Mass Spectrometry Research Center, Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA.
Nat Protoc. 2011 Oct 13;6(11):1695-709. doi: 10.1038/nprot.2011.388.
Archived formalin-fixed paraffin-embedded (FFPE) tissue collections represent a valuable informational resource for proteomic studies. Multiple FFPE core biopsies can be assembled in a single block to form tissue microarrays (TMAs). We describe a protocol for analyzing protein in FFPE-TMAs using matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS). The workflow incorporates an antigen retrieval step following deparaffinization, in situ trypsin digestion, matrix application and then mass spectrometry signal acquisition. The direct analysis of FFPE-TMA tissue using IMS allows direct analysis of multiple tissue samples in a single experiment without extraction and purification of proteins. The advantages of high speed and throughput, easy sample handling and excellent reproducibility make this technology a favorable approach for the proteomic analysis of clinical research cohorts with large sample numbers. For example, TMA analysis of 300 FFPE cores would typically require 6 h of total time through data acquisition, not including data analysis.
存档的福尔马林固定石蜡包埋（FFPE）组织收集物代表了蛋白质组学研究的有价值的信息资源。多个 FFPE 核心活检可以组装在一个单独的块中形成组织微阵列（TMA）。我们描述了一种使用基质辅助激光解吸/电离（MALDI）成像质谱（IMS）分析 FFPE-TMA 中蛋白质的方案。该工作流程包括脱蜡后进行抗原修复、原位胰蛋白酶消化、基质应用，然后进行质谱信号采集。使用 IMS 直接分析 FFPE-TMA 组织可以在单个实验中直接分析多个组织样本，而无需提取和纯化蛋白质。该技术具有速度快、通量高、易于处理样本和重现性好等优点，是对具有大量样本的临床研究队列进行蛋白质组分析的理想方法。例如，TMA 分析 300 个 FFPE 核心通常需要 6 小时的总时间进行数据采集，不包括数据分析。
