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DOI | 10.1038/s41467-019-10382-y |
Benchmarking common quantification strategies for large-scale phosphoproteomics | |
Hogrebe, Alexander; von Stechow, Louise; Bekker-Jensen, Dorte B.; Weinert, Brian T.; Kelstrup, Christian D.; Olsen, Jesper V. | |
2019-06-11 | |
发表期刊 | NATURE COMMUNICATIONS |
ISSN | 2041-1723 |
出版年 | 2018 |
卷号 | 9 |
文章类型 | Article |
语种 | 英语 |
国家 | Denmark |
英文摘要 | Comprehensive mass spectrometry (MS)-based proteomics is now feasible, but reproducible quantification remains challenging, especially for post-translational modifications such as phosphorylation. Here, we compare the most popular quantification techniques for global phosphoproteomics: label-free quantification (LFQ), stable isotope labeling by amino acids in cell culture (SILAC) and MS2- and MS3-measured tandem mass tags (TMT). In a mixed species comparison with fixed phosphopeptide ratios, we find LFQ and SILAC to be the most accurate techniques. MS2-based TMT yields the highest precision but lowest accuracy due to ratio compression, which MS3-based TMT can partly rescue. However, MS2-based TMT outperforms MS3-based TMT when analyzing phosphoproteome changes in the DNA damage response, since its higher precision and larger identification numbers allow detection of a greater number of significantly regulated phosphopeptides. Finally, we utilize the TMT multiplexing capabilities to develop an algorithm for determining phosphorylation site stoichiometry, showing that such applications benefit from the high accuracy of MS3-based TMT. |
领域 | 资源环境 |
收录类别 | SCI-E |
WOS记录号 | WOS:000427247900003 |
WOS关键词 | PEPTIDE IDENTIFICATION RATES ; QUANTITATIVE PROTEOMICS ; MASS-SPECTROMETER ; PHOSPHORYLATION STOICHIOMETRIES ; PROTEIN-PHOSPHORYLATION ; ENABLES ACCURATE ; LTQ ORBITRAP ; DNA-DAMAGE ; LABEL-FREE ; EXPRESSION |
WOS类目 | Multidisciplinary Sciences |
WOS研究方向 | Science & Technology - Other Topics |
URL | 查看原文 |
引用统计 | |
文献类型 | 期刊论文 |
条目标识符 | http://119.78.100.173/C666/handle/2XK7JSWQ/204404 |
专题 | 资源环境科学 |
作者单位 | Univ Copenhagen, Fac Hlth & Med Sci, Novo Nordisk Fdn Ctr Prot Res, Prote Program, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark |
推荐引用方式 GB/T 7714 | Hogrebe, Alexander,von Stechow, Louise,Bekker-Jensen, Dorte B.,et al. Benchmarking common quantification strategies for large-scale phosphoproteomics[J]. NATURE COMMUNICATIONS,2019,9. |
APA | Hogrebe, Alexander,von Stechow, Louise,Bekker-Jensen, Dorte B.,Weinert, Brian T.,Kelstrup, Christian D.,&Olsen, Jesper V..(2019).Benchmarking common quantification strategies for large-scale phosphoproteomics.NATURE COMMUNICATIONS,9. |
MLA | Hogrebe, Alexander,et al."Benchmarking common quantification strategies for large-scale phosphoproteomics".NATURE COMMUNICATIONS 9(2019). |
条目包含的文件 | 条目无相关文件。 |
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