jPOST database

2024/06/12

Web Site: https://globe.jpostdb.org/

jPOSTdb is a database containing re-analysis results with unified criteria for proteome data from jPOST repository.

README Content

1. Database Component
2. Data Description
3. License
4. Update History
5. Literature
6. Contact address

1. Database Component

1. README
2. Identified protein data
3. PSM peptide data
4. PSM peptide modification
5. jPOST database RDF

2. Data Description

2.1 README

Data name	README
Description of data contents	HTML file to describe "jPOST database" data.
File	README_e.html (English)

2.2 Identified protein data

Data name	Identified protein data
Description of data contents	This is the re-analysis summary results of proteome data in jPOST repository. They are idetified with UniProt protein data.
File	jpostdb_protein.zip (11.8MB)

Data items are the following:

Data item	Description
protein_id	jPOST internal protein ID
accession	UniProt ID
symbol	UniProt protein symbol
name	protein name
protein_type	protein type(Leading protein, Spectrum same-set protein Spectrum sub-set protein, Spectrum subsumable protein)
pep_count	identified peptide count
psm_count	peptide from psm(peptide specrum match) count
uniq_pep_count	unique peptide count

2.3 PSM peptide data

Data name	PSM peptide data
Description of data contents	Peptide data from protein spectrum match.
File	jpostdb_psm.zip (64.6MB)

Data items are the following:

Data item	Description
psm_id	Internal PSM ID
sequence	peptide sequence
accession	UniProt ID
exp_mz	M/Z value(ratio between mass m and chage z) obtained by experiment
calc_mz	M/Z value(ratio between mass m and chage z) value obtained by calculation
charge	charge
jpost_score	jPOST score

2.4 PSM peptide modification

Data name	PSM peptide modification
Description of data contents	Modification data of PSM peptide
File	jpostdb_psm_modification.zip (3035177)

Data items are the following:

Data item	Description
psm_id	Internal PSM ID
modification	modification type
site	modification site
position	position in peptide sequence

2.5 jPOST database RDF

Data name	jPOST database RDF
Description of data contents	jPOST database in RDF format. See https://integbio.jp/rdf/dataset/jpost about RDF schema.
File	-

3. License

You may use this database in compliance with the terms and conditions of the license described below. The license specifies the license terms regarding the use of this database and the requirements you must follow in using this database.

4. Update History

Date	Update contents
2024/06/12	Assigning DOIs.
2021/08/12	jPOST database archive site is opened.
2018/03/26	jPOST (https://repository.jpostdb.org/) is opened.

5. Literature

Yuki Moriya, Shin Kawano, Shujiro Okuda, Yu Watanabe, Masaki Matsumoto, Tomoyo Takami, Daiki Kobayashi, Yoshinori Yamanouchi, Norie Araki, Akiyasu C. Yoshizawa, Tsuyoshi Tabata, Mio Iwasaki, Naoyuki Sugiyama, Satoshi Tanaka, Susumu Goto, Yasushi Ishihama
The jPOST environment: an integrated proteomics data repository and database
Nucleic Acids Research, Volume 47, Issue D1, 08 January 2019, Pages D1218–D1224. doi: 10.1093/nar/gky899

6. Contact address

When you have any question about "jPOST database", contact the following:

https://jpostdb.org/contact/