jPOST environment accelerates the reuse and reanalysis of public proteome mass spectrometry data

• Published in: Nucleic acids research Vol. 53; no. D1; pp. D462 - D467
• Main Authors: Okuda, Shujiro, Yoshizawa, Akiyasu C, Kobayashi, Daiki, Takahashi, Yushi, Watanabe, Yu, Moriya, Yuki, Hatano, Atsushi, Takami, Tomoyo, Matsumoto, Masaki, Araki, Norie, Tabata, Tsuyoshi, Iwasaki, Mio, Sugiyama, Naoyuki, Kodera, Yoshio, Tanaka, Satoshi, Goto, Susumu, Kawano, Shin, Ishihama, Yasushi
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 06.01.2025
• Subjects: Database Issue; Databases, Protein; Humans; Mass Spectrometry - methods; Metadata; Proteome; Proteomics - methods; Search Engine; Tandem Mass Spectrometry - methods
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gkae1032

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.