Mapping Immune Responses In Acute Infection Across Multiple Pathogens by Proteomics and CITESeq

We used two novel, and previously optimized, analytical approaches, CITE-Seq and Quantitative Phopho-Proteomics, to perform detailed and cohesive characterization of the same paired PBMC and sera samples collected from patients at the acute and convalescent phases of infection with different microbial pathogens. Overall design: Samples were processed in four batches of 20-24 samples, each of which contained sets of all longitudinal samples for a given subject and subjects sampled from each infection cohort to minimize any coinciding batch effects between time points and infection groups. Each batch also contained replicate aliquots of two healthy donor PBMC samples to bridge across batches. Please note that each processed data was generated from a set of three samples (*_A, *_G, and *_H) and is linked to the corresponding [ADT-derived cDNA] sample records.

本研究采用两种已预先优化的新型分析方法——CITE-Seq与定量磷酸化蛋白质组学（Quantitative Phospho-Proteomics）——对不同微生物病原体感染患者在急性期与康复期采集的配对外周血单个核细胞（PBMC, Peripheral Blood Mononuclear Cell）与血清样本开展详细且连贯的表征分析。

整体实验设计：
样本按4批进行处理，每批包含20~24份样本，每批均涵盖单一名受试者的全部纵向样本，以及来自各感染队列的受试者样本，以最大程度减小不同时间点与感染组之间出现的混杂批次效应。
每批同时设置两份健康供者外周血单个核细胞样本的重复分装样本，用于实现不同批次间的衔接。
请注意，每份处理后的数据均由包含*_A、*_G与*_H的三份样本组合生成，并与对应的[抗体寡核苷酸偶联物（ADT）衍生的cDNA]样本记录相关联。