PXD028407

PXD028407 is an original dataset announced via ProteomeXchange.

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

Revision	Datetime	Status	ChangeLog Entry
0	2021-09-09 09:01:00	ID requested
⏵ 1	2022-05-19 10:13:12	announced

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]

submitter keyword: Mouse, Proximal Colon, Orbitrap, TMT, DDA, PRM

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

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

• PRIDE
  1. PXD028407
     1. Label: PRIDE project
     2. Name: Quantitative proteogenomic characterization of inflamed murine colon tissue using an integrated discovery, verification, and validation proteogenomic workflow