ProCan, Faculty of Medicine and Health, The University of Sydney, Children's Medical Research Institute, Westmead, NSW 2145, Australia.
Anal Chem. 2024 Mar 12;96(10):4093-4102. doi: 10.1021/acs.analchem.3c04708. Epub 2024 Mar 1.
Proteomic analysis by mass spectrometry of small (≤2 mg) solid tissue samples from diverse formats requires high throughput and comprehensive proteome coverage. We developed a nearly universal, rapid, and robust protocol for sample preparation, suitable for high-throughput projects that encompass most cell or tissue types. This end-to-end workflow extends from original sample to loading the mass spectrometer and is centered on a one-tube homogenization and digestion method called Heat 'n Beat (HnB). It is applicable to most tissues, regardless of how they were fixed or embedded. Sample preparation was divided into separate challenges. The initial sample washing and final peptide cleanup steps were adapted to three tissue sources: fresh frozen (FF), optimal cutting temperature (OCT) compound embedded (FF-OCT), and formalin-fixed paraffin embedded (FFPE). Third, for core processing, tissue disruption and lysis were decreased to a 7 min heat and homogenization treatment, and reduction, alkylation, and proteolysis were optimized into a single step. The refinements produced near doubled peptide yield when compared to our earlier method ABLE delivered a consistently high digestion efficiency of 85-90%, reported by ProteinPilot, and required only 38 min for core processing in a single tube, with the total processing time being 53-63 min. The robustness of HnB was demonstrated on six organ types, a cell line, and a cancer biopsy. Its suitability for high-throughput applications was demonstrated on a set of 1171 FF-OCT human cancer biopsies, which were processed for end-to-end completion in 92 h, producing highly consistent peptide yield and quality for over 3513 MS runs.
采用质谱技术对来自不同形式的小(≤2 毫克)固体组织样本进行蛋白质组学分析需要高通量和全面的蛋白质组覆盖。我们开发了一种几乎通用、快速且稳健的样品制备方案,适用于涵盖大多数细胞或组织类型的高通量项目。这个端到端的工作流程从原始样品延伸到质谱仪的加载,其核心是一种称为 Heat 'n Beat(HnB)的单管匀浆和消化方法。它适用于大多数组织,无论其固定或包埋方式如何。样品制备分为单独的挑战。最初的样品清洗和最终的肽净化步骤适用于三种组织来源:新鲜冷冻(FF)、最佳切割温度(OCT)化合物包埋(FF-OCT)和福尔马林固定石蜡包埋(FFPE)。第三,对于核心处理,将组织破坏和裂解减少到 7 分钟的热匀化处理,并且将还原、烷基化和蛋白水解优化为一个步骤。与我们早期的 ABLE 方法相比,这些改进使肽产量几乎增加了一倍,ProteinPilot 报告的消化效率始终保持在 85-90%,并且在单个管中仅需 38 分钟进行核心处理,总处理时间为 53-63 分钟。HnB 的稳健性在六种器官类型、一种细胞系和一个癌症活检中得到了证明。在一组 1171 个 FF-OCT 人类癌症活检上的高通量应用适用性证明,这些活检的处理时间为 92 小时,完成了端到端的处理,在超过 3513 次 MS 运行中产生了高度一致的肽产量和质量。