Single Amino Acid Variant Discovery in Small Numbers of Cells
文献类型：期刊论文
| 作者 | Tan, Zhijing1; Yi, Xinpei2,3; Carruthers, Nicholas J.4; Stemmer, Paul M.4; Lubman, David M.1 |
| 刊名 | JOURNAL OF PROTEOME RESEARCH
 |
| 出版日期 | 2019 |
| 卷号 | 18期号:1页码:417-425 |
| 关键词 | small number of cells sample fractionation LC-MS/MS single amino acid variants (SAAVs) cancer related SAAVs |
| ISSN号 | 1535-3893 |
| DOI | 10.1021/acs.jproteome.8b00694 |
| 英文摘要 | We have performed deep proteomic profiling down to as few as 9 Panc-1 cells using sample fractionation, TMT multiplexing, and a carrier/reference strategy. Off line fractionation of the TMT-labeled sample pooled with TMT-labeled carrier Panc-1 whole cell proteome was achieved using alkaline reversed phase spin columns. The fractionation in conjunction with the carrier/reference (C/R) proteome allowed us to detect 47414 unique peptides derived from 6261 proteins, which provided a sufficient coverage to search for single amino acid variants (SAAVs) related to cancer. This high sample coverage is essential in order to detect a significant number of SAAVs. In order to verify genuine SAAVs versus false SAAVs, we used the SAVControl pipeline and found a total of 79 SAAVs from the 9 -cell Panc-1 sample and 174 SAAVs from the 5000-cell Panc-1 C/R proteome. The SAAVs as sorted into high confidence and low confidence SAAVs were checked manually. All the high confidence SAAVs were found to be genuine SAAVs, while half of the low confidence SAAVs were found to be false SAAVs mainly related to PTMs. We identified several cancer-related SAAVs including KRAS, which is an important oncoprotein in pancreatic cancer. In addition, we were able to detect sites involved in loss or gain of glycosylation due to the enhanced coverage available in these experiments where we can detect both sites of loss and gain of glycosylation. |
| 资助项目 | NIH[R01GM49500] ; NIH[P30 ES020957] ; NIH[P30 CA 022453] ; NIH[S10 OD010700] |
| WOS研究方向 | Biochemistry & Molecular Biology |
| 语种 | 英语 |
| WOS记录号 | WOS:000455285900038 |
| 出版者 | AMER CHEMICAL SOC |
| 源URL | [http://ir.amss.ac.cn/handle/2S8OKBNM/32160]  |
| 专题 | 中国科学院数学与系统科学研究院 |
| 通讯作者 | Stemmer, Paul M.; Lubman, David M. |
| 作者单位 | 1.Univ Michigan, Dept Surg, Ann Arbor, MI 48109 USA 2.Chinese Acad Sci, Acad Math & Syst Sci, RCSDS, NCMIS, Beijing 100190, Peoples R China 3.Univ Chinese Acad Sci, Sch Math Sci, Beijing 100049, Peoples R China 4.Wayne State Univ, Inst Environm Hlth Sci, Detroit, MI 48202 USA |
| 推荐引用方式 GB/T 7714 | Tan, Zhijing,Yi, Xinpei,Carruthers, Nicholas J.,et al. Single Amino Acid Variant Discovery in Small Numbers of Cells[J]. JOURNAL OF PROTEOME RESEARCH,2019,18(1):417-425. |
| APA | Tan, Zhijing,Yi, Xinpei,Carruthers, Nicholas J.,Stemmer, Paul M.,&Lubman, David M..(2019).Single Amino Acid Variant Discovery in Small Numbers of Cells.JOURNAL OF PROTEOME RESEARCH,18(1),417-425. |
| MLA | Tan, Zhijing,et al."Single Amino Acid Variant Discovery in Small Numbers of Cells".JOURNAL OF PROTEOME RESEARCH 18.1(2019):417-425. |
入库方式： OAI收割
来源：数学与系统科学研究院
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