuantitator: A tool for protein expression inference using iTRAQ

BMC Bioinformatics

Volumn 10, Issue , 2009, Pages 342-

  Schwacke, John H ^a   Hill, Elizabeth G ^a   Krug, Edward L ^a   Comte Walters, Susana ^a   Schey, Kevin L ^b  

^a MEDICAL UNIVERSITY OF SOUTH CAROLINA   (United States)

^b VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SOFTWARE; DESIGN OF EXPERIMENTS; HYPERTEXT SYSTEMS; MARKOV PROCESSES; METADATA; PROTEINS;

COMPUTATIONAL CHALLENGES; EXPERIMENTAL CONDITIONS; HIERARCHICAL REGRESSION; MARKOV CHAIN MONTE CARLO METHOD; PARAMETER INFERENCE; PROCESS-BASED MODELING; QUANTITY OF INTEREST; REGRESSION COEFFICIENT;

MONTE CARLO METHODS;

ANIMAL CELL; ARTICLE; COMPUTER MODEL; COMPUTER PROGRAM; CONTROLLED STUDY; CYTOSOL; DATA ANALYSIS; MATHEMATICAL COMPUTING; MONTE CARLO METHOD; NONHUMAN; PROTEIN ANALYSIS; PROTEIN EXPRESSION; QUANTITATIVE ANALYSIS;

EID: 70450255179     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-342     Document Type: Article

References (22)

1. Aebersold R, Mann M. Mass spectrometry-based proteomics. Nature 2003, 422(6928):198-207. 10.1038/nature01511, 12634793.
2. Unlu M, Morgan ME, Minden JS. Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis 1997, 18(11):2071-2077. 10.1002/elps.1150181133, 9420172.
3. Mueller LN, Brusniak MY, Mani DR, Aebersold R. An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data. J Proteome Res 2008, 7(1):51-61. 10.1021/pr700758r, 18173218.
4. Ross PL, Huang YN, Marchese JN, Williamson B, Parker K, Hattan S, Khainovski N, Pillai S, Dey S, Daniels S. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 2004, 3(12):1154-1169. 10.1074/mcp.M400129-MCP200, 15385600.
5. Pierce A, Unwin RD, Evans CA, Griffiths S, Carney L, Zhang L, Jaworska E, Lee CF, Blinco D, Okoniewski MJ. Eight-channel iTRAQ enables comparison of the activity of 6 leukaemogenic tyrosine kinases. Mol Cell Proteomics 2008, 7(5):853-863. 10.1074/mcp.M700251-MCP200, 17951628.
6. Shadforth IP, Dunkley TP, Lilley KS, Bessant C. i-Tracker: for quantitative proteomics using iTRAQ. BMC Genomics 2005, 6:145. 10.1186/1471-2164-6-145, 1276793, 16242023.
7. Laderas T, Bystrom C, McMillen D, Fan G, McWeeney S. TandTRAQ: an open-source tool for integrated protein identification and quantitation. Bioinformatics 2007, 23(24):3394-3396. 10.1093/bioinformatics/btm467, 17895273.
8. Lin WT, Hung WN, Yian YH, Wu KP, Han CL, Chen YR, Chen YJ, Sung TY, Hsu WL. Multi-Q: a fully automated tool for multiplexed protein quantitation. J Proteome Res 2006, 5(9):2328-2338. 10.1021/pr060132c, 16944945.
9. Yu CY, Tsui YH, Yian YH, Sung TY, Hsu WL. The Multi-Q web server for multiplexed protein quantitation. Nucleic Acids Res 2007, (35 Web Server):W707-712. 10.1093/nar/gkm345, 1933177, 17553828.
10. Boehm AM, Putz S, Altenhofer D, Sickmann A, Falk M. Precise protein quantification based on peptide quantification using iTRAQ. BMC Bioinformatics 2007, 8:214. 10.1186/1471-2105-8-214, 1940031, 17584939.
11. Shifman MA, Li Y, Colangelo CM, Stone KL, Wu TL, Cheung KH, Miller PL, Williams KR. YPED: a web-accessible database system for protein expression analysis. J Proteome Res 2007, 6(10):4019-4024. 10.1021/pr070325f, 17867667.
12. Jones P, Cote RG, Cho SY, Klie S, Martens L, Quinn AF, Thorneycroft D, Hermjakob H. PRIDE: new developments and new datasets. Nucleic Acids Res 2008, (36 Database):D878-883. 2238846, 18033805.
13. Siepen JA, Swainston N, Jones AR, Hart SR, Hermjakob H, Jones P, Hubbard SJ. An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQ. Proteome Sci 2007, 5:4. 10.1186/1477-5956-5-4, 1796855, 17270041.
14. Oberg AL, Mahoney DW, Eckel-Passow JE, Malone CJ, Wolfinger RD, Hill EG, Cooper LT, Onuma OK, Spiro C, Therneau TM. Statistical Analysis of Relative Labeled Mass Spectrometry Data from Complex Samples Using ANOVA. J Proteome Res 2008, 7(1):225-233. 10.1021/pr700734f, 2528956, 18173221.
15. Hill EG, Schwacke JH, Comte-Walters S, Slate EH, Oberg AL, Eckel-Passow JE, Therneau TM, Schey KL. A statistical model for iTRAQ data analysis. J Proteome Res 2008, 7(8):3091-3101. 10.1021/pr070520u, 2722948, 18578521.
16. Liu H, Sadygov RG, Yates JR. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem 2004, 76(14):4193-4201. 10.1021/ac0498563, 15253663.
17. Carlin BP, Louis TA. Bayes and Empirical Bayes methods for data analysis. 2000, Boca Raton: Chapman & Hall/CRC, 2.
18. Gelman A. Analysis of variance - why it is more important than ever. Annals of Statistics 2005, 33(1):1-53.
19. Friedl JEF. Mastering regular expressions. 2006, Sebastapol, CA: O'Reilly, 3.
20. Plummer M, Best N, Cowles K, Vines K. CODA: Convergence Diagnosis and Output Analysis for MCMC. R News 2006, 6(1):7-11.
21. Adobe Systems Incorporated Adobe Reader 8. 2008, 8.1.2.
22. R Development Core Team R: A Language and Environment for Statistical Computing. 2006, Viena, Austria: R Foundation for Statistical Computing.