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. 2014 Apr 5;14:243. doi: 10.1186/1471-2407-14-243

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Copyright © 2014 Huang et al.; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Estimation of the correlation between log 2 phosphopeptide ratios in 2 independent experiments and quantitation error of SILAC ratios of DNP-regulated proteins. A, Two biological replicates were analyzed to compare absolute values of the log2 ratios for the phosphopeptides using scatter plot analysis. The “ratio-of-ratios” correlation between log2 phosphopeptide ratios obtained from 2 independent experiments. B, To determine the quantitation error of phosphopeptides, DNP-regulated protein expression changes were used to determine the median H/L ratio.