PXD002457

PXD002457 is an original dataset announced via ProteomeXchange.

Title	Characterizing cardiac molecular mechanisms of mammalian hibernation via quantitative proteogenomics.
Description	This study uses advanced proteogenomic approaches in a non-model organism to elucidate cardioprotective mechanisms used during mammalian hibernation. Mammalian hibernation is characterized by dramatic reductions in body temperature, heart rate, metabolism and oxygen consumption. These changes pose significant challenges to the physiology of hibernators, especially for the heart, which maintains function throughout extreme conditions resembling ischemia and reperfusion. To identify novel cardioadaptive strategies we merged large-scale RNA-seq data with large-scale iTRAQ-based proteomic data in heart tissue from thirteen-lined ground squirrels (Ictidomys tridecemlineatus) throughout the circannual cycle. Protein identification and data analysis were run through Galaxy-P, a new multi-omic data analysis platform enabling effective integration of RNA-seq and MS/MS proteomic data. Galaxy-P uses flexible, modular workflows that combine customized sequence database searching and iTRAQ quantification to identify novel ground squirrel-specific protein sequences and provide insight into molecular mechanisms of hibernation. This study allowed for the quantification of 2007 identified cardiac proteins, including over 350 peptide sequences derived from previously uncharacterized protein products. Identification of these peptides allows for improved genomic annotation of this non-model organism, as well as identification of potential splice variants, mutations, or genome re-organization that provide insights into novel cardioprotective mechanisms used during hibernation.
HostingRepository	PRIDE
AnnounceDate	2015-11-03
AnnouncementXML	Submission_2015-11-03_02:35:17.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Pratik Jagtap
SpeciesList	scientific name: Spermophilus tridecemlineatus (Thirteen-lined ground squirrel); NCBI TaxID: 43179;
ModificationList	monohydroxylated residue; iTRAQ8plex-116 reporter+balance reagent acylated residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2015-07-01 01:51:20	ID requested
⏵ 1	2015-11-03 02:35:18	announced

Vermillion KL, Jagtap P, Johnson JE, Griffin TJ, Andrews MT, Characterizing Cardiac Molecular Mechanisms of Mammalian Hibernation via Quantitative Proteogenomics. J Proteome Res, 14(11):4792-804(2015) [pubmed]

curator keyword: Biomedical, Biological

submitter keyword: Keywords: Proteogenomics, Galaxy-P, Hibernation, Heart.

Pratik Jagtap
contact affiliation	Pratik Jagtap, Managing Director, Center for Mass Spectrometry and Proteomics, 43 Gortner Laboratory, 1479 Gortner Avenue, St. Paul, MN 55108 Phone: 612-624-9275
contact email	pjagtap@umn.edu
lab head
Pratik Jagtap
contact affiliation	Center for Mass Spectrometry and Proteomics
contact email	pjagtap@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/2015/11/PXD002457

PRIDE project URI

• PRIDE
  1. PXD002457
     1. Label: PRIDE project
     2. Name: Characterizing cardiac molecular mechanisms of mammalian hibernation via quantitative proteogenomics.