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Proteomics
- Susumu Goto [contact]
- Yuki Moriya
- Yu Watanabe
- Shujiro Okuda
- Akiyasu C. Yoshizawa
- Satoshi Tanaka
- Tomoyo Takami
- Yuki Naito
Proteomics is a research field emerging owing to the advancement of mass spectrometry measurement technologies. To handle the rapid increase of proteomics data, it is quite important to develop proteomics database environments and application libraries for mass spectrometry data and protein/peptide sequence data analyses. The members of this working group have been developing the following proteomics related tools. jPOST database for linking proteome data to other omics data [1] Mass++ for developing mass spectrometry related applications [2] PPPeptide for fast and sensitive short peptide sequence search
The working group aimed to improve proteomics database ... International collaboration of data repository for proteomics data from mass spectrometry Started collaboration with NBDC regarding FTP archive Standard protocol for peptide and protein identification RDF-based database for reanalyzed proteomics data Variation data from TogoVar User data upload for comparisons Proteogenomics data
The following tasks were accomplished during the BH19: 1) Development of view for genetic variation data from TogoVar. 2) User data upload and comparison workflow using TogoDB database hosting service for differential expression analysis
Prepared for the poster presentation in HUPO (Human Proteome Organization World Congress) 2019 Adelaide Australia Made the poster on Skype meeting last night. Created some functions such as heat map, 3D viewer and importing identification results. The new version of Mass++ has not been released yet. We have to release it by 16 Sep as the presentation date is set to 17 Sep.
The working group made a solution for the problem.
Future!
Moriya, Y., Kawano, S., Okuda, S., Watanabe, Y., Matsumoto, M., Takami, T., Kobayashi, D., Yamanouchi, Y., Araki, N., Yoshizawa, A. C., Tabata, T., Iwasaki, M., Sugiyama, N., Tanaka, S., Goto, S., Ishihama, Y. (2019). The jPOST environment: an integrated proteomics data repository and database. Nucl. Acids Res. 47 (D1), D1218–D1224. doi: 10.1093/nar/gky899 Tanaka, S., Fujita, Y., Parry, H. E., Yoshizawa, A. C., Morimoto, K., Murase, M., Yamada, Y., Yao, J., Utsunomiya, S., Kajihara, S., Fukuda, M., Ikawa, M., Tabata, T., Takahashi, K., Aoshima, K., Nihei, Y., Nishioka, T., Oda, Y., Tanaka, K. (2014) Mass++: A visualization and analysis tool for mass spectrometry. J. Proteome Res., 13, 3846–3853. doi:10.1021/pr500155z