The ProteomeXchange consortium at 10 years: 2023 update.
The ProteomeXchange consortium at 10 years: 2023 update.
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DOI：
10.1093/nar/gkac1040
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发表时间：
2023-01-06
影响因子：
14.9
通讯作者：
Vizcaino, Juan Antonio
中科院分区：
文献类型：
--
作者：
Deutsch, Eric W.;Bandeira, Nuno;Perez-Riverol, Yasset;Sharma, Vagisha;Carver, Jeremy J.;Mendoza, Luis;Kundu, Deepti J.;Wang, Shengbo;Bandla, Chakradhar;Kamatchinathan, Selvakumar;Hewapathirana, Suresh;Pullman, Benjamin S.;Wertz, Julie;Sun, Zhi;Kawano, Shin;Okuda, Shujiro;Watanabe, Yu;MacLean, Brendan;MacCoss, Michael J.;Zhu, Yunping;Ishihama, Yasushi;Vizcaino, Juan Antonio
质谱 (MS) 是迄今为止高通量蛋白质组学中最常用的实验方法。 ProteomeXchange (PX) 蛋白质组学资源联盟 (http://www.proteomexchange.org) 最初成立的目的是标准化公共 MS 蛋白质组学数据的数据提交和传播。自最初的数据工作流程实施以来，现在已有 10 年了。在这份手稿中，我们描述了自 2020 年《核酸研究》上一篇更新手稿发表以来 PX 的主要进展。该联盟的六个成员是 PRIDE、PeptideAtlas（包括 PASSEL）、MassIVE、jPOST、iProX 和 Panorama Public。我们报告了当前的数据提交统计数据，表明提交到 PX 资源的数据集数量每年都在持续增加。截至 2022 年 6 月，已有超过 34 233 个数据集提交给 PX 资源，其中仅在过去三年就有 20 062 个数据集 (58.6%)。我们还报告了通用频谱标识符的开发以及捕获实验元数据注释的改进。与此同时，我们强调公共数据集的数据重用活动不断增加，从而实现 PX 资源与其他流行生物信息学资源、新颖研究和新数据资源之间的连接。最后，我们总结了敏感人类（临床）蛋白质组数据的数据管理实践的最新技术。
Mass spectrometry (MS) is by far the most used experimental approach in high-throughput proteomics. The ProteomeXchange (PX) consortium of proteomics resources (http://www.proteomexchange.org) was originally set up to standardize data submission and dissemination of public MS proteomics data. It is now 10 years since the initial data workflow was implemented. In this manuscript, we describe the main developments in PX since the previous update manuscript in Nucleic Acids Research was published in 2020. The six members of the Consortium are PRIDE, PeptideAtlas (including PASSEL), MassIVE, jPOST, iProX and Panorama Public. We report the current data submission statistics, showcasing that the number of datasets submitted to PX resources has continued to increase every year. As of June 2022, more than 34 233 datasets had been submitted to PX resources, and from those, 20 062 (58.6%) just in the last three years. We also report the development of the Universal Spectrum Identifiers and the improvements in capturing the experimental metadata annotations. In parallel, we highlight that data re-use activities of public datasets continue to increase, enabling connections between PX resources and other popular bioinformatics resources, novel research and also new data resources. Finally, we summarise the current state-of-the-art in data management practices for sensitive human (clinical) proteomics data.
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DOI：
10.1093/bioinformatics/btaa864
发表时间：
2021-07-19
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Bernal-Llinares M;Ferrer-Gómez J;Juty N;Goble C;Wimalaratne SM;Hermjakob H
通讯作者：
Hermjakob H
影响因子：
48
作者：
Choi M;Carver J;Chiva C;Tzouros M;Huang T;Tsai TH;Pullman B;Bernhardt OM;Hüttenhain R;Teo GC;Perez-Riverol Y;Muntel J;Müller M;Goetze S;Pavlou M;Verschueren E;Wollscheid B;Nesvizhskii AI;Reiter L;Dunkley T;Sabidó E;Bandeira N;Vitek O
通讯作者：
Vitek O
影响因子：
4.4
作者：
LeDuc RD;Deutsch EW;Binz PA;Fellers RT;Cesnik AJ;Klein JA;Van Den Bossche T;Gabriels R;Yalavarthi A;Perez-Riverol Y;Carver J;Bittremieux W;Kawano S;Pullman B;Bandeira N;Kelleher NL;Thomas PM;Vizcaíno JA
通讯作者：
Vizcaíno JA
影响因子：
14.9
作者：
Chen T;Ma J;Liu Y;Chen Z;Xiao N;Lu Y;Fu Y;Yang C;Li M;Wu S;Wang X;Li D;He F;Hermjakob H;Zhu Y
通讯作者：
Zhu Y
影响因子：
16.6
作者：
Adhikari S;Nice EC;Deutsch EW;Lane L;Omenn GS;Pennington SR;Paik YK;Overall CM;Corrales FJ;Cristea IM;Van Eyk JE;Uhlén M;Lindskog C;Chan DW;Bairoch A;Waddington JC;Justice JL;LaBaer J;Rodriguez H;He F;Kostrzewa M;Ping P;Gundry RL;Stewart P;Srivastava S;Srivastava S;Nogueira FCS;Domont GB;Vandenbrouck Y;Lam MPY;Wennersten S;Vizcaino JA;Wilkins M;Schwenk JM;Lundberg E;Bandeira N;Marko-Varga G;Weintraub ST;Pineau C;Kusebauch U;Moritz RL;Ahn SB;Palmblad M;Snyder MP;Aebersold R;Baker MS
通讯作者：
Baker MS