Translational Medicine, Oncology R&D, AstraZeneca, One MedImmune Way, Gaithersburg, MD, 20878, USA.
Data Science & AI, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA.
Sci Rep. 2022 Aug 16;12(1):13876. doi: 10.1038/s41598-022-16358-1.
Mass spectrometry-based targeted proteomics allows objective protein quantitation of clinical biomarkers from a single section of formalin-fixed, paraffin-embedded (FFPE) tumor tissue biopsies. We combined high-field asymmetric waveform ion mobility spectrometry (FAIMS) and parallel reaction monitoring (PRM) to increase assay sensitivity. The modular nature of the FAIMS source allowed direct comparison of the performance of FAIMS-PRM to PRM. Limits of quantitation were determined by spiking synthetic peptides into a human spleen matrix. In addition, 20 clinical samples were analyzed using FAIMS-PRM and the quantitation of HER2 was compared with that obtained with the Ventana immunohistochemistry assay. FAIMS-PRM improved the overall signal-to-noise ratio over that from PRM and increased assay sensitivity in FFPE tissue analysis for four (HER2, EGFR, cMET, and KRAS) of five proteins of clinical interest. FAIMS-PRM enabled sensitive quantitation of basal HER2 expression in breast cancer samples classified as HER2 negative by immunohistochemistry. Furthermore, we determined the degree of FAIMS-dependent background reduction and showed that this correlated with an improved lower limit of quantitation with FAIMS. FAIMS-PRM is anticipated to benefit clinical trials in which multiple biomarker questions must be addressed and the availability of tumor biopsy samples is limited.
基于质谱的靶向蛋白质组学可以从福尔马林固定、石蜡包埋（FFPE）的肿瘤组织活检的单个切片中客观地定量分析临床生物标志物。我们结合了高场非对称波形离子淌度谱（FAIMS）和并行反应监测（PRM）来提高检测灵敏度。FAIMS 源的模块化特性允许直接比较 FAIMS-PRM 和 PRM 的性能。通过向人类脾脏基质中添加合成肽来确定定量下限。此外，使用 FAIMS-PRM 分析了 20 个临床样本，并将 HER2 的定量与 Ventana 免疫组织化学测定进行了比较。FAIMS-PRM 提高了整体信噪比，并提高了 5 种临床相关蛋白中 4 种（HER2、EGFR、cMET 和 KRAS）在 FFPE 组织分析中的检测灵敏度。FAIMS-PRM 能够灵敏地定量免疫组织化学检测为 HER2 阴性的乳腺癌样本中的基础 HER2 表达。此外，我们确定了 FAIMS 依赖性背景减少的程度，并表明这与 FAIMS 具有更好的定量下限有关。FAIMS-PRM 有望受益于需要解决多个生物标志物问题且肿瘤活检样本有限的临床试验。
