Over the last two decades, EDTA-plasma has been used as the preferred sample matrix for human blood proteomic profiling. Serum has also been employed widely. Only a few studies have assessed the difference and relevance of the proteome profiles obtained from plasma samples, such as EDTA-plasma or lithium-heparin-plasma, and serum. A more complete evaluation of the use of EDTA-plasma, heparin-plasma, and serum would greatly expand the comprehensiveness of shotgun proteomics of blood samples. In this study, we evaluated the use of heparin-plasma with respect to EDTA-plasma and serum to profile blood proteomes using a scalable automated proteomic pipeline (ASAP²). The use of plasma and serum for mass-spectrometry-based shotgun proteomics was first tested with commercial pooled samples. The proteome coverage consistency and the quantitative performance were compared. Furthermore, protein measurements in EDTA-plasma and heparin-plasma samples were comparatively studied using matched sample pairs from 20 individuals from the Australian Imaging, Biomarkers and Lifestyle (AIBL) Study. We identified 442 proteins in common between EDTA-plasma and heparin-plasma samples. Overall agreement of the relative protein quantification between the sample pairs demonstrated that shotgun proteomics using workflows such as the ASAP² is suitable in analyzing heparin-plasma and that such sample type may be considered in large-scale clinical research studies. Moreover, the partial proteome coverage overlaps (e.g., ∼70%) showed that measures from heparin-plasma could be complementary to those obtained from EDTA-plasma.

中文翻译：

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对基于血浆的Shot弹枪蛋白质组学中人类血浆和血清使用情况的系统评价

在过去的二十年中，EDTA血浆已被用作人类血液蛋白质组分析的首选样品基质。血清也被广泛使用。只有少数研究评估了从血浆样品（如EDTA-血浆或锂-肝素-血浆）和血清中获得的蛋白质组图谱的差异和相关性。对EDTA-血浆，肝素-血浆和血清的使用进行更完整的评估将大大扩展血液样本的gun弹枪蛋白质组学的全面性。在这项研究中，我们评估了肝素血浆相对于EDTA血浆和血清的使用，并使用可扩展的自动化蛋白质组学方法来分析血液蛋白质组（ASAP ²）。血浆和血清在基于质谱的shot弹枪蛋白质组学中的使用首先与商业化的混合样品进行了测试。比较了蛋白质组覆盖率一致性和定量性能。此外，使用来自澳大利亚影像，生物标记和生活方式研究（AIBL）的20个人的匹配样本对，对EDTA-血浆和肝素-血浆样品中的蛋白质测量值进行了比较研究。我们确定了EDTA-血浆和肝素-血浆样品之间共有442种蛋白质。样品对之间相对蛋白质定量的总体一致性表明，使用ASAP ²等工作流程的shot弹枪蛋白质组学适用于分析肝素血浆，此类样品类型可在大规模临床研究中考虑。此外，部分蛋白质组覆盖重叠（例如，约70％）表明，肝素血浆检测结果可与EDTA血浆检测结果互补。