PRIDE and "Database on Demand" as Valuable Tools for Computational Proteomics
PRIDE and "Database on Demand" as Valuable Tools for Computational Proteomics
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DOI：
10.1007/978-1-60761-987-1_6
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发表时间：
2011-01-01
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影响因子：
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通讯作者：
Martens, Lennart
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作者：
Vizcaino, Juan Antonio;Reisinger, Florian;Martens, Lennart
蛋白质组学鉴定数据库（PRIDE, http://www.ebi.ac.uk/pride）为用户提供了探索和比较基于质谱的蛋白质组学实验的能力，这些实验揭示了在广泛的分类组、组织和疾病状态中发现的蛋白质表达的细节。PRIDE实验通常包括蛋白质、多肽和蛋白质修饰的鉴定。此外，许多提交的实验还包括为这些鉴定提供证据的质谱。最后，与其他蛋白质组学知识库相比，PRIDE的最大优势之一是它包含的元数据量，这是将上述数据置于生物学和/或技术背景下的关键点。已经开发了若干信息学工具来支持PRIDE数据库。最近的一个被称为“按需数据库”（DoD），它允许自定义序列数据库的建立，以优化搜索引擎的结果。我们将在本章中描述DoD的用法。此外，为了展示PRIDE作为数据挖掘源的潜力，我们还使用联合BioMart查询探索复杂查询，将PRIDE数据与其他资源（如Ensembl、Reactome或UniProt）集成。
The Proteomics Identifications Database (PRIDE, http://www.ebi.ac.uk/pride) provides users with the ability to explore and compare mass spectrometry-based proteomics experiments that reveal details of the protein expression found in a broad range of taxonomic groups, tissues, and disease states. A PRIDE experiment typically includes identifications of proteins, peptides, and protein modifications. Additionally, many of the submitted experiments also include the mass spectra that provide the evidence for these identifications. Finally, one of the strongest advantages of PRIDE in comparison with other proteomics repositories is the amount of metadata it contains, a key point to put the above-mentioned data in biological and/or technical context. Several informatics tools have been developed in support of the PRIDE database. The most recent one is called "Database on Demand" (DoD), which allows custom sequence databases to be built in order to optimize the results from search engines. We describe the use of DoD in this chapter. Additionally, in order to show the potential of PRIDE as a source for data mining, we also explore complex queries using federated BioMart queries to integrate PRIDE data with other resources, such as Ensembl, Reactome, or UniProt.