PeptideDepot: flexible relational database for visual analysis of quantitative proteomic data and integration of existing protein information.
PeptideDepot: flexible relational database for visual analysis of quantitative proteomic data and integration of existing protein information.
复制标题
PeptideDepot：灵活的关系数据库，用于定量蛋白质组数据的可视化分析和现有蛋白质信息的整合。
DOI：
10.1002/pmic.200900119
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发表时间：
2009
期刊：
影响因子：
3.4
通讯作者：
Salomon,ArthurR
中科院分区：
文献类型：
--
作者：
Yu,Kebing;Salomon,ArthurR
最近，在扩大能够通过MS/MS片段化和识别肽的质谱仪的灵敏度、分辨率、质量准确度和扫描速率方面已经取得了巨大的进展。不幸的是，这种增强的获取蛋白质组数据的能力并没有伴随着灵活工具的可用性的伴随增加，从而允许用户快速吸收、探索、分析和鉴定肽。并分析这些数据，以最小的用户干预适应各种实验工作流程。在这里，我们填补了这一关键的差距，提供了一个灵活的关系数据库，称为PeptideDepot的组织广泛的蛋白质组数据集，整理蛋白质组数据与可用的蛋白质信息资源，和多个定量蛋白质组学实验的视觉比较。我们的软件设计建立在MySQL数据库（用于蛋白质组数据的安全仓储）与FileMaker驱动的图形用户界面（用于灵活适应不同的工作流程）的协同组合之上，使蛋白质组学最终用户能够直接定制蛋白质组学数据的呈现，以满足各个蛋白质组学实验室的独特分析要求。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。
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.