International Centre for Cancer Vaccine Science, University of Gdańsk, Gdańsk, Poland.
International Centre for Cancer Vaccine Science, University of Gdańsk, Gdańsk, Poland.
Anal Chim Acta. 2022 Apr 29;1204:339695. doi: 10.1016/j.aca.2022.339695. Epub 2022 Mar 12.
Developments in quantitative proteomics and data-independent acquisition (DIA) methodology is enabling quantification of proteins in biological samples. Currently, there are a few reports on DIA mass spectrometry (MS) approaches for proteome analysis of formalin-fixed paraffin-embedded (FFPE) tissues. Therefore, to facilitate detection and quantification of immune- and glioblastoma (GBM)-relevant proteins from FFPE patient materials, we established a simple and precise DIA-MS workflow. We first evaluated different lysis buffers for their efficiency in protein extractions from FFPE GBM tissues. Our results showed that more than 1700 proteins were detected and over 1400 proteins were quantified from GBM FFPE tissue microdissections. GBM-relevant proteins (e.g., GFAP, FN1, VIM, and MBP) were quantified with high precision (median coefficient of variation <12%). In addition, immune-related proteins (e.g., ILF2, MIF, and CD38) were consistently detected and quantified. The strategy holds great potential for routinizing protein quantification in FFPE tissue samples.
定量蛋白质组学和数据非依赖性采集 (DIA) 方法的发展使得在生物样本中定量蛋白质成为可能。目前，已有一些关于 DIA 质谱 (MS) 方法在福尔马林固定石蜡包埋 (FFPE) 组织中的蛋白质组分析的报道。因此，为了促进从 FFPE 患者材料中检测和定量免疫和神经胶质瘤 (GBM) 相关蛋白，我们建立了一种简单而精确的 DIA-MS 工作流程。我们首先评估了不同的裂解缓冲液在从 FFPE GBM 组织中提取蛋白质方面的效率。结果表明，从 GBM FFPE 组织微切割中检测到了超过 1700 种蛋白质，并且定量了超过 1400 种蛋白质。GBM 相关蛋白（例如 GFAP、FN1、VIM 和 MBP）的定量具有很高的精度（中位数变异系数 <12%）。此外，还一致检测和定量了免疫相关蛋白（例如 ILF2、MIF 和 CD38）。该策略在 FFPE 组织样本中的蛋白质定量方面具有很大的潜力。
