基于微流控纳升液滴样品制备和超灵敏纳升液相色谱-质谱联用的单细胞蛋白质组学分析。
Proteomic Analysis of Single Mammalian Cells Enabled by Microfluidic Nanodroplet Sample Preparation and Ultrasensitive NanoLC-MS.
机构信息
Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA.
Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA.
出版信息
Angew Chem Int Ed Engl. 2018 Sep 17;57(38):12370-12374. doi: 10.1002/anie.201802843. Epub 2018 Jun 14.
Abstract
We report on the quantitative proteomic analysis of single mammalian cells. Fluorescence-activated cell sorting was employed to deposit cells into a newly developed nanodroplet sample processing chip, after which samples were analyzed by ultrasensitive nanoLC-MS. An average of circa 670 protein groups were confidently identified from single HeLa cells, which is a far greater level of proteome coverage for single cells than has been previously reported. We demonstrate that the single-cell proteomics platform can be used to differentiate cell types from enzyme-dissociated human lung primary cells and identify specific protein markers for epithelial and mesenchymal cells.
摘要
我们报告了对单个哺乳动物细胞的定量蛋白质组学分析。通过荧光激活细胞分选将细胞沉积到新开发的纳升液滴样品处理芯片中，然后通过超灵敏纳升 LC-MS 对样品进行分析。从单个 HeLa 细胞中可鉴定出平均约 670 个蛋白质组，这比以前报道的单细胞蛋白质组覆盖率高得多。我们证明，单细胞蛋白质组学平台可用于区分酶解的人肺原代细胞的细胞类型，并鉴定上皮细胞和间充质细胞的特定蛋白质标志物。
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Int J Mass Spectrom. 2018 Apr;427:4-10. doi: 10.1016/j.ijms.2017.08.016. Epub 2017 Sep 1.
2
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Nat Commun. 2018 Feb 28;9(1):882. doi: 10.1038/s41467-018-03367-w.
3
The promise of spatial transcriptomics for neuroscience in the era of molecular cell typing.空间转录组学在分子细胞分型时代对神经科学的承诺。
Science. 2017 Oct 6;358(6359):64-69. doi: 10.1126/science.aan6827.
4
Evaluation of FASP, SP3, and iST Protocols for Proteomic Sample Preparation in the Low Microgram Range.评价 FASP、SP3 和 iST 三种方法在低微克范围内进行蛋白质组学样品制备的效果。
J Proteome Res. 2017 Nov 3;16(11):4060-4072. doi: 10.1021/acs.jproteome.7b00433. Epub 2017 Oct 11.
5
Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single-cell resolution using RNA sequencing.利用RNA测序以单细胞分辨率剖析成年斑马鱼的造血细胞和肾细胞异质性。
J Exp Med. 2017 Oct 2;214(10):2875-2887. doi: 10.1084/jem.20170976. Epub 2017 Sep 6.
6
Single-cell spatial reconstruction reveals global division of labour in the mammalian liver.单细胞空间重建揭示了哺乳动物肝脏中的全局分工。
Nature. 2017 Feb 16;542(7641):352-356. doi: 10.1038/nature21065. Epub 2017 Feb 6.
7
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8
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Anal Chem. 2016 Sep 20;88(18):8957-64. doi: 10.1021/acs.analchem.6b01915. Epub 2016 Aug 26.
10
Visualization and analysis of gene expression in tissue sections by spatial transcriptomics.空间转录组学在组织切片中基因表达的可视化和分析。
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