Laboratory for Proteomics and Protein Engineering, Carlos Chagas Institute, Fiocruz, Paraná, Brazil.
J Proteomics. 2013 Aug 26;89:179-82. doi: 10.1016/j.jprot.2013.06.013. Epub 2013 Jun 21.
Mass-spectrometry-based shotgun proteomics has become a widespread technology for analyzing complex protein mixtures. Here we describe a new module integrated into PatternLab for Proteomics that allows the pinpointing of differentially expressed domains. This is accomplished by inferring functional domains through our cloud service, using HMMER3 and Pfam remotely, and then mapping the quantitation values into domains for downstream analysis. In all, spotting which functional domains are changing when comparing biological states serves as a complementary approach to facilitate the understanding of a system's biology. We exemplify the new module's use by reanalyzing a previously published MudPIT dataset of Cryptococcus gattii cultivated under iron-depleted and replete conditions. We show how the differential analysis of functional domains can facilitate the interpretation of proteomic data by providing further valuable insight.
基于质谱的鸟枪法蛋白质组学已成为分析复杂蛋白质混合物的广泛应用技术。在这里，我们描述了 PatternLab for Proteomics 中集成的一个新模块，该模块允许精确定位差异表达的结构域。这是通过使用 HMMER3 和 Pfam 在远程的云服务中推断功能结构域来实现的，然后将定量值映射到结构域中进行下游分析。总的来说，在比较生物状态时，确定哪些功能结构域发生了变化，这是一种辅助理解系统生物学的补充方法。我们通过重新分析以前发表的在缺铁和富铁条件下培养的隐球菌的 MudPIT 数据集来举例说明新模块的用途。我们展示了如何通过提供更有价值的见解，通过对功能结构域的差异分析来促进对蛋白质组学数据的解释。
