Insights from the First Phosphopeptide Challenge of the MS Resource Pillar of the HUPO Human Proteome Project.
Insights from the First Phosphopeptide Challenge of the MS Resource Pillar of the HUPO Human Proteome Project.
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DOI：
10.1021/acs.jproteome.0c00648
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发表时间：
2020-12-04
影响因子：
4.4
通讯作者：
Moritz RL
中科院分区：
文献类型：
--
作者：
Hoopmann MR;Kusebauch U;Palmblad M;Bandeira N;Shteynberg DD;He L;Xia B;Stoychev SH;Omenn GS;Weintraub ST;Moritz RL
质谱法极大地改善了复杂生物系统中大规模磷酸化事件的分析。尽管取得了相当大的进展，磷酸化位点的正确识别，它们的定量，以及它们关于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MS资源支柱发起了磷酸肽挑战赛，作为帮助社区评估方法，学习程序和数据分析程序的资源，并通过比较从标准的94种磷酸肽组中获得的结果来建立自己的工作流程（丝氨酸、苏氨酸、酪氨酸）和它们的非磷酸化对应物以不同比例混合在纯样品和酵母背景中。参与者用他们选择的方法分析了两种样品，以报告这些肽的鉴定和位点定位，确定其相对丰度，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。我们使用单一软件管道重新分析了提交的数据，并强调了正确磷酸盐定位的成功和挑战。所有来自这一合作奋进的数据都作为一种资源共享，以鼓励为各种磷酸化蛋白质组学应用开发更好的方法和工具。所有提交的数据和检索结果均上传至MassIVE（https：//musve.ucsd.edu/），作为数据集MSV 000085932，ProteomeXchange标识符为PXD 020801。
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.
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影响因子：
14.9
作者：
Deutsch EW;Csordas A;Sun Z;Jarnuczak A;Perez-Riverol Y;Ternent T;Campbell DS;Bernal-Llinares M;Okuda S;Kawano S;Moritz RL;Carver JJ;Wang M;Ishihama Y;Bandeira N;Hermjakob H;Vizcaíno JA
通讯作者：
Vizcaíno JA
DOI：
10.1074/mcp.o113.034181
发表时间：
2013-12
期刊：
Molecular & cellular proteomics : MCP
影响因子：
--
作者：
Olsen JV;Mann M
通讯作者：
Mann M
影响因子：
4.3
作者：
Bakalarski, Corey E.;Haas, Wilhelm;Gygi, Steven P.
通讯作者：
Gygi, Steven P.
影响因子：
3.4
作者：
Eng, Jimmy K.;Jahan, Tahmina A.;Hoopmann, Michael R.
通讯作者：
Hoopmann, Michael R.
影响因子：
9.9
作者：
Leutert, Mario;Rodriguez-Mias, Ricard A.;Villen, Judit
通讯作者：
Villen, Judit