Cancer Proteomics Mass Spectrometry, Scilifelab, Department of Oncology and Pathology, Karolinska Institutet, SE-141 86 Stockholm, Sweden.
Research and Development, ITB-Med AB, SE-113 66 Stockholm, Sweden.
J Proteome Res. 2021 Sep 3;20(9):4610-4620. doi: 10.1021/acs.jproteome.1c00378. Epub 2021 Jul 28.
High abundant protein depletion is a common strategy applied to increase analytical depth in global plasma proteomics experiment setups. The standard strategies for depletion of the highest abundant proteins currently rely on multiple-use HPLC columns or multiple-use spin columns. Here we evaluate the performance of spin columns for plasma depletion and show that the single-use spin reduces handling time by allowing parallelization and is easily adapted to a nonspecialized lab environment without reducing the high plasma proteome coverage and reproducibility. In addition, we evaluate the effect of viral heat inactivation on the plasma proteome, an additional step in the plasma preparation workflow that allows the sample preparation of SARS-Cov2-infected samples to be performed in a BSL3 laboratory, and report the advantage of performing the heat inactivation postdepletion. We further show the possibility of expanding the use of the depletion column cross-species to macaque plasma samples. In conclusion, we report that single-use spin columns for high abundant protein depletion meet the requirements for reproducibly in in-depth plasma proteomics and can be applied on a common animal model while also reducing the sample handling time.
高丰度蛋白质去除是一种常用于增加全局血浆蛋白质组学实验方案分析深度的常用策略。目前，高丰度蛋白质去除的标准策略依赖于多用途 HPLC 柱或多用途离心柱。在这里，我们评估了离心柱用于血浆去除的性能，并表明单用途离心柱通过允许并行处理而大大减少了处理时间，并且易于适应非专业实验室环境，而不会降低高血浆蛋白质组覆盖率和重现性。此外，我们评估了病毒热失活对血浆蛋白质组的影响，这是血浆制备工作流程中的一个额外步骤，允许在 BSL3 实验室中对 SARS-CoV2 感染样本进行样品制备，并报告在去除后进行热失活的优势。我们进一步展示了将消耗柱交叉物种扩展到猕猴血浆样本的可能性。总之，我们报告说，用于高丰度蛋白质去除的一次性离心柱满足可重复性的深入血浆蛋白质组学要求，可应用于常见的动物模型，同时还减少了样品处理时间。
