蛋白质组
等压标记
蛋白质组学
质谱法
计算机科学
定量蛋白质组学
无标记量化
串联质量标签
计算生物学
化学
生物
生物信息学
色谱法
生物化学
基因
作者
Tommy K. Cheung,Chien-Yun Lee,Florian Bayer,Atticus McCoy,Bernhard Küster,Christopher M. Rose
出处
期刊:Nature Methods
[Springer Nature]
日期:2020-12-07
卷期号:18 (1): 76-83
被引量:140
标识
DOI:10.1038/s41592-020-01002-5
摘要
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.
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