PXD050904-1

PXD050904 is an original dataset announced via ProteomeXchange.

Title	Long-read Proteogenomics Internal Standard triggered PRM (LRP-IS-PRM)
Description	Long-read proteogenomic data was used to create sample-matched protein database for WTC11 sample. This includes many potential alternative protein isoforms (major and minor isoforms) per gene. The IS-PRM method called Tomahto was tested versus DDA to demonstrate improved coverage of isoform-specific peptides. We called this overall method of long-read RNA informed Tomahto targeting LRP-IS-PRM and used it for protein-level evidence of multiple isoforms derived from alternative splicing.
HostingRepository	PRIDE
AnnounceDate	2024-07-17
AnnouncementXML	Submission_2024-07-17_05:36:33.608.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Erin Jeffery
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2024-03-22 08:16:07	ID requested
⏵ 1	2024-07-17 05:36:34	announced

Korchak JA, Jeffery ED, Bandyopadhyay S, Jordan BT, Lehe MD, Watts EF, Fenix A, Wilhelm M, Sheynkman GM, IS-PRM-Based Peptide Targeting Informed by Long-Read Sequencing for Alternative Proteome Detection. J Am Soc Mass Spectrom, ():(2024) [pubmed]

10.1021/jasms.4c00119;

submitter keyword: Proteogenomics, IS-PRM, Tomahto

Gloria Sheynkman
contact affiliation	Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA USA
contact email	gs9yr@virginia.edu
lab head
Erin Jeffery
contact affiliation	University of Virginia, Department of Molecular Physiology and Biological Physics
contact email	edf4n@virginia.edu
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/2024/07/PXD050904

PRIDE project URI

• PRIDE
  1. PXD050904
     1. Label: PRIDE project
     2. Name: Long-read Proteogenomics Internal Standard triggered PRM (LRP-IS-PRM)