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A Proteome Catalog of Drosophila melanogaster: An Essential Resource for Targeted Quantitative Proteomics
Christian Ahrens, Erich Brunner, Ernst Hafen, Ruedi Aebersold and Konrad Basler
volume 1 | issue 3
May/June 2007Pages: 182 - 186
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Proteomic analyses are critically important for systems biology because important aspects related to the structure, function and control of biological systems are only amenable by direct protein measurements. It has become apparent that the current proteomics technologies are unlikely to allow routine, quantitative measurements of whole proteomes. We have therefore suggested and largely implemented a two-step strategy for quantitative proteome analysis. In a first step, the discovery phase, the proteome observable by mass spectrometry is extensively analyzed. The resulting proteome catalog can then be used to select peptides specific to only one protein, so-called proteotypic peptides (PTPs). It represents the basis to realize sensitive, robust and reproducible measurements based on targeted mass spectrometry of these PTPs in a subsequent scoring phase. In this "Extra View" we describe the need for such proteome catalogs and their multiple benefits for catalyzing the shift towards targeted quantitative proteomic analysis and beyond. We use the Insulin signaling cascade as a representative example to illustrate the limitations of currently used proteomics approaches for the specific analysis of individual pathway components, and describe how the recently published Drosophila proteome catalog already helped to overcome many of these limitations.
Authors
Christian Ahrens
Swiss Institute of Technology, Functional Genomics Center Zurich, Zürich, Switzerland
Erich Brunner
University of Zurich, Center for Model Organism Proteomes, Zurich, Switzerland
Ernst Hafen
Swiss Institute of Technology, Institute of Molecular Systems Biology, Zurich, Switzerland
Ruedi Aebersold
Swiss Institute of Technology, Institute of Molecular Systems Biology, Zurich, Switzerland
Konrad Basler
University of Zurich, Zurich, Switzerland
We now provide open access to journal articles published online for one year or more. This article may be downloaded at the following link:
Download PDF If the document does not open, please right-click on the link (control-click on a Macintosh) and select the option to save the file to disk.