SEPepQuant enhances the detection of possible isoform regulations in shotgun proteomics
文献类型：期刊论文
| 作者 | Dou, Yongchao6,7; Liu, Yuejia5; Yi, Xinpei6,7; Olsen, Lindsey K.6,7; Zhu, Hongwen3,4; Gao, Qiang1,2; Zhou, Hu3,4,5 ; Zhang, Bing6,7
|
| 刊名 | NATURE COMMUNICATIONS
 |
| 出版日期 | 2023-09-19 |
| 卷号 | 14期号:1页码:15 |
| DOI | 10.1038/s41467-023-41558-2 |
| 通讯作者 | Zhang, Bing(bing.zhang@bcm.edu) |
| 英文摘要 | Shotgun proteomics is essential for protein identification and quantification in biomedical research, but protein isoform characterization is challenging due to the extensive number of peptides shared across proteins, hindering our understanding of protein isoform regulation and their roles in normal and disease biology. We systematically assess the challenge and opportunities of shotgun proteomics-based protein isoformcharacterization using in silico and experimental data, and then present SEPepQuant, a graph theory-based approach to maximize isoform characterization. Using published data from one induced pluripotent stem cell study and two human hepatocellular carcinoma studies, we demonstrate the ability of SEPepQuant in addressing the key limitations of existing methods, providing more comprehensive isoformlevel characterization, identifying hundreds of isoform-level regulation events, and facilitating streamlined cross-study comparisons. Our analysis provides solid evidence to support a widespread role of protein isoform regulation in normal and disease processes, and SEPepQuant has broad applications to biological and translational research. |
| WOS关键词 | PROTEOGENOMIC CHARACTERIZATION ; PEPTIDE IDENTIFICATION ; STATISTICAL-MODEL ; INFERENCE ; ACCURACY ; INSIGHTS ; PLATFORM ; DATABASE ; SLK |
| 资助项目 | National Cancer Institute (NCI)[U24 CA210954] ; National Cancer Institute (NCI)[U24 CA271076] ; National Cancer Institute (NCI)[R01 CA245903] ; Cancer Prevention & Research Institutes of Texas (CPRIT)[RR160027] ; McNair Medical Institute at The Robert and Janice McNair Foundation ; Shanghai Young Excellent Academic Leader Program[20XD1424900] ; Shanghai Municipal Science and Technology Major Project |
| WOS研究方向 | Science & Technology - Other Topics |
| 语种 | 英语 |
| WOS记录号 | WOS:001189045900002 |
| 出版者 | NATURE PORTFOLIO |
| 源URL | [http://119.78.100.183/handle/2S10ELR8/310381]  |
| 专题 | 中国科学院上海药物研究所 |
| 通讯作者 | Zhang, Bing |
| 作者单位 | 1.Minist Educ, Key Lab Carcinogenesis & Canc Invas, 180 Fenglin Rd, Shanghai 200032, Peoples R China 2.Fudan Univ, Zhongshan Hosp, Liver Canc Inst, Dept Liver Surg & Transplantat, 180 Fenglin Rd, Shanghai 200032, Peoples R China 3.Chinese Acad Sci, Shanghai Inst Mat Med, CAS Key Lab Receptor Res, 555 Zuchongzhi Rd, Shanghai 201203, Peoples R China 4.Chinese Acad Sci, Shanghai Inst Mat Med, Dept Analyt Chem, State Key Lab Drug Res, 555 Zuchongzhi Rd, Shanghai 201203, Peoples R China 5.Nanjing Univ Chinese Med, Sch Chinese Mat Med, 138 Xianlin Ave, Nanjing 210023, Jiangsu, Peoples R China 6.Baylor Coll Med, Dept Mol & Human Genet, Houston, TX 77030 USA 7.Baylor Coll Med, Lester & Sue Smith Breast Ctr, Houston, TX 77030 USA |
| 推荐引用方式 GB/T 7714 | Dou, Yongchao,Liu, Yuejia,Yi, Xinpei,et al. SEPepQuant enhances the detection of possible isoform regulations in shotgun proteomics[J]. NATURE COMMUNICATIONS,2023,14(1):15. |
| APA | Dou, Yongchao.,Liu, Yuejia.,Yi, Xinpei.,Olsen, Lindsey K..,Zhu, Hongwen.,...&Zhang, Bing.(2023).SEPepQuant enhances the detection of possible isoform regulations in shotgun proteomics.NATURE COMMUNICATIONS,14(1),15. |
| MLA | Dou, Yongchao,et al."SEPepQuant enhances the detection of possible isoform regulations in shotgun proteomics".NATURE COMMUNICATIONS 14.1(2023):15. |
入库方式： OAI收割
来源：上海药物研究所
浏览0
下载0
收藏0
其他版本
除非特别说明，本系统中所有内容都受版权保护，并保留所有权利。