Toward the Standardization of Mitochondrial Proteomics: The Italian Mitochondrial Human Proteome Project Initiative
Toward the Standardization of Mitochondrial Proteomics: The Italian Mitochondrial Human Proteome Project Initiative
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DOI：
10.1021/acs.jproteome.7b00350
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发表时间：
2017-12-01
影响因子：
4.4
通讯作者：
Fasano, Mauro
中科院分区：
文献类型：
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作者：
Alberio, Tiziana;Pieroni, Luisa;Fasano, Mauro
线粒体人类蛋白质组项目旨在了解线粒体蛋白质组的功能及其与其他细胞器蛋白质组的串扰。能够根据下游蛋白质组学分析的具体需求选择合适且经过验证的功能性线粒体富集方案，将极大地帮助该领域的研究人员。使用三种富集方案制备来自十个模型细胞系的线粒体组分，并在七个不同的 LCMS/MS 平台上进行分析。所有数据均使用 neXtProt 作为参考数据库进行处理。这些数据可通过 ProteomeXchange 联盟（标识符为 PXD007053）用于人类蛋白质组项目。使用一套 R 例程对处理后的数据集进行分析，以执行统计分析并检索亚细胞和软骨下定位。尽管鉴定出的总蛋白和线粒体蛋白的总数并不显着依赖于富集方案，但观察到了特定的线与线之间的差异。此外，蛋白质列表被映射到代表功能性线粒体蛋白质组的网络，包括线粒体蛋白质及其第一个相互作用子。超过 80% 的已识别蛋白质产生了该网络的节点，但对于每个富集方案/细胞系对，共分离线粒体相关结构的能力不同。
The Mitochondrial Human Proteome Project aims at understanding the function of the mitochondrial proteome and its crosstalk with the proteome of other organelles. Being able to choose a suitable and validated enrichment protocol of functional mitochondria, based on the specific needs of the downstream proteomics analysis, would greatly help the researchers in the field. Mitochondrial fractions from ten model cell lines were prepared using three enrichment protocols and analyzed on seven different LCMS/MS platforms. All data were processed using neXtProt as reference database. The data are available for the Human Proteome Project purposes through the ProteomeXchange Consortium with the identifier PXD007053. The processed data sets were analyzed using a suite of R routines to perform a statistical analysis and to retrieve subcellular and submitochondrial localizations. Although the overall number of identified total and mitochondrial proteins was not significantly dependent on the enrichment protocol, specific line to line differences were observed. Moreover, the protein lists were mapped to a network representing the functional mitochondrial proteome, encompassing mitochondrial proteins and their first interactors. More than 80% of the identified proteins resulted in nodes of this network but with a different ability in coisolating mitochondria-associated structures for each enrichment protocol/cell line pair.