PXD050904 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2024-03-22 08:16:07 | ID requested | |
⏵ 1 | 2024-07-17 05:36:34 | announced | |
Publication List
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; |
Keyword List
submitter keyword: Proteogenomics, IS-PRM, Tomahto |
Contact List
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 | |
Full Dataset Link List
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 |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD050904
- Label: PRIDE project
- Name: Long-read Proteogenomics Internal Standard triggered PRM (LRP-IS-PRM)