Enrichment for Mitochondrial Proteins by MS

<div><p>(A) shows the 546 proteins (in rows) identified from 28 datasets (columns). The proteins are sorted in decreasing order down rows by the number of experiments in which peptide tags were identified by MS and binned into three classes of detection frequency. The number at the bottom of each class indicates the total number of proteins in the class. Proteins that are part of the reference set, and thus are previously known mitochondrial proteins (M), are marked to the left. The experiments are divided according to fermentable (F) and nonfermentable (NF) mitochondrial preparations.</p> <p>(B) Proportions of proteins identified in membrane and matrix fractions. Whether a protein was detected predominantly in either the membrane or matrix fraction, or equal in both fractions, was determined based on where it was detected with an average higher tag number. Shown are the proportions for all 546 proteins, for known matrix proteins (i.e., matrix and intermembrane space, <i>n</i> = 109), for known membrane proteins (i.e., inner and outer membrane, <i>n</i> = 101), and for detected proteins not previously known to be mitochondrial (<i>n</i> = 290).</p> <p>(C) Distribution of proteins identified under fermentable and nonfermentable conditions by proteomics, and overlap with previously known mitochondrial proteins. Total numbers are given in parentheses.</p> <p>(D) Breakdown by localization of the 546 proteins identified. For mitochondrial localization the reference set was chosen; for localization outside mitochondria the GFP fusion protein data were used (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020160#pbio-0020160-Huh1" target="_blank">Huh et al. 2003</a>). The inner circle represents the distribution for all proteins in yeast.</p> <p>(E) Distribution of median mRNA expression under fermentable and nonfermentable conditions, protein abundance under fermentable conditions (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020160#pbio-0020160-Ghaemmaghami1" target="_blank">Ghaemmaghami et al. 2003</a>), and protein length across bins of confidence of identification (maximum number of tags identified in any of the 28 datasets). The bars indicate fold differences from the median for the known mitochondrial proteins that were not detected by MS (“M not det.”).</p>