BIOINFORMATICS: INTEGRATION OF PROTEOMICS DATA

这个子项目是利用由NIH/NCRR资助的中心拨款提供的资源的许多研究子项目之一。子项目和调查员(PI)可能从另一个NIH来源获得了主要资金，因此可能会出现在其他CRISE条目中。列出的机构是针对中心的，而不一定是针对调查员的机构。在过去的几年里，蛋白质组学受到了学术界和工业界的广泛关注。该领域发展非常迅速，目前正在经历一个过渡期，需要在技术上实现飞跃，以实现其承诺。为此，许多Labpratpry信息管理系统(LIMS)公司已经投资于非专利系统的开发，并试图让蛋白质组实验室能够使用它们。其他公司已经投资于基因组学/蛋白质组学信息的数据挖掘，以帮助我们进一步了解生物系统的行为。由此产生的软件包在它们所开发的上下文中运行良好。不幸的是，依赖这些包的实验室发现，他们不得不花费大量资金购买许多这样的专门包，然后花费大量努力将它们整合在一起，使其变得有用。对于学术用户来说，目前的成本很高，新的高通量技术的引入可能会受到修改蛋白质组学LIMS所需时间的限制。通常情况下，这些混合系统不容易使用，相当僵硬，而且往往不符合研究人员或分析师的期望。最重要的是，许多可以完成的数据收集和链接自动化以及数据采集后的自动处理没有完成，这主要是因为需要有一系列专业知识来适当地解决这些问题。巨大的开发成本和所需的专业知识范围会产生惯性效应，这些混合系统不能很快适应该领域发生的变化，对研究人员的有用性随着时间的推移而下降。除了这些系统的专有性质之外，我们经常发现软件供应商迅速移交或可能不再支持该软件包。我们在功能注释和开发工具和数据库以实现基因组数据的功能注释方面的工作将受益于整合蛋白质组学中心的提议。我们特别感兴趣的是开发用于存储质谱学数据的数据库，特别是用于存储从质谱学确定的基于MS/MS的序列信息的名为DBMST的数据库，以及名为DBPTM的数据库，用于跟踪从磷蛋白质组分析中识别的翻译后修饰。与您的团队和您的数据合作，使这样的数据库成为可能，这将对我们有极大的帮助。我们还有兴趣将您对BIND格式的研究产生的交互信息存档，并将与您合作将您的软件和数据库链接到BIND。我们还可以通过设置像我们的SeqHound集成数据库系统这样的服务，为您构建LIMS系统的努力提供支持。SeqHound提供在BIND操作中以及在MDS蛋白质组学中使用的支持生物信息学数据库服务。它是在GNU许可下免费提供的，它将允许您在NCBI RefSeq登录号的上下文中跟踪实验样本信息，以及其他几个序列、结构和文献信息的标准数据库。此外，我们正在开发几个新工具，这些工具将允许您将您的研究工作放在我们将收集的全球功能蛋白质组学信息的背景下，并分析您自己的工作，以便您可以发布和交流出现的新发现。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Proteomics in the last few years has received a lot of interest from academia and industry. The field is growing very rapidly and is now going through a transitional period where a leap in technology is needed to allow for the fulfillment of its promise. To this end, many Labpratpry Infrmation Management Systems (LIMS) companies have invested in development of generic systems and are attempting to make them accessible to proteomics laboratories. Other companies have invested in the data mining of genomics/proteomics information to help further our knowledge of how biological systems behave. The resulting software packages are ones that work well within the context they were developed. Unfortunately, laboratories that depend on these packages find that they have to spend a significant amount of their capital in the purchase of many such specialized packages and then a significant effort in integrating them in such a way as to become useful. The ongoing costs are high for academic users and introduction of new high-throughput technologies may be limited by the time required to modify the proteomics LIMS. Very frequently these hybrid systems are not easy to use, are rather inflexible, and often do not meet the expectations of the researchers or analysts. Most importantly, much of the data gathering and linking automation and the post data acquisition automatic processing that could be done is not, mostly because of the range of expertise needed to attack these problems appropriately. The significant development costs and the range of expertise needed gives rise to an inertia effect where these hybrid systems cannot adapt very quickly to changes that occur in this field and the usefulness to the researcher drops over time. In addition to the proprietary nature of these systems, we frequently find that the software vendors turn over rapidly or may no longer support the software package. Our work in functional annotation and development of tools and databases to enable functional annotation of genome data will benefit from the Center for integrative proteomics being proposed. We are specifically interested in developing databases for storing mass spectrometry data, in particular a database called dbMST for storing MS/MS based sequence information determined from mass spectrometry, as well as a database called dbPTM to track post-translational modifications identified from phosphoproteomic analyses. It would be of tremendous help for us to work with your group and your data in making such databases possible. We are also interested in archiving of interaction information generated from your research into BIND format and will work with you to link your software and databases to BIND. We can also provide support to your efforts to build LIMS systems by setting up services like our SeqHound integrated database system. SeqHound provides the supporting bioinformatics database services that are used within the BIND operation, and also at MDS Proteomics. It is freely available under the GNU license, and it will allow you to track experimental sample information in the context of NCBI RefSeq accession numbers as well as several other standard databases of sequence, structure and literature information. In addition, we have several new tools under development that will allow you to put your research efforts into context of the global assembly of functional Proteomics information that we will be collecting, and analyze your own work so that you may publish and communicate novel findings that arise.