Department of Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA, USA.
Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.
Nat Methods. 2021 Jan;18(1):76-83. doi: 10.1038/s41592-020-01002-5. Epub 2020 Dec 7.
Single-cell proteomics by mass spectrometry (SCoPE-MS) is a recently introduced method to quantify multiplexed single-cell proteomes. While this technique has generated great excitement, the underlying technologies (isobaric labeling and mass spectrometry (MS)) have technical limitations with the potential to affect data quality and biological interpretation. These limitations are particularly relevant when a carrier proteome, a sample added at 25-500× the amount of a single-cell proteome, is used to enable peptide identifications. Here we perform controlled experiments with increasing carrier proteome amounts and evaluate quantitative accuracy, as it relates to mass analyzer dynamic range, multiplexing level and number of ions sampled. We demonstrate that an increase in carrier proteome level requires a concomitant increase in the number of ions sampled to maintain quantitative accuracy. Lastly, we introduce Single-Cell Proteomics Companion (SCPCompanion), a software tool that enables rapid evaluation of single-cell proteomic data and recommends instrument and data analysis parameters for improved data quality.
基于质谱的单细胞蛋白质组学（SCoPE-MS）是一种最近提出的方法，可定量分析多重单细胞蛋白质组。虽然这项技术引起了极大的兴趣，但潜在的技术（等压标记和质谱（MS））具有潜在影响数据质量和生物学解释的技术限制。当使用载体蛋白质组（一种添加到单细胞蛋白质组的 25-500 倍的样品）来实现肽鉴定时，这些限制尤其重要。在这里，我们进行了增加载体蛋白质组量的对照实验，并评估了定量准确性，因为它与质量分析仪动态范围、多重化水平和采样离子数量有关。我们证明，载体蛋白质组水平的增加需要相应增加采样离子的数量以保持定量准确性。最后，我们引入了单细胞蛋白质组学伴侣（SCPCompanion），这是一种软件工具，可快速评估单细胞蛋白质组学数据，并为提高数据质量推荐仪器和数据分析参数。
