PXD005667

PXD005667 is an original dataset announced via ProteomeXchange.

Title	Quantitative metaproteomics and activity-based probe enrichment on fecal samples from a mouse model of inflammatory bowel disease
Description	Tandem mass spectrometry based shotgun proteomics of distal gut microbiomes is exceedingly difficult due to the inherent complexity and taxonomic diversity of the samples. We introduce two new methodologies to improve metaproteomic studies of microbiome samples. These methods include the stable isotope labeling in mammals to permit protein quantitation across the two mouse cohorts, as well as the application of activity-based probes to enrich and analyze both host and microbial proteins with specific functionalities. We used these technologies to study the microbiota from the adoptive T cell transfer mouse model of inflammatory bowel disease (IBD) and compare these samples to an isogenic control; thereby, limiting genetic and environmental variables that influence microbiome composition.
HostingRepository	PRIDE
AnnounceDate	2017-01-16
AnnouncementXML	Submission_2017-01-16_07:32:31.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Mike Mayers
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	biotinylated residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2017-01-09 01:38:25	ID requested
⏵ 1	2017-01-16 07:32:33	announced

Mayers MD, Moon C, Stupp GS, Su AI, Wolan DW, Quantitative Metaproteomics and Activity-Based Probe Enrichment Reveals Significant Alterations in Protein Expression from a Mouse Model of Inflammatory Bowel Disease. J Proteome Res, 16(2):1014-1026(2017) [pubmed]

curator keyword: Biomedical

submitter keyword: LC-MSMS, mouse, metaproteomics, SILAM, activity-based probes, microbiome, MudPIT, quantitative proteomics

Dennis W. Wolan
contact affiliation	Department of Molecular and Experimental Medicine, Department of Chemical Physiology, The Scripps Research Institute, USA
contact email	wolan@scripps.edu
lab head
Mike Mayers
contact affiliation	The Scripps Research Institute
contact email	mmayers@scripps.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/2017/01/PXD005667

PRIDE project URI

• PRIDE
  1. PXD005667
     1. Label: PRIDE project
     2. Name: Quantitative metaproteomics and activity-based probe enrichment on fecal samples from a mouse model of inflammatory bowel disease