PXD003164

PXD003164 is an original dataset announced via ProteomeXchange.

Title	Cross-species proteomics in analysis of mammalian sperm proteins C4PR_LIV
Description	Many proteomics studies are conducted in ‘model’ organisms for which a fully annotated and detailed, high quality proteome is available. By contrast, many studies in ecology and evolution lack a high quality proteome data set that can be used for protein discovery and quantification. This is particularly true of proteins in the reproductive system that have an immune function or drive sexual conflict, sperm competition and secondary sexual characteristics, as these are anticipated to have a high rate of evolution. This can compromise the potential for cross-species proteomics to yield confident identification. Here, we analysed the sperm proteome from a range of ungulates and rodents and explored the potential of proteomics, using routine data workflows, to be able to yield characterisation and quantification. We report that database searching is robust to cross-species matching for a core proteome, but that classes of proteins, notably those involved in sperm-egg interaction, are not readily analysed by this approach. Using iBAQ label free quantitative proteomics, we were also able to define a ‘core sperm proteome’ that was consistent across the ungulate and rodent groups, and which could be used as a reference for quantitative analysis of species-specific protein characterisation.
HostingRepository	PRIDE
AnnounceDate	2017-10-24
AnnouncementXML	Submission_2017-10-24_00:49:27.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Dean Hammond
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Bos taurus (Bovine); NCBI TaxID: 9913; scientific name: Sus scrofa domesticus (domestic pig); NCBI TaxID: 9825; scientific name: Rattus norvegicus (Rat); NCBI TaxID: 10116; scientific name: Equus caballus (Horse); NCBI TaxID: 9796;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2015-11-09 02:55:58	ID requested
1	2016-01-13 09:12:15	announced
2	2016-01-18 09:00:04	announced	Updated publication reference for PubMed record(s): 26768581.
3	2017-02-16 00:30:42	announced	Updated project metadata.
⏵ 4	2017-10-24 00:49:28	announced	Updated project metadata.

Bayram HL, Claydon AJ, Brownridge PJ, Hurst JL, Mileham A, Stockley P, Beynon RJ, Hammond DE, Cross-species proteomics in analysis of mammalian sperm proteins. J Proteomics, 135():38-50(2016) [pubmed]

curator keyword: Biological

submitter keyword: Cross-species, Sperm, Proteins, LC-MS, Rodents, Ungulates

Robert J Beynon
contact affiliation	Centre for Proteome Research Institute of Intergrative Biology University of Liverpool
contact email	r.beynon@liv.ac.uk
lab head
Dean Hammond
contact affiliation	University of Liverpool
contact email	d.e.hammond@liv.ac.uk
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/2016/01/PXD003164

PRIDE project URI

• PRIDE
  1. PXD003164
     1. Label: PRIDE project
     2. Name: Cross-species proteomics in analysis of mammalian sperm proteins C4PR_LIV