BBSRC-NSF/BIO PTMeXchange: Globally harmonized re-analysis and sharing of data on post-translational modifications

BBSRC-NSF/BIO PTMeXchange：全球统一的翻译后修饰数据重新分析和共享

• 批准号: BB/S01781X/1
• 负责人: Juan Antonio Vizcaino
• 金额: $ 59万
• 依托单位: European Bioinformatics Institute
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2019
• 资助国家: 英国
• 起止时间: 2019 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FS01781X%2F1
• 关键词: BBSRC; NSF; BIO; PTMeXchange; Globally

Proteins are the key functional molecules in cells, performing multiple biological tasks. This includes catalysing reactions, providing structure to cellular components, signaling between different cells and regulating the production of other genes among many others. Proteins are composed of chains of individual amino acids that are formed initially into a long sequence, which forms into a strictly controlled 3D structure, giving the highly specific function to each protein. The advent of genome sequencing has transformed our ability to study these molecules into a "Big Data" discipline, coupled to advances in mass spectrometry and allied computing techniques. This particular branch of "'omics" is referred to as proteomics - the high-throughput study (identification and quantification) of all the proteins that can be detected in a given biological sample. Proteomics is used right across biological and biomedical research for profiling systems as varied as human, model organisms including plants, and infectious diseases/microbes, among many others. Many biological functions are dependent on chemical modifications that proteins can undergo, called Post-translational Modifications (PTMs). Due to the occurrence of PTMs, one particular gene can produce a great number of different protein entities which can potentially have different biological functions. PTMs can provide a rapid mechanism for changing function, such as switching an enzyme (biological catalyst) "on" and "off". Due to their functional importance, sites of PTMs on proteins are frequently the targets for drug design, particularly against cancer. In this grant, we will study, using high-quality data analysis pipelines, the occurrence of the main types of PTMs across hundreds of proteomics datasets in the public domain, involving human and the main model organisms (e.g. mouse, rat and the model plant Arabidopsis). Three world-leading bioinformatics resources are involved in this proposal, namely PRIDE and PeptideAtlas (proteomics resources), and UniProtKB (protein knowledge-base). We expect that UniProtKB will be the main resource to disseminate the outputs of the project to thousands of researchers, working in varied disciplines. We will also showcase possible research applications of this huge amount of data that will be generated, for example studying how PTMs have evolved in different groups of species. We will ensure that all the outputs of the project are disseminated via different training and outreach activities, including e.g. delivering workshops, training and online help/tutorials.

蛋白质是细胞中的关键功能分子，执行多种生物学任务。这包括催化反应，为细胞成分提供结构，不同细胞之间的信号传递，以及调节其他基因的产生等。蛋白质是由单个氨基酸组成的链，这些氨基酸最初形成一个长序列，形成一个严格控制的3D结构，赋予每个蛋白质高度特定的功能。基因组测序的出现，将我们研究这些分子的能力转变为一门“大数据”学科，再加上质谱学和相关计算技术的进步。“组学”的这一特殊分支被称为蛋白质组学--对给定生物样本中可以检测到的所有蛋白质进行高通量研究(鉴定和量化)。蛋白质组学直接用于生物和生物医学研究，包括人类、包括植物在内的模式生物和传染病/微生物等不同的图谱系统。许多生物功能依赖于蛋白质可以经历的化学修饰，称为翻译后修饰(PTM)。由于PTMS的发生，一个特定的基因可以产生大量不同的蛋白质实体，这些实体可能具有不同的生物学功能。PTMS可以提供一种快速改变功能的机制，例如将一种酶(生物催化剂)“开”和“关”。由于它们的功能重要性，PTMS在蛋白质上的位置经常是药物设计的靶点，尤其是抗癌药物。在这笔赠款中，我们将利用高质量的数据分析管道，研究公共领域数百个蛋白质组学数据集上主要类型的PTM的出现情况，涉及人类和主要模式生物(例如小鼠、大鼠和模式植物拟南芥)。这项提议涉及三个世界领先的生物信息学资源，即Pride and PeptideAtlas(蛋白质组学资源)和UniProtKB(蛋白质知识库)。我们预计UniProtKB将成为向在不同学科工作的数千名研究人员传播项目成果的主要资源。我们还将展示这些将产生的大量数据的可能研究应用，例如研究PTM如何在不同的物种群体中进化。我们将确保通过不同的培训和外联活动传播该项目的所有成果，包括举办讲习班、培训和在线帮助/教程。

项目成果

The ProteomeXchange consortium at 10 years: 2023 update.

• DOI: 10.1093/nar/gkac1040
• 发表时间: 2023-01-06
• 期刊: NUCLEIC ACIDS RESEARCH
• 影响因子: 14.9
• 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
• 通讯作者: Vizcaino, Juan Antonio

UniProt and Mass Spectrometry-Based Proteomics-A 2-Way Working Relationship.

• DOI: 10.1016/j.mcpro.2023.100591
• 发表时间: 2023-08
• 期刊: MOLECULAR & CELLULAR PROTEOMICS
• 影响因子: 7
• 作者: Bowler-Barnett, E. H.;Fan, J.;Luo, J.;Magrane, M.;Martin, M. J.;Orchard, S.
• 通讯作者: Orchard, S.

The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences.

• DOI: 10.1093/nar/gkab1038
• 发表时间: 2022-01-07
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Perez-Riverol Y;Bai J;Bandla C;García-Seisdedos D;Hewapathirana S;Kamatchinathan S;Kundu DJ;Prakash A;Frericks-Zipper A;Eisenacher M;Walzer M;Wang S;Brazma A;Vizcaíno JA
• 通讯作者: Vizcaíno JA

Proteomic repository data submission, dissemination, and reuse: key messages.

• DOI: 10.1080/14789450.2022.2160324
• 发表时间: 2022-07
• 期刊: Expert review of proteomics
• 影响因子: 3.4
• 作者: Perez-Riverol Y

Searching and Navigating UniProt Databases.

搜索和导航 UniProt 数据库。

• DOI: 10.1002/cpz1.700
• 发表时间: 2023
• 期刊: Current protocols
• 作者: Lussi,YvonneC;Magrane,Michele;Martin,MariaJ;Orchard,Sandra;UniProtConsortium
• 通讯作者: UniProtConsortium