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PXD029362

PXD029362 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleGeneration of ENSEMBL-based proteogenomics databases boost the identification of novel peptides - Mouse dataset
DescriptionA 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.
HostingRepositoryPRIDE
AnnounceDate2025-02-09
AnnouncementXMLSubmission_2025-02-09_00:31:08.093.xml
DigitalObjectIdentifierhttps://dx.doi.org/10.6019/PXD029362
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterYasset Perez-Riverol
SpeciesList scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationListacetylated residue; monohydroxylated residue; deaminated residue
InstrumentQ Exactive HF; LTQ
Dataset History
RevisionDatetimeStatusChangeLog Entry
02021-10-26 08:43:55ID requested
12021-10-26 13:12:44announced
22025-02-09 00:31:09announced2025-02-09: 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 affiliationEMBL-EBI
contact emailyperez@ebi.ac.uk
lab head
Yasset Perez-Riverol
contact affiliationEBI
contact emailyperez@ebi.ac.uk
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
Repository Record List
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