Individual Variability of Protein Expression in Human Tissues,Journal of Proteome Research

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Individual Variability of Protein Expression in Human Tissues
Journal of Proteome Research ( IF 3.8 ) Pub Date : 2018-10-18 , DOI: 10.1021/acs.jproteome.8b00580
Irena K. Kushner ₁ , Geremy Clair ₁ , Samuel Owen Purvine ₁ , Joon-Yong Lee ₁ , Joshua N. Adkins ₁ , Samuel H. Payne ₁

Affiliation

Human tissues are known to exhibit interindividual variability, but a deeper understanding of the different factors affecting protein expression is necessary to further apply this knowledge. Our goal was to explore the proteomic variability between individuals as well as between healthy and diseased samples, and to test the efficacy of machine learning classifiers. In order to investigate whether disparate proteomics data sets may be combined, we performed a retrospective analysis of proteomics data from 9 different human tissues. These data sets represent several different sample prep methods, mass spectrometry instruments, and tissue health. Using these data, we examined interindividual and intertissue variability in peptide expression, and analyzed the methods required to build accurate tissue classifiers. We also evaluated the limits of tissue classification by downsampling the peptide data to simulate situations where less data is available, such as clinical biopsies, laser capture microdissection or potentially single-cell proteomics. Our findings reveal the strong potential for utilizing proteomics data to build robust tissue classifiers, which has many prospective clinical applications for evaluating the applicability of model clinical systems.

中文翻译：

人组织中蛋白质表达的个体差异

已知人体组织表现出个体间的变异性，但是需要进一步深入了解影响蛋白质表达的不同因素，以进一步应用这一知识。我们的目标是探索个体之间以及健康和患病样本之间的蛋白质组变异性，并测试机器学习分类器的功效。为了研究是否可以组合不同的蛋白质组学数据集，我们对来自9个不同人体组织的蛋白质组学数据进行了回顾性分析。这些数据集代表几种不同的样品制备方法，质谱仪和组织健康状况。使用这些数据，我们检查了肽表达的个体间和组织间变异性，并分析了建立准确的组织分类器所需的方法。我们还通过对肽数据进行下采样以模拟可用数据较少的情况（例如临床活检，激光捕获显微解剖或可能的单细胞蛋白质组学）来评估组织分类的局限性。我们的发现揭示了利用蛋白质组学数据构建强大的组织分类器的强大潜力，该分类器在评估模型临床系统的适用性方面具有许多前瞻性临床应用。

更新日期：2018-10-19

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