PXD029360

PXD029360 is an original dataset announced via ProteomeXchange.

Title	Generation of ENSEMBL-based proteogenomics databases boost the identification of novel peptides
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 generation by the algorithm DecoyPyrat. Finally, we perform a reanalysis of four public datasets in PRIDE by generating cell-type specific databases for 65 cell lines using the pypgatk and pgdb workflow, revealing a wealth of non-canonical or cryptic peptides amounting to more than 10% of the total number of peptides identified (43,501 out of 402,512).
HostingRepository	PRIDE
AnnounceDate	2021-10-26
AnnouncementXML	Submission_2021-10-26_13:27:02.081.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD029360
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Yasset Perez-Riverol
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; monohydroxylated residue
Instrument	Q Exactive HF; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2021-10-26 04:13:09	ID requested
⏵ 1	2021-10-26 13:27:02	announced

Dataset with its publication pending

submitter keyword: proteogenomics, ENSEMBL, reanalysis

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

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.pride.ebi.ac.uk/pride/data/archive/2021/10/PXD029360

PRIDE project URI

• PRIDE
  1. PXD029360
     1. Label: PRIDE project
     2. Name: Generation of ENSEMBL-based proteogenomics databases boost the identification of novel peptides