jPOST repository
2021/01/28Web Site: https://repository.jpostdb.org/
HTTPS Site: https://dbarchive.biosciencedbc.jp/data/jpost/
The repository of mass spectrometry (MS) raw data, peak lists and analyzed data.
README Content
1. Database Component
- README
- Metadata
- File list
- Profile list
- Sample list
- Fractionation list
- Enzyme/Mod. List
- MS mode List
- Data directory
2. Data Description
2.1 README
| Data name | README |
|---|---|
| Description of data contents | HTML file to describe "jPOST repository" data. |
| File | README_e.html (English) |
2.2 Metadata
| Data name | Metadata |
|---|---|
| Description of data contents | The main body of jPOST repository metadata |
| File | jpost_metadata.zip (80 KB) |
Data items are the following:
| Data item | Description |
|---|---|
| jPOST ID | Project ID |
| PXID | ProtemoeXchange (PX) ID |
| Project title | Project title |
| Keywords | Keywords |
| Description | Description |
| Mode | Data analysis mode ("Complete" or "Partial") |
| PubMed ID(s) | PubMed ID(s) if articles are published |
| PubMed Info | References if articles are published |
| Principal investigator | Principal investigator |
| Created date | Data registration date |
| Announcement date | Data publication date |
| Note | Note |
| Contact | Contact |
| Revision | Revision |
| Files | Registered file list (Only simple search) |
2.3 File list
| Data name | File list |
|---|---|
| Description of data contents | The list of files registered in jPOST repository |
| File | jpost_file_list.zip (414 KB) |
Data items are the following:
| Data item | Description |
|---|---|
| jPOST ID | Project ID |
| File ID | File ID |
| File Name | File Name |
| Download | Download link (Only simple search) |
| File size | File size |
| Profiles | The list of profiles in this file (Only simple search) |
2.4 Profile list
| Data name | Profile list |
|---|---|
| Description of data contents | The list of expeerimental profiles such as sample or enzymes etc. It is refered from "metadata". |
| File | jpost_profile_list.zip (236 KB) |
Data items are the following:
| Data item | Description |
|---|---|
| jPOST ID | Project ID |
| File ID | File ID |
| Profile plex | Profile name |
| Sample - ID | Sample ID |
| Sample - Title | Sample name |
| Fractionation - ID | Fractionation ID |
| Fractionation - Title | Fractionation name |
| Enzyme/Mod. - ID | Enzyme/Mod. reaction ID |
| Enzyme/Mod. - Title | Enzyme/Mod. reaction name |
| MS mode - ID | MS mode ID |
| MS mode - Title | MS mode name |
2.5 Sample list
| Data name | Sample list |
|---|---|
| Description of data contents | The list of experimental samples It is refered from "profile list". |
| File | jpost_sample_list.zip (21 KB) |
Data items are the following:
| Data item | Description |
|---|---|
| ID | Sample ID |
| Title | Sample name |
| Species | Species |
| Tissue | Tissue |
| Cell type | Cell type |
| Disease | Disease |
| Note | Note |
2.6 Fractionation list
| Data name | Fractionation list |
|---|---|
| Description of data contents | The list of fractionations It is refered from "profile list". |
| File | jpost_fractionation_list.zip (13 KB) |
Data items are the following:
| Data item | Description |
|---|---|
| ID | Fractionation ID |
| Title | Fractionation name |
| Subcellular | Subcellular |
| Protein | Protein |
| Peptide | Peptide |
| Note | Note |
2.7 Enzyme/Mod. List
| Data name | Enzyme/Mod. List |
|---|---|
| Description of data contents | The list of enzyme/mod. It is refered from "profile list". |
| File | jpost_enzyme_mod_list.zip (7.7 KB) |
Data items are the following:
| Data item | Description |
|---|---|
| ID | Enzyme/Mod. reaction ID |
| Title | Enzyme/Mod. reaction name |
| Enzyme | Enzyme |
| Fixed modification | Modification prepared before the experiment |
| Variable modification | Other modifications |
| Taxonomy | Taxonomy |
| Note | Note |
2.8 MS mode List
| Data name | MS mode List |
|---|---|
| Description of data contents | The list of MS mode It is refered from "profile list". |
| File | jpost_ms_mode_list.zip (6.7 KB) |
Data items are the following:
| Data item | Description |
|---|---|
| ID | MS mode ID |
| Title | MS mode name |
| Instrument | Instrument |
| Instrument mode | Instrument mode |
| Purpose | Purpose |
| Quantification platform | Quantification platform |
| Plex | Plex |
| Label | Label |
| Note | Note |
2.9 Data directory
| Data name | Data directory |
|---|---|
| Description of data contents | Data registered in jPOST and published. Those contain mass spectrometry (MS) raw data, peak lists, analyzed data and metadata etc. |
| File | jpostrepos (11 TB) |
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.
This database is provided under CC0 Public Domein.
E-mail: jpostdb[at]gmail[dot]com
About Providing Links to This Database
You can freely provide links to all contents in this database. But, contents might be changed without notice.
4. Update History
| Date | Update contents |
|---|---|
| 2021/01/28 | License is updated. |
| 2019/12/26 | According to archiving jPOST original data, the archive name is changed to "jPOST repository". The following data are updated. "Original metadata" is changed to "Data Directory". "Data Directory" contains not only metadata also mass spectrometry (MS) raw data, peak lists and analyzed data etc. |
| 2018/02/28 | jPOST repository metadata English archive site is opened. |
| 2016/05/02 | jPOST (https://repository.jpostdb.org/) is opened. |
5. Literature
Shujiro Okuda, Yu Watanabe, Yuki Moriya, Shin Kawano, Tadashi Yamamoto, Masaki Matsumoto, Tomoyo Takami, Daiki Kobayashi, Norie Araki, Akiyasu C. Yoshizawa, Tsuyoshi Tabata, Naoyuki Sugiyama, Susumu Goto, Yasushi IshihamajPOSTrepo: an international standard data repository for proteomes
Nucleic Acids Research, Volume 45, Issue D1, 4 January 2017, Pages D1107–D1111
PMID: 27899654