PXD029362 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Generation of ENSEMBL-based proteogenomics databases boost the identification of novel peptides - Mouse dataset |
Description | A novel bioinformatics tool pypgatk and the pgdb workflow is presented in study to create proteogenomics databases based on ENSEMBL resources. The tools allow the generation of protein sequences from novel protein-coding transcripts by performing a three-frame translation of pseudogenes, lncRNAs, and other non-canonical transcripts, such as those produced by alternative splicing events. It also includes exonic out-of-frame translation from otherwise canonical protein-coding mRNAs. Moreover, the tool enables the generation of variant protein sequences from multiple sources of genomic variants including COSMIC, cBioportal, gnomAD, and mutations detected from sequencing of patient samples. pypgatk and pgdb provide multiple functionalities for database handling, notably optimized target/decoy generati on by the algorithm DecoyPyrat. |
HostingRepository | PRIDE |
AnnounceDate | 2025-02-09 |
AnnouncementXML | Submission_2025-02-09_00:31:08.093.xml |
DigitalObjectIdentifier | https://dx.doi.org/10.6019/PXD029362 |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Supported dataset by repository |
PrimarySubmitter | Yasset Perez-Riverol |
SpeciesList | scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; |
ModificationList | acetylated residue; monohydroxylated residue; deaminated residue |
Instrument | Q Exactive HF; LTQ |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2021-10-26 08:43:55 | ID requested | |
1 | 2021-10-26 13:12:44 | announced | |
⏵ 2 | 2025-02-09 00:31:09 | announced | 2025-02-09: Updated project metadata. |
Publication List
Umer HM, Audain E, Zhu Y, Pfeuffer J, Sachsenberg T, Lehti, รถ J, Branca RM, Perez-Riverol Y, Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides. Bioinformatics, 38(5):1470-1472(2022) [pubmed] |
10.1093/bioinformatics/btab838; |
10.6019/PXD029362; |
Keyword List
submitter keyword: Mouse, Mice |
Contact List
Yasset Perez-Riverol |
contact affiliation | EMBL-EBI |
contact email | yperez@ebi.ac.uk |
lab head | |
Yasset Perez-Riverol |
contact affiliation | EBI |
contact email | yperez@ebi.ac.uk |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD029362
- Label: PRIDE project
- Name: Generation of ENSEMBL-based proteogenomics databases boost the identification of novel peptides - Mouse dataset