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Review
. 2009 Feb 15;72(1):4-11.
doi: 10.1016/j.jprot.2008.11.017. Epub 2008 Dec 7.

Evolution of organelle-associated protein profiling

Wei Yan  1 , Ruedi Aebersold, Elaine W Raines
Affiliations
Review

Evolution of organelle-associated protein profiling

Wei Yan et al. J Proteomics. .

Abstract

Identification of the protein constituents of cell organelles forms the basis for studies to define the roles of specific proteins in organelle structure and functions. Over the past decade, the use of mass spectrometry-based proteomics has dissected various organelles and allowed the association of many novel proteins with particular organelles. This review chronicles the evolution of organelle proteomics technology, and discusses how many limitations, such as organelle heterogeneity and purity, can be avoided with recently developed quantitative profiling approaches. Although many challenges remain, quantitative profiling of organelles holds the promise to begin to address the complex and dynamic shuttling of proteins among organelles that will be critical for application of this advanced technology to disease-based changes in organelle function.

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Figures

Figure 1
Figure 1. Development of new strategies for proteomics analysis to more accurately associate proteins with specific organelles
Partial separation of 3 organelles (individual organelles displayed with different colors and shapes) by density gradient fractionation are shown schematically on the left. The middle panel demonstrates a typical distribution pattern of individual fractions analyzed by immunoblot analysis of organelle marker proteins. Three different approaches to analyze the mass spectrometric data are illustrated in the right panel: A. direct identification of proteins in specific fractions of purified organelle; B. organelle fraction identifications after subtraction of proteins in background fractions using different qualitative and quantitative approaches; C. identification and quantification of proteins in all fractions, and establishment of a quantitative distribution pattern among all of the fractions for each protein to create an organelle signature based on the distribution of organelle marker proteins. The third approach can be used to profile organelles and predict subcellular localization of unknown proteins.
See this image and copyright information in PMC

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