Brunner Erich, Ahrens Christian H, Mohanty Sonali, Baetschmann Hansruedi, Loevenich Sandra, Potthast Frank, Deutsch Eric W, Panse Christian, de Lichtenberg Ulrik, Rinner Oliver, Lee Hookeun, Pedrioli Patrick G A, Malmstrom Johan, Koehler Katja, Schrimpf Sabine, Krijgsveld Jeroen, Kregenow Floyd, Heck Albert J R, Hafen Ernst, Schlapbach Ralph, Aebersold Ruedi
Center for Model Organism Proteomes, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
Nat Biotechnol. 2007 May;25(5):576-83. doi: 10.1038/nbt1300. Epub 2007 Apr 22.
Understanding how proteins and their complex interaction networks convert the genomic information into a dynamic living organism is a fundamental challenge in biological sciences. As an important step towards understanding the systems biology of a complex eukaryote, we cataloged 63% of the predicted Drosophila melanogaster proteome by detecting 9,124 proteins from 498,000 redundant and 72,281 distinct peptide identifications. This unprecedented high proteome coverage for a complex eukaryote was achieved by combining sample diversity, multidimensional biochemical fractionation and analysis-driven experimentation feedback loops, whereby data collection is guided by statistical analysis of prior data. We show that high-quality proteomics data provide crucial information to amend genome annotation and to confirm many predicted gene models. We also present experimentally identified proteotypic peptides matching approximately 50% of D. melanogaster gene models. This library of proteotypic peptides should enable fast, targeted and quantitative proteomic studies to elucidate the systems biology of this model organism.
了解蛋白质及其复杂的相互作用网络如何将基因组信息转化为一个动态的生物体，是生物科学领域的一项基本挑战。作为迈向理解复杂真核生物系统生物学的重要一步，我们通过从498,000个冗余和72,281个不同的肽段鉴定中检测到9,124种蛋白质，对预测的黑腹果蝇蛋白质组的63%进行了编目。通过结合样本多样性、多维生化分级分离和分析驱动的实验反馈回路，实现了对复杂真核生物前所未有的高蛋白组覆盖率，其中数据收集由先前数据的统计分析指导。我们表明，高质量的蛋白质组学数据为修正基因组注释和确认许多预测的基因模型提供了关键信息。我们还展示了实验鉴定的与约50%的黑腹果蝇基因模型匹配的蛋白型肽段。这个蛋白型肽段文库应能实现快速、靶向和定量的蛋白质组学研究，以阐明这种模式生物的系统生物学。
