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

IF 16.6 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Nucleic Acids Research Pub Date : 2024-11-11 DOI:10.1093/nar/gkae1032

Shujiro Okuda, Akiyasu C Yoshizawa, Daiki Kobayashi, Yushi Takahashi, Yu Watanabe, Yuki Moriya, Atsushi Hatano, Tomoyo Takami, Masaki Matsumoto, Norie Araki, Tsuyoshi Tabata, Mio Iwasaki, Naoyuki Sugiyama, Yoshio Kodera, Satoshi Tanaka, Susumu Goto, Shin Kawano, Yasushi Ishihama

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引用次数: 0

Abstract

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.

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jPOST 环境加速了公共蛋白质组质谱数据的再利用和再分析

jPOST (https://jpostdb.org/) 包括 jPOSTrepo (https://repository.jpostdb.org/) （2000 多个项目）和 jPOSTdb (https://globe.jpostdb.org/) （600 多个数据集），前者是蛋白质组质谱数据的储存库，后者是根据使用 UniScore 的标准化协议对原始蛋白质组数据进行的再分析，后者是整合了再分析数据的数据库。jPOST 重新分析协议使用新的尺度 UniScore 对 MS/MS 图谱进行重新评分，以评估图谱峰与搜索引擎确定的氨基酸序列的对应程度。然而，资源库数据库中登记的元数据不足以进行重新分析。为了解决这个问题，日本蛋白质组学学会创办了一份数据期刊--《蛋白质组数据与方法期刊》（JPDM），该期刊接受数据描述符文章，其中详细介绍了可以重新分析的元数据。在 jPOST 中，根据 JPDM 数据描述符文章中描述的元数据，利用 UniScore 对原始蛋白质组数据进行重新分析。重新分析后的数据将存入 jPOSTdb，并在 jPOSTrepo 中添加 JPDM 文章的链接。这些在 jPOST 环境中的再分析加速将促进 FAIR 数据原则和开放科学。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Nucleic Acids Research 生物-生化与分子生物学

CiteScore

27.10

自引率

4.70%

发文量

1057

审稿时长

2 months

期刊介绍： Nucleic Acids Research (NAR) is a scientific journal that publishes research on various aspects of nucleic acids and proteins involved in nucleic acid metabolism and interactions. It covers areas such as chemistry and synthetic biology, computational biology, gene regulation, chromatin and epigenetics, genome integrity, repair and replication, genomics, molecular biology, nucleic acid enzymes, RNA, and structural biology. The journal also includes a Survey and Summary section for brief reviews. Additionally, each year, the first issue is dedicated to biological databases, and an issue in July focuses on web-based software resources for the biological community. Nucleic Acids Research is indexed by several services including Abstracts on Hygiene and Communicable Diseases, Animal Breeding Abstracts, Agricultural Engineering Abstracts, Agbiotech News and Information, BIOSIS Previews, CAB Abstracts, and EMBASE.