PXD008960

PXD008960 is an original dataset announced via ProteomeXchange.

Title	Improvements to the rice genome annotation through large-scale analysis of RNA-Seq and proteomics data sets
Description	We have performed a Proteogenomics meta-analysis of data sets deposited in ProteomeXchange: PXD000265, PXD000313, PXD000923, PXD001030, PXD001058, PXD002291, PXD002739, PXD002740 and PXD003156 and using 29 RNA-Seq data sets on rice (Oryza sativa). We created a search database comprising translated reads that had been mapped onto the rice genome, as well as officially annotated rice proteins sequences. The RNA Seq database was pre-processed to identify “novel transcripts” for those not mapping fully to an existing exon, and “novel junctions” for those reads mapped with a gap, implying a potential novel splice site that was not annotated in the official gene set. Confidentially identified “novel peptides” i.e. those mapping to a novel junction or novel transcript were post-processed to ensure that there were no other better explanations for the corresponding spectra e.g. peptide from a canonical gene with a modification or amino acid substitution. Data were exported from the pipeline in PSI mzIdentML 1.2 format, containing chromosomal coordinates, and further converted to PSI proBed format for genome visualisation. Novel peptides were searched against other plant databases using BLAST to see if they had predicted in genes from other species. A total of 1584 novel peptides were identified, mapping to ~700 genomic loci in which either new genes have been predicted (~100) or updates to existing gene models have been predicted (~600).
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:48:09.660.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD008960
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Da Qi
SpeciesList	scientific name: Oryza sativa (Rice); NCBI TaxID: 4530;
ModificationList	Ammonia-loss; iTRAQ8plex:13C(6)15N(2); Oxidation; Carbamidomethyl; Gly->Val; Gln->pyro-Glu; Phospho; Glu->pyro-Glu; Deamidated; cysTMT6plex; iTRAQ8plex; Acetyl; Sulfo; Trimethyl
Instrument	LTQ Orbitrap Velos; TripleTOF 5600; Q Exactive; LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2018-02-15 01:12:25	ID requested
1	2018-10-30 09:30:03	announced
2	2019-02-15 09:06:41	announced	Updated publication reference for PubMed record(s): 30293062.
⏵ 3	2024-10-22 04:48:18	announced	2024-10-22: Updated project metadata.

10.6019/PXD008960;

Ren Z, Qi D, Pugh N, Li K, Wen B, Zhou R, Xu S, Liu S, Jones AR, Improvements to the Rice Genome Annotation Through Large-Scale Analysis of RNA-Seq and Proteomics Data Sets. Mol Cell Proteomics, 18(1):86-98(2019) [pubmed]

10.1074/mcp.RA118.000832;

curator keyword: Technical, Biological

submitter keyword: Rice,Proteogenomics, Proteomics, RNA-Seq, Big data analysis

Andrew R Jones
contact affiliation	Institute of Integrative Biology, University of Liverpool
contact email	andrew.jones@liverpool.ac.uk
lab head
Da Qi
contact affiliation	BGI-Shenzhen
contact email	qida@genomics.cn
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD008960
     1. Label: PRIDE project
     2. Name: Improvements to the rice genome annotation through large-scale analysis of RNA-Seq and proteomics data sets