Department of Chemistry, Brown University, Providence, RI 02903, USA.
Proteomics. 2009 Dec;9(23):5350-8. doi: 10.1002/pmic.200900119.
Recently, dramatic progress has been achieved in expanding the sensitivity, resolution, mass accuracy, and scan rate of mass spectrometers able to fragment and identify peptides through MS/MS. Unfortunately, this enhanced ability to acquire proteomic data has not been accompanied by a concomitant increase in the availability of flexible tools allowing users to rapidly assimilate, explore, and analyze this data and adapt to various experimental workflows with minimal user intervention. Here we fill this critical gap by providing a flexible relational database called PeptideDepot for organization of expansive proteomic data sets, collation of proteomic data with available protein information resources, and visual comparison of multiple quantitative proteomic experiments. Our software design, built upon the synergistic combination of a MySQL database for safe warehousing of proteomic data with a FileMaker-driven graphical user interface for flexible adaptation to diverse workflows, enables proteomic end-users to directly tailor the presentation of proteomic data to the unique analysis requirements of the individual proteomics lab. PeptideDepot may be deployed as an independent software tool or integrated directly with our high throughput autonomous proteomic pipeline used in the automated acquisition and post-acquisition analysis of proteomic data.
最近，在提高能够通过 MS/MS 对肽进行片段化和鉴定的质谱仪的灵敏度、分辨率、质量精度和扫描速度方面取得了巨大进展。不幸的是，这种增强的获取蛋白质组学数据的能力并没有伴随着灵活工具的可用性的相应增加，这些工具允许用户快速吸收、探索和分析这些数据，并在最小的用户干预下适应各种实验工作流程。在这里，我们通过提供一个名为 PeptideDepot 的灵活关系数据库来填补这一关键空白，用于组织扩展的蛋白质组数据集，将蛋白质组数据与可用的蛋白质信息资源进行整理，并对多个定量蛋白质组学实验进行可视化比较。我们的软件设计基于 MySQL 数据库的协同组合，用于安全地存储蛋白质组数据，以及 FileMaker 驱动的图形用户界面，用于灵活适应各种工作流程，使蛋白质组学终端用户能够直接根据个人蛋白质组学实验室的独特分析要求来定制蛋白质组数据的呈现方式。PeptideDepot 可以作为一个独立的软件工具部署，也可以直接与我们的高通量自主蛋白质组学管道集成，用于蛋白质组学数据的自动采集和采集后分析。
