| Name | MassBase |
|---|
| Aliases | A comprehensive mass spectral tags archive for plant metabolomics. |
|---|
| Description | The concept of metabolomics is emerged as a new omics layer of system biology in this several years, but a flood of publicly available data for bioinformatics research is not observed yet. MassBase is an archive of a huge amount of mass spectrum tags (MST) include both known and unknown assigned (or predicted) peaks which are found in biological samples (mainly from plants) and standard chemical reagents for peak annotation. The aim of the database is to enhance the bioinformatics research of metabolomics using a huge metabolomics dataset. Over 39,100,000 peaks from 7,600 MSTs by GC-MS, 7,100 MSTs by LC-MS, and 28,800 MSTs by CE-MS are archived as text format files with its binary raw data files. Scanned mass spectra (SMS), a text format list of mass signals in all scans of a binary raw data are also archived. It should help to verify a computational peak assignment and to study an improvement of a quality of peak assignment. All dataset is freely downloadable from this site. To expand the dataset by using another type of MS instruments (e.g. CE-MS) are planned in near future. MassBase developed at Kazusa DNA research institute and supported by the NEDO project. (cited from the original site) |
|---|
| Type | DB |
|---|
| Main Institutes of management | Kazusa DNA Research Institute (KDRI) |
|---|
| Country of the Institute | Japan |
|---|
| URL of the site | http://webs2.kazusa.or.jp/massbase/index.php/ |
|---|
| Interface | GUI |
|---|
| Input example | Push "GO" button after Inputing the keyword "Arabidopsis" in the search text box. |
|---|
| Keyword | MST | SMS | Plant | Huge Data |
|---|
| Amount of the all data for download（Mbyte） | Method to obtain the all data. | 1100000|Donwload from the page http://webs2.kazusa.or.jp/massbase/index.php?action=Massbase_ShowDownload |
|---|
| External resources (databases) in building the product. | None |
|---|
| Data type | Metabolite repression |
|---|
| Biological species in the main concern | Acacia mangium | Arabidopsis thaliana | Cosmos bipinnatus | Acacia mangium [Taxonomy_id: 224085] | Arabidopsis thaliana [Taxonomy_id: 3702, thale cress] | Cosmos bipinnatus [Taxonomy_id: 51277] | Dicksonia antarctica [Taxonomy_id: 3271] | Escherichia coli [Taxonomy_id: 562] | Glycine max [Taxonomy_id: 3847, soybean] | Hevea brasiliensis [Taxonomy_id: 3981, jebe] | Jatropha curcas [Taxonomy_id: 180498] | Lotus japonicus [Taxonomy_id: 34305] | Medicago sativa [Taxonomy_id: 3879, lucerne] | Medicago truncatula [Taxonomy_id: 3880, barrel medic] | Mus musculus [Taxonomy_id: 10090, house mouse] | Nicotiana tabacum [Taxonomy_id: 4097, common tobacco] | Saccharomyces cerevisiae [Taxonomy_id: 4932, baker's yeast] | Solanum lycopersicum [Taxonomy_id: 4081, tomato] | Solanum pimpinellifolium [Taxonomy_id: 4084] | Thellungiella halophila [Taxonomy_id: 98038] |
|---|
| Conditions of use | None |
|---|
| Frequency of updates (in last two years) | 21 |
|---|
| Last date of updates (date of confirmation) | 2017/03/31 (2019/07/03) |
|---|
| Main IDs used in the products | MD ID |
|---|
| How to make a link to get access to each IDs. | http://webs2.kazusa.or.jp/massbase/index.php?action=Massbase_ShowPeakListPage&md_id=[MD ID] |
|---|
| external databases to which this database/tool have links | None |
|---|
| Published papers (PubMed IDs) | pmid:34177338 |
|---|
| Operational Status | available |
|---|
