PXD028407 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Quantitative proteogenomic characterization of inflamed murine colon tissue using an integrated discovery, verification, and validation proteogenomic workflow |
Description | Rag2-/-Il10-/- mice were subjected to infection by Helicobacter hepaticus and allowed to develop long-term infections. Proximal colon tissue was then harvested from the mice for analysis. RNA was isolated from the samples and submitted for transcriptomic analysis; this data was then used to create a custom RNA-based FASTA database. Protein isolated from the proximal colon samples were digested and analyzed via bottom-up mass spectrometry. The custom FASTA database was then used for proteogenomic analysis of the raw mass spectrometry data in the Galaxy for proteomics (Galaxy-P) platform. |
HostingRepository | PRIDE |
AnnounceDate | 2022-05-19 |
AnnouncementXML | Submission_2022-05-19_10:13:12.120.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Andrew Rajczewski |
SpeciesList | scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; |
ModificationList | TMT6plex-126 reporter+balance reagent acylated residue; phosphorylated residue; iodoacetamide derivatized residue |
Instrument | Q Exactive; Orbitrap Fusion |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2021-09-09 09:01:00 | ID requested | |
⏵ 1 | 2022-05-19 10:13:12 | announced | |
Publication List
Rajczewski AT, Han Q, Mehta S, Kumar P, Jagtap PD, Knutson CG, Fox JG, Tretyakova NY, Griffin TJ, Quantitative Proteogenomic Characterization of Inflamed Murine Colon Tissue Using an Integrated Discovery, Verification, and Validation Proteogenomic Workflow. Proteomes, 10(2):(2022) [pubmed] |
Keyword List
submitter keyword: Mouse, Proximal Colon, Orbitrap, TMT, DDA, PRM |
Contact List
Timothy J Griffin |
contact affiliation | Professor, Department of Biochemistry, Molecular Biology and Biophysics Director, Center for Mass Spectrometry and Proteomics |
contact email | tgriffin@umn.edu |
lab head | |
Andrew Rajczewski |
contact affiliation | University of Minnesota |
contact email | rajcz001@umn.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/2022/05/PXD028407 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD028407
- Label: PRIDE project
- Name: Quantitative proteogenomic characterization of inflamed murine colon tissue using an integrated discovery, verification, and validation proteogenomic workflow