Content area
Full Text
Figure 1. Linear correlation between label-free abundance estimates (mean of 14 replicates) and absolute protein abundance (in 1000 copies per cell) is shown for 12 proteins from Jurkat whole-cell lysate sequenced 14 times. Absolute protein abundance for the 12 quantified proteins was obtained using the AQUA method [70]. Abundances ranged from 16,000 to 4.2 million copies per cell, and sizes ranged from 9 to 182 kDa. Sequenced Jurkat whole-cell lysate and mRNA abundances were previously reported in Wu
et al. [10]. (A) Known protein abundance is plotted as a function of raw spectral count and resulting squared Pearson correlation coefficient is 0.90. (B) The enclosed area in the lower left portion of plot A is expanded. Error bars show one standard deviation on each side of mean. (C) Known protein abundance is plotted as a function of emPAI [55] , with squared Pearson correlation coefficient of 0.77. (D) Known protein abundance is plotted as a function of size-normalized SC (SC/MM), with squared Pearson correlation coefficient of 0.69. (E) Heat map shows position of mass spectrometry-detected proteins (bright turquoise) relative to their measured mRNA abundance. Positions of the 12 quantified proteins are indicated. emPAI: Exponentially modified protein abundance index; MM: Molecular mass; SC: Spectral count.
(Figure omitted. See article PDF.)
Figure 2. Normal versus Poisson distributions. These are compared for the following theoretical distributions: µ = 2, s = 1.41; µ = 3, s = 1.73; µ = 5, s = 2.24; and µ = 10, s = 3.16.
(Figure omitted. See article PDF.)
Figure 3. FDR versus sensitivity plots show how type of analysis, number of replicates and magnitude of fold-change all affect detection of differential regulation. (A-D) Results based on synthetic yeast cell datasets from [53]. (E & F) Results based on an unpublished synthetic human Jurkat leukemic T-cell dataset for which 15% of proteins are up- or down-regulated (5% twofold, 5% fourfold and 5% eightfold) [101]. PLGEM was applied to both raw spectral count and NSAF. QSpec results were the same using both spectral count and NSAF; thus, only NSAF results are shown. (A) Two-replicate, twofold; (B) two-replicate, fourfold; (C) four-replicate, twofold; (D) four-replicate, fourfold; (E) two-replicate, combined two-, four- and eight-fold; and (F) two-replicate, separate two-, four-, and eight-fold comparisons are...