Genome annotation improvements from cross-phyla proteogenomics and time-of-day differences in malaria mosquito proteins using untargeted quantitative proteomics

The malaria mosquito, Anopheles stephensi, and other mosquitoes modulate their biology to match the time-of-day. In the present work, we used a non-hypothesis driven approach (untargeted proteomics) to identify proteins in mosquito tissue, and then quantified the relative abundance of the identified proteins from An. stephensi bodies. Using these quantified protein levels, we then analyzed the data for proteins that were only detectable at certain times-of-the day, highlighting the need to consider time-of-day in experimental design. Further, we extended our time-of-day analysis to look for proteins which cycle in a rhythmic 24-hour (“circadian”) manner, identifying 31 rhythmic proteins. Finally, to maximize the utility of our data, we performed a proteogenomic analysis to improve the genome annotation of An. stephensi. We compare peptides that were detected using mass spectrometry but are ‘missing’ from the An. stephensi predicted proteome, to reference proteomes from 38 other primaril...

疟疾蚊子——斯氏按蚊（Anopheles stephensi）及其他蚊子会调节自身生物学特性以适应昼夜节律。本研究采用非假设驱动的方法（非靶向蛋白质组学，untargeted proteomics）对蚊子组织中的蛋白质进行鉴定，随后对斯氏按蚊（An. stephensi）虫体中已鉴定蛋白质的相对丰度进行了定量分析。基于这些定量的蛋白质水平数据，我们进一步分析了仅在一天中特定时段可检测到的蛋白质，这凸显了在实验设计中考虑昼夜时间因素的必要性。此外，我们扩展了昼夜时间分析范围，以寻找呈24小时节律性（即“昼夜节律性”，circadian）循环的蛋白质，共鉴定出31种节律性蛋白质。最后，为最大化数据的利用价值，我们开展了蛋白质基因组学（proteogenomic）分析，以完善斯氏按蚊（An. stephensi）的基因组注释。我们将通过质谱检测到但未出现在斯氏按蚊（An. stephensi）预测蛋白质组中的肽段，与来自其他38种主要……的参考蛋白质组进行了比较。