PXD004603
PXD004603 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Rice (Oryza sativa) proteome |
| Description | Here, we present OryzaPG-DB, a rice proteome database based on shotgun proteogenomics, which incorporates the genomic features of experimental shotgun proteomics data. This version of the database was created from the results of 27 nanoLC-MS/MS runs on a hybrid ion trap-orbitrap mass spectrometer, which offers high accuracy for analyzing tryptic digests from undifferentiated cultured rice cells. Peptides were identified by searching the product ion spectra against the protein, cDNA, transcript and genome databases from Michigan State University, and were mapped to the rice genome. Approximately 3200 genes were covered by these peptides and 40 of them contained novel genomic features. Users can search, download or navigate the database per chromosome, gene, protein, cDNA or transcript and download the updated annotations in standard GFF3 format, with visualization in PNG format. In addition, the database scheme of OryzaPG was designed to be generic and can be reused to host similar proteogenomic information for other species. OryzaPG is the first proteogenomics-based database of the rice proteome, providing peptide-based expression profiles, together with the corresponding genomic origin, including the annotation of novelty for each peptide. |
| HostingRepository | jPOST |
| AnnounceDate | 2016-07-20 |
| AnnouncementXML | Submission_2022-09-18_04:00:09.746.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Natsumi Ishikawa |
| SpeciesList | scientific name: Oryza sativa; NCBI TaxID: 4530; |
| ModificationList | S-carboxamidomethyl-L-cysteine; alpha-amino acetylated residue; 2-pyrrolidone-5-carboxylic acid (Gln); 2-pyrrolidone-5-carboxylic acid (Glu); L-methionine sulfoxide |
| Instrument | LTQ Orbitrap |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2016-07-19 19:14:55 | ID requested | |
| 1 | 2016-07-19 19:24:53 | announced | |
| 2 | 2016-07-19 22:29:56 | announced | Updated PubMed ID. |
| 3 | 2016-07-20 00:39:23 | announced | Updated PubMed ID. |
| 4 | 2016-11-17 18:21:28 | announced | Updated PubMed ID. |
| 5 | 2018-09-18 22:43:27 | announced | Updated CV, FTP location and Modification list. |
| 6 | 2021-02-04 16:39:59 | announced | 2021-02-04: Updated FTP location. |
| ⏵ 7 | 2022-09-18 04:00:10 | announced | 2022-09-18: Updated FTP location. |
Publication List
| Helmy M, Tomita M, Ishihama Y, OryzaPG-DB: rice proteome database based on shotgun proteogenomics. BMC Plant Biol, 11():63(2011) [pubmed] |
Keyword List
| submitter keyword: Rice, Oryza sativa, proteogenomics |
Contact List
| Yasushi Ishihama | |
|---|---|
| lab head | |
| Natsumi Ishikawa | |
| contact affiliation | Kyot Univ. |
| dataset submitter | |
Full Dataset Link List
| jPOST dataset URI |
| Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.jpostdb.org/JPST000156/ |
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