jPOST environment accelerates the reuse and reanalysis of public proteome mass spectrometry data
jPOST (https://jpostdb.org/) comprises jPOSTrepo (https://repository.jpostdb.org/) (over 2000 projects), a repository for proteome mass spectrometry data, the reanalysis of raw proteome data based on a standardised protocol using UniScore, and jPOSTdb (https://globe.jpostdb.org/) (over 600 datasets), a database that integrates the reanalysed data. The jPOST reanalysis protocol rescores MS/MS spectra using a new scale, UniScore, to evaluate the extent to which the spectral peaks correspond to the amino acid sequences identified by search engines. However, the metadata registered in the repository database is insufficient for conducting the reanalysis. To address this issue, the Japanese Proteomics Society launched a data journal, the Journal of Proteome Data and Methods (JPDM), which accepts data descriptor articles detailing metadata that can be reanalysed. Within jPOST, raw proteome data is reanalysed based on the metadata described in the JPDM data descriptor articles, utilising UniScore. The reanalysed data is deposited in jPOSTdb, and a link to the JPDM articles is added to jPOSTrepo. These reanalysis accelerations within the jPOST environment will promote FAIR data principles and open science.
Authors
- Akiyasu C. Yoshizawa (ORCID: https://orcid.org/0000-0002-0870-5502)
- Yasushi Ishihama (ORCID: https://orcid.org/0000-0001-7714-203X)
- Naoyuki Sugiyama (ORCID: https://orcid.org/0000-0001-7633-8495)
- Satoshi Tanaka (ORCID: https://orcid.org/0000-0002-7101-0690)
- Yuki Moriya (ORCID: https://orcid.org/0000-0001-8195-5893)
- Shin Kawano (ORCID: https://orcid.org/0000-0002-7969-2972)
- Masaki Matsumoto (ORCID: https://orcid.org/0000-0002-6987-0288)
- Yushi Takahashi (ORCID: https://orcid.org/0000-0002-9210-6413)
- Shujiro Okuda (ORCID: https://orcid.org/0000-0002-7704-8104)
- Tsuyoshi Tabata (ORCID: https://orcid.org/0000-0003-2077-5244)
- Mio Iwasaki (ORCID: https://orcid.org/0000-0003-2085-732X)
- Tomoyo Takami (ORCID: https://orcid.org/0000-0002-6974-8119)
- Atsushi Hatano (ORCID: https://orcid.org/0000-0002-0386-5080)
- Daiki Kobayashi (ORCID: https://orcid.org/0000-0003-4131-5220)
- Yu Watanabe (ORCID: https://orcid.org/0000-0003-1265-1591)
- Yoshio Kodera (ORCID: https://orcid.org/0000-0002-6661-8677)
- Norie Araki (ORCID: https://orcid.org/0000-0001-9987-6229)
- Susumu Goto (ORCID: https://orcid.org/0000-0003-2989-8486)
Institutions
- Kyoto University (JP)
- National Institute of Biomedical Innovation, Health and Nutrition (JP)
- National Cerebral and Cardiovascular Center (JP)
- Niigata University Medical and Dental Hospital (JP)
- Research Organization of Information and Systems (JP)
- Kitasato University (JP)
- Niigata University (JP)
- Kumamoto University (JP)
Publication Details
- Journal
- Nucleic Acids Research
- Published
- 2024-11-11
- DOI
- https://doi.org/10.1093/nar/gkae1032
- Citations
- 62
- Primary Topic
- Advanced Proteomics Techniques and Applications
- Type
- article
- Field-Weighted Citation Impact
- 14.93
Funders
- Japan Society for the Promotion of Science
- Japan Science and Technology Agency
- National Bioscience Database Center