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. 2012 Oct 26;151(3):671–683. doi: 10.1016/j.cell.2012.09.019

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© 2012 ELL & Excerpta Medica.

Open Access under CC BY 3.0 license

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Figure S2 — Calibration of Proteomics Data and Functional Properties of Fission Yeast Proteome, Related to Figure 5

(A) Natural logarithm of extracted precursor ion intensities plotted against the natural logarithm of copies per cell for 39 proteins quantified by heavy peptide standards for proliferating cells.

(B) Distribution of error rates determined by bootstrapping for protein quantities from proliferating cells.

(C) Natural logarithm of extracted precursor ion intensities plotted against the natural logarithm of copies per cell for 39 proteins quantified by heavy peptide standards for quiescent cells.

(D) Distribution of error rates determined by bootstrapping for protein quantities from quiescent cells.

(E) Distributions of Identified (blue bars) and all Database Protein Entries (red bars) for Clusters of orthologous groups (COG).

(F) Distributions of Identified (blue bars) and all Database Protein Entries (red bars) for number of transmembrane domains per protein.

(G) Distributions of Identified (blue bars) and all Database Protein Entries (red bars) for number of predicted MS-suitable peptides based on a precursor mass of 700–6000 daltons.

(H) Comparison of expression levels of 17 cytokinesis proteins in asynchronous cultures as measured in this study or in a quantitative fluorescence microscopy study (Wu and Pollard, 2005). Dotted lines represent 2 and 4 fold difference. The coefficient of determination is shown in the bottom right corner.

(I) Cumulative plot of the percentage of total protein count in proliferating cells as a function of the percentage expression rank of individual proteins (red curve), and of the percentage of total mRNA count as a function of the percentage expression rank of individual mRNAs (black curve). Blue and green lines mark 20 and 80% respectively.

(J) Log-log plots of mRNA frequencies as a function of their expression rank. Numbers indicate the exponents of selected power-law distributions shown as black curves. The red vertical lines on the left panel delimitate the three mRNA expression zones (see main text). For more information about Pareto and Zipf laws, see (Furusawa and Kaneko, 2003; Kuznetsov et al., 2002; Newman, 2005).

(K) Log-log plots of protein (right panel) frequencies as a function of their expression rank. Numbers indicate the exponents of selected power-law distributions shown as black curves. Our data thus extend Zipf's law to protein abundance.