iTRAQ experimental design for plasma biomarker discovery.

@article{citeulike:3175424, abstract = {There is considerable interest in using mass spectrometry for biomarker discovery in human blood plasma. We investigated aspects of experimental design for large studies that require analysis of multiple sample sets using iTRAQ reagents for sample multiplexing and quantitation. Immunodepleted plasma samples from healthy volunteers were compared to immunodepleted plasma from patients with osteoarthritis in eight separate iTRAQ experiments. Our analyses utilizing ProteinPilot software for peptide identification and quantitation showed that the methodology afforded excellent reproducibility from run to run for determining protein level ratios (coefficient of variation 11.7\%), in spite of considerable quantitative variances observed between different peptides for a given protein. Peptides with high variances were associated with lower intensity iTRAQ reporter ions, while immunodepletion prior to sample analysis had a negligible affect on quantitative variance. We examined the influence of different reference samples, such as pooled samples or individual samples on calculating quantitative ratios. Our findings are discussed in the context of optimizing iTRAQ experimental design for robust plasma-based biomarker discovery.}, address = {Australian Proteome Analysis Facility Ltd., Macquarie University, Sydney, Australia.}, author = {Song, X. and Bandow, J. and Sherman, J. and Baker, J. D. and Brown, P. W. and McDowell, M. T. and Molloy, M. P. }, citeulike-article-id = {3175424}, doi = {http://dx.doi.org/10.1021/pr800072x}, issn = {1535-3893}, journal = {Journal of proteome research}, keywords = {biomarker, blood, itraq}, month = {July}, number = {7}, pages = {2952--2958}, posted-at = {2008-08-31 02:59:41}, priority = {2}, title = {iTRAQ experimental design for plasma biomarker discovery.}, url = {http://dx.doi.org/10.1021/pr800072x}, volume = {7}, year = {2008} }

TY - JOUR ID - citeulike:3175424 L3 - citeulike-article-id:3175424 N2 - There is considerable interest in using mass spectrometry for biomarker discovery in human blood plasma. We investigated aspects of experimental design for large studies that require analysis of multiple sample sets using iTRAQ reagents for sample multiplexing and quantitation. Immunodepleted plasma samples from healthy volunteers were compared to immunodepleted plasma from patients with osteoarthritis in eight separate iTRAQ experiments. Our analyses utilizing ProteinPilot software for peptide identification and quantitation showed that the methodology afforded excellent reproducibility from run to run for determining protein level ratios (coefficient of variation 11.7%), in spite of considerable quantitative variances observed between different peptides for a given protein. Peptides with high variances were associated with lower intensity iTRAQ reporter ions, while immunodepletion prior to sample analysis had a negligible affect on quantitative variance. We examined the influence of different reference samples, such as pooled samples or individual samples on calculating quantitative ratios. Our findings are discussed in the context of optimizing iTRAQ experimental design for robust plasma-based biomarker discovery. IS - 7 JF - Journal of proteome research SN - 1535-3893 AD - Australian Proteome Analysis Facility Ltd., Macquarie University, Sydney, Australia. EP - 2958 TI - iTRAQ experimental design for plasma biomarker discovery. VL - 7 SP - 2952 KW - biomarker KW - blood KW - itraq AU - Song, X AU - Bandow, J AU - Sherman, J AU - Baker, JD AU - Brown, PW AU - McDowell, MT AU - Molloy, MP PY - 2008/07// UR - http://dx.doi.org/10.1021/pr800072x ER -