PXD008381

PXD008381 is an original dataset announced via ProteomeXchange.

Title	ProteomeGenerator analysis of K052
Description	To improve identification of canonical and non-canonical protein isoforms, we introduced ProteomeGenerator, a framework for reference-guided and de novo proteogenomic database generation from transcriptomic sequencing dataset. The proteomic databases output by ProteomeGenerator contain only proteins encoded by actively transcribed genes, and includes sample-specific protein isoforms resulting from non-canonical transcription and mRNA editing. We applied this workflow to the proteogenomic analysis of spliceosome-defective K052 SRSF2(P95H) cells, demonstrating high-confidence identification of proteins isoforms arising from intron inclusion and non-canonical splicing, as well as improved overall estimation of false-discovery rate from the focused database assembled by ProteomeGenerator.
HostingRepository	PRIDE
AnnounceDate	2018-10-11
AnnouncementXML	Submission_2018-10-11_07:18:58.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Alex Kentsis
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	deaminated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion ETD

Revision	Datetime	Status	ChangeLog Entry
0	2017-12-07 01:27:35	ID requested
⏵ 1	2018-10-11 07:18:59	announced

Cifani P, Dhabaria A, Chen Z, Yoshimi A, Kawaler E, Abdel-Wahab O, Poirier JT, Kentsis A, ProteomeGenerator: A Framework for Comprehensive Proteomics Based on de Novo Transcriptome Assembly and High-Accuracy Peptide Mass Spectral Matching. J Proteome Res, 17(11):3681-3692(2018) [pubmed]

curator keyword: Technical, Biological

submitter keyword: ProteomeGenerator proteogenomics shotgun K052 non-canonical isoforms

Alex Kentsis
contact affiliation	Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
contact email	kentsisresearchgroup@gmail.com
lab head
Alex Kentsis
contact affiliation	Memorial Sloan Kettering Cancer Center
contact email	kentsisresearchgroup@gmail.com
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/2018/10/PXD008381

PRIDE project URI

• PRIDE
  1. PXD008381
     1. Label: PRIDE project
     2. Name: ProteomeGenerator analysis of K052