BIOINFORMATICS: INTEGRATION OF PROTEOMICS DATA

本子项目是利用由NIH/NCRR资助的中心赠款提供的资源的众多研究子项目之一。子项目和研究者（PI）可能已经从另一个NIH来源获得了主要资金，因此可以在其他CRISP条目中表示。列出的机构是中心的，不一定是研究者的机构。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，现在正在经历一个过渡时期，需要技术上的飞跃才能实现其承诺。为此，许多labprpry信息管理系统（LIMS）公司已经投资于通用系统的开发，并试图使它们能够被蛋白质组学实验室使用。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方式。最终的软件包是在它们被开发的环境中工作良好的软件包。不幸的是，依赖这些包的实验室发现，他们不得不花费大量的资金来购买许多这样的专门包，然后花费大量的精力将它们以这样一种方式整合起来，使其变得有用。对于学术用户来说，持续的成本很高，并且引入新的高通量技术可能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，相当不灵活，而且往往不能满足研究人员或分析人员的期望。最重要的是，许多数据收集和链接自动化以及数据采集后的自动处理都无法完成，这主要是因为适当地解决这些问题所需的专业知识范围太广。巨大的开发成本和所需专业知识的范围产生了惯性效应，这些混合系统不能很快适应该领域发生的变化，并且随着时间的推移，对研究人员的有用性也会下降。除了这些系统的专有性质之外，我们经常发现软件供应商很快就会更换，或者可能不再支持软件包。我们在功能注释和开发工具和数据库方面的工作，以实现基因组数据的功能注释，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存储质谱数据的数据库，特别是一个名为dbMST的数据库，用于存储从质谱测定的基于MS/MS的序列信息，以及一个名为dbPTM的数据库，用于跟踪从磷蛋白质组学分析中确定的翻译后修饰。与你们的团队和你们的数据合作，使这样的数据库成为可能，对我们将有巨大的帮助。我们也有兴趣将您的研究产生的交互信息存档为BIND格式，并将与您合作将您的软件和数据库连接到BIND。我们也可以通过建立我们的SeqHound集成数据库系统等服务，为您建立LIMS系统提供支持。SeqHound提供支持生物信息学数据库服务，用于BIND操作，也用于MDS蛋白质组学。它是在GNU许可下免费提供的，它将允许您在NCBI RefSeq登录号以及其他几个序列、结构和文献信息的标准数据库的背景下跟踪实验样本信息。此外，我们有几个正在开发的新工具，将允许您将您的研究工作纳入我们将收集的功能蛋白质组学信息的全球集合的背景下，并分析您自己的工作，以便您可以发表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.