The regulatory landscape of the yeast phosphoproteome – ultra-deep reference phosphoproteomic DDA data

We systematically exposed the yeast Saccharomyces cerevisiae to a wide array of 101 perturbations and generated a quantitative mass spectrometry-based atlas of early phosphoproteomic responses. Perturbations covered broad classes of environmental, chemical, and drug perturbations and systematically targeted diverse aspects of yeast cell biology. Importantly, most perturbations focused on capturing early signaling responses (5 min treatments). An ultra-deep yeast phosphoproteome was generated from a pooled sample of all 5 min perturbations by multi protease digestion, deep offline fractionations using two different peptide separation methods, and data-dependent acquisition (DDA). This submission includes 120 DDA-MS raw files that were used to generate a deep yeast phosphoproteome.

本研究系统地将酿酒酵母（Saccharomyces cerevisiae）暴露于101种多样化扰动条件下，并基于定量质谱技术构建了早期磷酸化蛋白质组响应图谱。本次实验涉及的扰动类型涵盖环境、化学及药物等多个类别，且系统性地靶向酵母细胞生物学的诸多不同维度。尤为关键的是，绝大多数扰动实验均以捕捉早期信号通路响应为核心目标，处理时长均为5分钟。研究人员通过多蛋白酶酶解、采用两种不同肽段分离方法的深度离线分级分离，结合数据依赖性采集（data-dependent acquisition, DDA）技术，对全部5分钟扰动处理的混合样本进行分析，成功构建了超深度酵母磷酸化蛋白质组。本次提交的数据集包含120个用于构建该深度酵母磷酸化蛋白质组的DDA-MS原始文件。