PDF(Pubmed)
Abstract：
We recently revealed significant variability in protein corona characterization across various proteomics facilities, indicating that data sets are not comparable between independent studies. This heterogeneity mainly arises from differences in sample preparation protocols, mass spectrometry workflows, and raw data processing. To address this issue, we developed standardized protocols and unified sample preparation workflows, distributing uniform protein corona digests to several top-performing proteomics centers from our previous study. We also examined the influence of using similar mass spectrometry instruments on data homogeneity and standardized database search parameters and data processing workflows. Our findings reveal a remarkable stepwise improvement in protein corona data uniformity, increasing overlaps in protein identification from 11% to 40% across facilities using similar instruments and through a uniform database search. We identify the key parameters behind data heterogeneity and provide recommendations for designing experiments. Our findings should significantly advance the robustness of protein corona analysis for diagnostic and therapeutics applications.
摘要：
我们最近揭示了各种蛋白质组学设施中蛋白质电晕表征的显着变异性，这表明独立研究之间的数据集没有可比性。这种异质性主要来自样品制备方案的差异，质谱工作流程，和原始数据处理。为了解决这个问题，我们制定了标准化的协议和统一的样品制备工作流程，从我们之前的研究中，将均匀的蛋白质电晕消化物分配到几个表现最好的蛋白质组学中心。我们还研究了使用类似的质谱仪器对数据均匀性，标准化的数据库搜索参数和数据处理工作流程的影响。我们的发现揭示了蛋白质电晕数据均匀性的显着逐步改善，使用类似的仪器和通过统一的数据库搜索，在不同的设施中，蛋白质鉴定的重叠度从11%增加到40%。我们确定了数据异质性背后的关键参数，并为设计实验提供了建议。我们的发现将显着提高蛋白质电晕分析在诊断和治疗应用中的稳健性。
