PROTEOMIC ANALYSIS OF MITOCHONDRIAL PROTEINS Mary F. Lopez,* Simon Melov, y Felicity Johnson, y Nicole Nagulko, y Eva Golenko,* Scott Kuzdzal, z Suzanne Ackloo, x and Alvydas Mikulskis* *PerkinElmer Life and Analytical Sciences, Boston, Massachusetts 02118 y Buck Institute for Age Research, Novato, California 94945 z PerkinElmer Life and Analytical Sciences, Shelton, Connecticut 06484 x MDS Sciex, Concord, Ontario, Canada L4K 4V8 I. Introduction II. Model Systems III. Technological Approaches A. Mass Spectrometry-Based Proteomics B. Descriptive Proteomics C. Functional Proteomics IV. DiVerential Expression of Proteins in Mouse Brain Mitochondria from Cortex and Synaptosomes V. Conclusions References I. Introduction Approximately one billion years ago eukaryotic cells acquired the distant -proteobacterial progenitors of modern mitochondria (Burger and Lang, 2003). Over the course of mitochondrial evolution, many of the bacterial progenitor genes were lost and many proteins of nonmitochondrial origin were added to the mitochondrial proteome (Hermann and Neupert, 2003). As a result, the mito- chondria in modern organisms are composed of approximately 1000 proteins, with only a handful of very hydrophobic proteins being contributed directly by the mitochondrial genome. The rest of the mitochondrial proteins are derived from genes that reside in the host’s nucleus and are translocated into the organelle. Eukaryotes exhibit a large diversity of mitochondrial DNA (mtDNA). Mitochondrial genomes range in size from 15.8 (Chlamydomonas reinhardtii) to 366.9 (Arabidopsis thaliana) kilobases, with the human circular mitochondrial genome weighing in at 16.6 kilobases. However, mammalian mitochondria are extraordinarily well conserved among species, hence their utility in inferring evolutionary relationships (Boore, 1999). INTERNATIONAL REVIEW OF 31 NEUROBIOLOGY, VOL. 61 Copyright 2004, Elsevier Inc. All rights reserved. 0074-7742/04 $35.00