In-Depth Proteomics of Ovarian Cancer Ascites: Combining Shotgun Proteomics and Selected Reaction Monitoring Mass Spectrometry
In-Depth Proteomics of Ovarian Cancer Ascites: Combining Shotgun Proteomics and Selected Reaction Monitoring Mass Spectrometry
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DOI：
10.1021/pr1011087
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发表时间：
2011-05-01
影响因子：
4.4
通讯作者：
Kislinger, Thomas
中科院分区：
文献类型：
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作者：
Elschenbroich, Sarah;Ignatchenko, Vladimir;Kislinger, Thomas
上皮性卵巢癌（EOC）是最常见的妇科癌症，也是第九常见的癌症。与EOC相关的主要问题包括疾病进展特征不佳、疾病异质性、缺乏早期检测标记物和耐药性的发展。EOC的早期发现和治疗将大大受益于对现有生物液体的常规筛查试验。我们在分析卵巢癌腹水的经验的基础上，提出了一个分析管道，该管道结合了基于发现的蛋白质组学，生物信息学优先级和使用选择反应监测质谱（SRM-MS）的靶向蛋白质组学定量。采用全面的鸟枪蛋白质组学分析浆液性上皮性卵巢癌患者的腹水，并与良性卵巢肿瘤患者的非癌性腹水进行比较。我们的数据与已发表的mRNA转录组学和蛋白质组学数据集的整合导致了一组51个候选蛋白质。使用合成肽（13种蛋白质）和稳定同位素标记的标准品（4种蛋白质）对这些蛋白质的子集进行系统性SRM-MS测定开发。随后，通过稳定同位素稀释-SRM（SID-SRM）在独立腹水和血清样本中进行精确相对定量，作为概念验证。本文概述的分析策略为未来使用大量患者样本和其他候选蛋白质的实验奠定了基础，并为基于蛋白质组学的癌症生物标志物发现提供了模板。
Epithelial ovarian cancer (EOC) is the most common gynecological cancer and the ninth most common cancer overall. Major problems associated with EOC include poorly characterized disease progression, disease heterogeneity, lack of early detection markers and the development of chemoresistance. Early detection and treatment of EOC would significantly benefit from routine screening tests on available biofluids. We built on our experience in analyzing ovarian cancer ascites and present an analysis pipeline that combines discovery-based proteomics, bioinformatics prioritization and targeted proteornics quantification using Selected Reaction Monitoring Mass Spectrometry (SRM-MS). Ascitic fluids from patients with serous-type epithelial ovarian cancer were analyzed using comprehensive shotgun proteomics and compared to noncancerous ascitic fluids from patients with benign ovarian tumors. Integration of our data with published mRNA transcriptomic and proteomic data sets led to a panel of 51 candidate proteins. Systematic SRM-MS assay development was performed for a subset of these proteins using both synthetic peptides (13 proteins) and stable isotope labeled standards (4 proteins). Subsequently, precise relative quantification by stable isotope dilution-SRM (SID-SRM) in independent ascites and serum samples was performed as a proof-of-concept validation. The analysis strategy outlined here lays the foundation for future experiments using both larger numbers of patient samples and additional candidate proteins, and provides a template for the proteomics-based discovery of cancer biomarkers.