Multicenter Collaborative Study to Optimize Mass Spectrometry Workflows of Clinical Specimens

The foundation for integrating mass spectrometry (MS)-based proteomics into systems medicine is the development of standardized start-to-finish and fit-for-purpose workflows for clinical specimens. An essential step in this pursuit is to highlight the common ground in a diverse landscape of different sample preparation techniques and liquid chromatography–mass spectrometry (LC–MS) setups. With the aim to benchmark and improve the current best practices among the proteomics MS laboratories of the CLINSPECT-M consortium, we performed two consecutive round-robin studies with full freedom to operate in terms of sample preparation and MS measurements. The six study partners were provided with two clinically relevant sample matrices: plasma and cerebrospinal fluid (CSF). In the first round, each laboratory applied their current best practice protocol for the respective matrix. Based on the achieved results and following a transparent exchange of all lab-specific protocols within the consortium, each laboratory could advance their methods before measuring the same samples in the second acquisition round. Both time points are compared with respect to identifications (IDs), data completeness, and precision, as well as reproducibility. As a result, the individual performances of participating study centers were improved in the second measurement, emphasizing the effect and importance of the expert-driven exchange of best practices for direct practical improvements.将基于质谱（mass spectrometry, MS）的蛋白质组学整合入系统医学的基础，在于为临床样本开发标准化的全流程且适配临床需求的工作流程。此进程中的关键一步，是梳理多样化样本制备技术与液相色谱-质谱联用（liquid chromatography–mass spectrometry, LC–MS）平台格局中的共通之处。为在CLINSPECT-M联盟的蛋白质组学质谱实验室中基准测试并优化当前最佳实践，我们开展了两项连续的循环比对研究，允许各实验室在样本制备与质谱检测环节自由采用既定方案。六家参与实验室获得了两种临床相关样本基质：血浆与脑脊液（cerebrospinal fluid, CSF）。首轮实验中，各实验室针对对应样本基质采用其当前的最佳实验流程。基于首轮实验结果，并在联盟内部完成所有实验室专属实验流程的透明共享与交流后，各实验室可优化自身实验方法，随后针对同一批样本开展第二轮检测。我们从蛋白质鉴定数（identification, IDs）、数据完整性、精密度与重现性多个维度对两轮实验结果进行对比分析。结果显示，第二轮检测中各参与实验室的实验表现均有所提升，凸显了专家主导的最佳实践交流对实现直接实用改进的作用与重要价值。