Applied Research Lab, Faculty of Natural and Applied Sciences, Trinity Western University Canada, Langley, BC, Canada.
BMC Bioinformatics. 2014 Oct 31;15(1):344. doi: 10.1186/1471-2105-15-344.
A typical affinity purification coupled to mass spectrometry (AP-MS) experiment includes the purification of a target protein (bait) using an antibody and subsequent mass spectrometry analysis of all proteins co-purifying with the bait (aka prey proteins). Like any other systems biology approach, AP-MS experiments generate a lot of data and visualization has been challenging, especially when integrating AP-MS experiments with orthogonal datasets.
We present Circular Interaction Graph for Proteomics (CIG-P), which generates circular diagrams for visually appealing final representation of AP-MS data. Through a Java based GUI, the user inputs experimental and reference data as file in csv format. The resulting circular representation can be manipulated live within the GUI before exporting the diagram as vector graphic in pdf format. The strength of CIG-P is the ability to integrate orthogonal datasets with each other, e.g. affinity purification data of kinase PRPF4B in relation to the functional components of the spliceosome. Further, various AP-MS experiments can be compared to each other.
CIG-P aids to present AP-MS data to a wider audience and we envision that the tool finds other applications too, e.g. kinase - substrate relationships as a function of perturbation. CIG-P is available under: http://sourceforge.net/projects/cig-p/
典型的亲和纯化结合质谱（AP-MS）实验包括使用抗体对靶蛋白（诱饵）进行纯化，以及随后对与诱饵共纯化的所有蛋白质（即猎物蛋白）进行质谱分析。与任何其他系统生物学方法一样，AP-MS 实验会产生大量数据，可视化一直具有挑战性，尤其是在将 AP-MS 实验与正交数据集集成时。
我们提出了用于蛋白质组学的环形交互图（CIG-P），它为 AP-MS 数据的可视化最终表示生成了圆形图。通过基于 Java 的 GUI，用户可以将实验和参考数据作为 csv 格式的文件输入。在将图表以 pdf 格式的矢量图形导出之前，可以在 GUI 中实时操作生成的圆形表示。CIG-P 的优势在于能够将正交数据集相互集成，例如激酶 PRPF4B 的亲和纯化数据与剪接体的功能成分之间的关系。此外，还可以相互比较各种 AP-MS 实验。
CIG-P 有助于将 AP-MS 数据呈现给更广泛的受众，我们设想该工具还会有其他应用，例如激酶-底物关系作为干扰的函数。CIG-P 可在以下网址获得：http://sourceforge.net/projects/cig-p/
