German Cancer Research Center (DKFZ), Heidelberg, Germany.
Heidelberg University, Medical Faculty, Heidelberg, Germany.
Methods Mol Biol. 2023;2718:181-211. doi: 10.1007/978-1-0716-3457-8_11.
Mass spectrometry (MS)-based proteomics is a rapidly maturing discipline, thus gaining momentum for routine molecular profiling of clinical specimens to improve disease classification, diagnostics, and therapy development. Yet, hurdles need to be overcome to enhance reproducibility in preanalytical sample processing, especially in large, quantity-limited sample cohorts. Therefore, automated sonication and single-pot solid-phase-enhanced sample preparation (autoSP3) was developed as a streamlined workflow that integrates all tasks from tissue lysis and protein extraction, protein cleanup, and proteolysis. It enables the concurrent processing of 96 clinical samples of any type (fresh-frozen or FFPE tissue, liquid biopsies, or cells) on an automated liquid handling platform, which can be directly interfaced to LC-MS for proteome analysis of clinical specimens with high sensitivity, high reproducibility, and short turn-around times.
基于质谱（MS）的蛋白质组学是一个快速发展的学科，因此正在为常规分析临床标本的分子特征以改善疾病分类、诊断和治疗开发而努力。然而，在分析前的样品处理中，仍需要克服许多障碍以提高重现性，特别是在大型、样本数量有限的样本队列中。因此，自动化超声处理和单管固相增强样品制备（autoSP3）作为一种简化的工作流程被开发出来，该流程集成了从组织裂解和蛋白质提取、蛋白质纯化和蛋白水解的所有任务。它可以在自动化液体处理平台上同时处理 96 个临床样本（新鲜冷冻或 FFPE 组织、液体活检或细胞），并可直接与 LC-MS 接口，以实现高灵敏度、高重现性和短周转时间的临床标本的蛋白质组分析。
