2 0 0 0 OA Dataset for in-depth proteome analysis of cell culture supernatants containing fetal bovine serum
- 著者
- Yusuke Kawashima
- 出版者
- Japanese Proteomics Society
- 雑誌
- Journal of Proteome Data and Methods (ISSN:24346454)
- 巻号頁・発行日
- vol.5, pp.2, 2023 (Released:2023-03-08)
- 参考文献数
- 8
We established a deep proteome analysis method of cell-derived proteins in fetal bovine serum-containing culture supernatants and successfully detected more than 3500 cell-derived proteins.
- 著者
- Yusuke Kawashima Natsumi Mori Norihito Kawashita Yu-Shi Tian Tatsuya Takagi
- 出版者
- Chem-Bio Informatics Society
- 雑誌
- Chem-Bio Informatics Journal (ISSN:13476297)
- 巻号頁・発行日
- vol.21, pp.1-10, 2021-01-29 (Released:2021-01-29)
- 参考文献数
- 16
- 被引用文献数
- 1
Fragment molecular orbital (FMO) calculation is a useful ab initio method for analyzing protein–ligand interactions in the current structure-based drug design. When multiple ligands exist for one receptor, a post-FMO calculation tool is required because of large numbers of interaction energy decomposition terms calculated using this method. In this study, a method that combines self-organizing maps (SOM) and hierarchical clustering analysis (HCA) was proposed to analyze the results of the FMO energy components. This method could effectively compress the high-dimensional energy terms and is expected to be useful to analyze the interaction between protein and ligands. A case study of antitype 2 diabetes mellitus target DPP-IV and its inhibitors was analyzed to verify the feasibility of the proposed method. After performing dimensional compression using SOM and further grouping using HCA, we obtained superclasses of the inhibitors based on the dispersion energy (DI), which showed consistency with structural information, indicating that further analyses of detailed energies per superclass can be an effective approach for obtaining important ligand–protein interactions.
- 著者
- Daisuke Nakajima Yusuke Kawashima Osamu Ohara
- 出版者
- Japanese Proteomics Society
- 雑誌
- Journal of Proteome Data and Methods (ISSN:24346454)
- 巻号頁・発行日
- vol.5, pp.8, 2023 (Released:2023-04-29)
- 参考文献数
- 4
To analyse deep protein profiling of dried blood spot (DBS). We developed a simple method using sodium carbonate precipitation (SCP). SCP enriches hydrophobic proteins from DBS, allowing substantial removal of soluble proteins. In combination with SCP, we used quantitative LC-MS/MS proteome analysis in a data-independent acquisition mode (DIA) to enhance the sensitivity and quantification limits of proteome analysis.