ISPIDER Central: an integrated database web-server for proteomics.
ISPIDER Central: an integrated database web-server for proteomics.
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ISPIDER Central：蛋白质组学集成数据库网络服务器。
DOI：
10.1093/nar/gkn196
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发表时间：
2008
影响因子：
14.9
通讯作者：
Siepen JA
中科院分区：
文献类型：
--
作者：
Siepen JA
尽管蛋白质组学数据量不断增加，但由于格式、采集的数据、蛋白质加入和各个储存库提供的服务存在差异，基础结果的整合仍然存在问题。为了解决这个问题，我们提出了ISPIDER中央蛋白质组数据库搜索（http://www.ispider.manchester.ac.uk/cgi-bin/ProteomicSearch.pl），一个集成服务，提供领先的，成熟的，蛋白质组库，包括PRoteomics IDEntifications数据库（PRIDE），PepSeeker，PeptideAtlas和全球蛋白质组机器的新的搜索功能。它使用户能够搜索存储在不同数据库中的不同群体的蛋白质组学实验中表征的蛋白质和肽，并与专业观众/客户一起查看整理结果。为了克服个别实验室使用的蛋白质加入的巨大变化所带来的限制，欧洲生物信息学研究所的蛋白质标识符交叉引用（PICR）服务被用来解决来自不同序列库的加入。定制的客户端允许用户查看来自多个实验和存储库的不同背景下的肽/蛋白质鉴定，以及与Dasty 2客户端的集成，该客户端支持分布式注释系统服务器提供的任何注释。关于蛋白质命中的进一步信息也可以通过能够将蛋白质作为输入的外部网络服务来添加。这个网络服务器提供了第一个真正集成的访问蛋白质组学知识库，并提供了一个独特的服务，生物学家感兴趣的质谱为基础的蛋白质组学。
Despite the growing volumes of proteomic data, integration of the underlying results remains problematic owing to differences in formats, data captured, protein accessions and services available from the individual repositories. To address this, we present the ISPIDER Central Proteomic Database search ( http://www.ispider.manchester.ac.uk/cgi-bin/ProteomicSearch.pl ), an integration service offering novel search capabilities over leading, mature, proteomic repositories including PRoteomics IDEntifications database (PRIDE), PepSeeker, PeptideAtlas and the Global Proteome Machine. It enables users to search for proteins and peptides that have been characterised in mass spectrometry-based proteomics experiments from different groups, stored in different databases, and view the collated results with specialist viewers/clients. In order to overcome limitations imposed by the great variability in protein accessions used by individual laboratories, the European Bioinformatics Institute's Protein Identifier Cross-Reference (PICR) service is used to resolve accessions from different sequence repositories. Custom-built clients allow users to view peptide/protein identifications in different contexts from multiple experiments and repositories, as well as integration with the Dasty2 client supporting any annotations available from Distributed Annotation System servers. Further information on the protein hits may also be added via external web services able to take a protein as input. This web server offers the first truly integrated access to proteomics repositories and provides a unique service to biologists interested in mass spectrometry-based proteomics.