iTRAQ protein quantification: A quality-controlled workflow

Proteomics

Volumn 11, Issue 6, 2011, Pages 1125-1134

  Burkhart, Julia M ^a   Vaudel, Marc ^a   Zahedi, René P ^a   Martens, Lennart ^b,c   Sickmann, Albert ^a,d  

^a LEIBNIZ INSTITUT FÜR ANALYTISCHE WISSENSCHAFTEN ISAS E V   (Germany)

^b DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

^c GHENT UNIVERSITY   (Belgium)

^d RUHR UNIVERSITY BOCHUM   (Germany)

Author keywords

ITRAQ; Mass spectrometry; Quantification; Technology

Indexed keywords

ARTICLE; CHEMICAL LABELING; CONTROLLED STUDY; ITRAQ; PRIORITY JOURNAL; PROTEIN ANALYSIS; QUALITY CONTROL; WORKFLOW;

INDICATORS AND REAGENTS; IONS; ISOTOPES; MITOCHONDRIAL PROTEINS; PEPTIDES; PROTEINS; PROTEOMICS; QUALITY CONTROL; SACCHAROMYCES CEREVISIAE PROTEINS; TANDEM MASS SPECTROMETRY; WORKFLOW;

EID: 79952288667     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201000711     Document Type: Article

References (32)

1. Chakraborty, A., Regnier, F. E., Global internal standard technology for comparative proteomics. J. Chromatogr. A 2002, 949, 173-184.
2. Dayon, L., Hainard, A., Licker, V., Turck, N. et al., Relative quantification of proteins in human cerebrospinal fluids by MS/MS using 6-plex isobaric tags. Anal. Chem. 2008, 80, 2921-2931.
3. Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F. et al., Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 1999, 17, 994-999.
4. Ross, P. L., Huang, Y. N., Marchese, J. N., Williamson, B. et al., Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics 2004, 3, 1154-1169.
5. Ong, S., Kratchmarova, I., Mann, M., Properties of 13C-substituted arginine in stable isotope labeling by amino acids in cell culture (SILAC). J. Proteome Res. 2003, 2, 173-181.
6. Wang, W., Zhou, H., Lin, H., Roy, S. et al., Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards. Anal. Chem. 2003, 75, 4818-4826.
7. Silva, J. C., Gorenstein, M. V., Li, G., Vissers, J. P. C., Geromanos, S. J., Absolute quantification of proteins by LCMSE: a virtue of parallel MS acquisition. Mol. Cell. Proteomics 2006, 5, 144-156.
8. Lange, V., Picotti, P., Domon, B., Aebersold, R., Selected reaction monitoring for quantitative proteomics: a tutorial. Mol. Syst. Biol. 2008, 4, 222.
9. Zhang, G., Neubert, T. A., Automated comparative proteomics based on multiplex tandem mass spectrometry and stable isotope labeling. Mol. Cell. Proteomics 2006, 5, 401-411.
10. Ishihama, Y., Oda, Y., Tabata, T., Sato, T. et al., Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol. Cell. Proteomics 2005, 4, 1265-1272.
11. Pichler, P., Kocher, T., Holzmann, J., Mazanek, M. et al., 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, 6549-6558.
12. Simpson, D. M., Beynon, R. J., Acetone precipitation of proteins and the modification of peptides. J. Proteome Res. 2010, 9, 444-450.
13. Sickmann, A., Reinders, J., Wagner, Y., Joppich, C. et al., The proteome of Saccharomyces cerevisiae mitochondria. Proc. Natl. Acad. Sci. USA 2003, 100, 13207-13212.
14. Green, N. M., Neurath, H., The effects of divalent cations on trypsin. J. Biol. Chem. 1953, 204, 379-390.
15. Olsen, J. V., de Godoy, L. M. F., Li, G., Macek, B. et al., Parts per million mass accuracy on an Orbitrap mass spectrometer via lock mass injection into a C-trap. Mol. Cell. Proteomics 2005, 4, 2010-2021.
16. Martens, L., Chambers, M., Sturm, M., Kessner, D. et al., mzML - a community standard for mass spectrometry data. Mol. Cell. Proteomics 2010.
17. Kessner, D., Chambers, M., Burke, R., Agus, D., Mallick, P., ProteoWizard: open source software for rapid proteomics tools development. Bioinformatics 2008, 24, 2534-2536.
18. Sturm, M., Bertsch, A., Gropl, C., Hildebrandt, A. et al., OpenMS - an open-source software framework for mass spectrometry. BMC Bioinformatics 2008, 9, 163.
19. 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.
20. 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, 207-214.
21. Martens, L., Vandekerckhove, J., Gevaert, K., DBToolkit: processing protein databases for peptide-centric proteomics. Bioinformatics 2005, 21, 3584-3585.
22. Storey, J. D., Tibshirani, R., Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. USA 2003, 100, 9440-9445.
23. Vaudel, M., Sickmann, A., Martens, L., Peptide and protein quantification: a map of the minefield. Proteomics 2010, 10, 650-670.
24. Carrillo, B., Yanofsky, C., Laboissiere, S., Nadon, R., Kearney, R. E., Methods for combining peptide intensities to estimate relative protein abundance. Bioinformatics 2010, 26, 98-103.
25. Rosner, B., Percentage points for a generalized ESD many-outlier procedure. Technometrics 1983, 25, 165-172.
26. Dixon, W., Processing data for outliers. Biometrics 1953, 9, 74-89.
27. Russell, W. K., Park, Z. Y., Russell, D. H., Proteolysis in mixed organic-aqueous solvent systems: applications for peptide mass mapping using mass spectrometry. Anal. Chem. 2001, 73, 2682-2685.
28. Rodriguez, J., Gupta, N., Smith, R. D., Pevzner, P. A., Does trypsin cut before proline?. J. Proteome Res. 2008, 7, 300-305.
29. Chertov, O., Biragyn, A., Kwak, L. W., Simpson, J. T. et al., Organic solvent extraction of proteins and peptides from serum as an effective sample preparation for detection and identification of biomarkers by mass spectrometry. Proteomics 2004, 4, 1195-1203.
30. Kay, R., Barton, C., Ratcliffe, L., Matharoo-Ball, B. et al., Enrichment of low molecular weight serum proteins using acetonitrile precipitation for mass spectrometry based proteomic analysis. Rapid Commun. Mass Spectrom. 2008, 22, 3255-3260.
31. Kirkpatrick, D. S., Gerber, S. A., Gygi, S. P., The absolute quantification strategy: a general procedure for the quantification of proteins and post-translational modifications. Methods 2005, 35, 265-273.
32. Holzmann, J., Pichler, P., Madalinski, M., Kurzbauer, R., Mechtler, K., Stoichiometry determination of the MP1-p14 complex using a novel and cost-efficient method to produce an equimolar mixture of standard peptides. Anal. Chem. 2009, 81, 10254-10261.