Hoopmann Michael R, Kusebauch Ulrike, Palmblad Magnus, Bandeira Nuno, Shteynberg David D, He Lingjie, Xia Bin, Stoychev Stoyan H, Omenn Gilbert S, Weintraub Susan T, Moritz Robert L
Institute for Systems Biology, Seattle, Washington 98109, United States.
Center for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands.
J Proteome Res. 2020 Dec 4;19(12):4754-4765. doi: 10.1021/acs.jproteome.0c00648. Epub 2020 Nov 9.
Mass spectrometry has greatly improved the analysis of phosphorylation events in complex biological systems and on a large scale. Despite considerable progress, the correct identification of phosphorylated sites, their quantification, and their interpretation regarding physiological relevance remain challenging. The MS Resource Pillar of the Human Proteome Organization (HUPO) Human Proteome Project (HPP) initiated the Phosphopeptide Challenge as a resource to help the community evaluate methods, learn procedures and data analysis routines, and establish their own workflows by comparing results obtained from a standard set of 94 phosphopeptides (serine, threonine, tyrosine) and their nonphosphorylated counterparts mixed at different ratios in a neat sample and a yeast background. Participants analyzed both samples with their method(s) of choice to report the identification and site localization of these peptides, determine their relative abundances, and enrich for the phosphorylated peptides in the yeast background. We discuss the results from 22 laboratories that used a range of different methods, instruments, and analysis software. We reanalyzed submitted data with a single software pipeline and highlight the successes and challenges in correct phosphosite localization. All of the data from this collaborative endeavor are shared as a resource to encourage the development of even better methods and tools for diverse phosphoproteomic applications. All submitted data and search results were uploaded to MassIVE (https://massive.ucsd.edu/) as data set MSV000085932 with ProteomeXchange identifier PXD020801.
质谱技术极大地改进了对复杂生物系统中磷酸化事件的大规模分析。尽管取得了显著进展，但磷酸化位点的正确识别、定量以及对其生理相关性的解释仍然具有挑战性。人类蛋白质组组织（HUPO）人类蛋白质组计划（HPP）的质谱资源支柱发起了磷酸肽挑战赛，作为一种资源，帮助研究团体评估方法、学习实验步骤和数据分析程序，并通过比较从一组标准的94种磷酸肽（丝氨酸、苏氨酸、酪氨酸）及其非磷酸化对应物以不同比例混合在纯样品和酵母背景中所获得的结果来建立自己的工作流程。参与者用他们选择的方法分析这两种样品，以报告这些肽的识别和位点定位，确定它们的相对丰度，并在酵母背景中富集磷酸化肽。我们讨论了来自22个实验室的结果，这些实验室使用了一系列不同的方法、仪器和分析软件。我们用单一的软件管道重新分析了提交的数据，并强调了正确磷酸化位点定位方面的成功与挑战。这项合作努力的所有数据都作为一种资源共享，以鼓励开发用于各种磷酸蛋白质组学应用的更好方法和工具。所有提交的数据和搜索结果都作为数据集MSV000085932上传到了MassIVE（https://massive.ucsd.edu/），其蛋白质组交换标识符为PXD020801。
