NSAF and GeneChip datasets have a similar variance-versus-mean dependence.A–C, the rowMean and the rowS.D. of the abundance values for each transcript.

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binding sites 58 of the 473 unambiguously assigned phosphorylation sites are predicted by Scansite to be sites for binding. 50 of these correspond.

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NSAF and GeneChip data have similar distribution properties.

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NSAF and GeneChip datasets have similar PLGEM parameters.

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Identification of differentially abundant proteins in the yeast growth phase NSAF dataset. Identification of differentially abundant proteins in the yeast.

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Percentage of proteins identified in envelope membrane extracts according to the purification method and the number of transmembrane domains. Percentage.

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SCX chromatography at low pH permits strong enrichment of phosphopeptides of distinct solution charge states.A, the number of phosphopeptides (blue triangles)

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NSAF and GeneChip datasets have a similar variance-versus-mean dependence.A–C, the rowMean and the rowS.D. of the abundance values for each transcript or protein were measured across all available replicates in the indicated dataset and subsequently transformed to their corresponding base 10 logarithms. NSAF and GeneChip datasets have a similar variance-versus-mean dependence.A–C, the rowMean and the rowS.D. of the abundance values for each transcript or protein were measured across all available replicates in the indicated dataset and subsequently transformed to their corresponding base 10 logarithms. Scatter plots of log10(rowS.D.) versus log10(rowMean) were color-coded according to the same scheme described in the legend of Fig. 1. D–F, the rowCV of each transcript or protein was measured as the ratio between the rowS.D. and the rowMean in the indicated dataset and subsequently transformed to its corresponding base 10 logarithm. Scatter plots of log10(rowCV) versus log10(rowMean) were color-coded according to the same scheme described in the legend of Fig. 1. Note that a linear relationship in a log-log space is mathematically equivalent to a power law relationship in a linear-linear space. A and D represent mouse GeneChip data, B and E represent yeast NSAF data, and C and F represent Mediator NSAF data. Norman Pavelka et al. Mol Cell Proteomics 2008;7:631-644 © 2008 The American Society for Biochemistry and Molecular Biology