PXD000112

PXD000112 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Zebrafish plasma analyzed by CE- and LC-MS/MS
Description	Single analyses of a Zebrafish whole plasma digest were analyzed by both CE-MS/MS and LC-MS/MS. The identified peptides and their corresponding retention or migration times were used to train a 'blind' retention/migration time model using linear regression. This trained model provided us with information on the migration/retention coefficients resulting from the individual amino acids. All acquired tandem mass spectrometry data was processed in the Trans-Proteomic Pipeline (TPP) embedded in the Taverna scientific workflow manager. The raw data was converted to mzXML using compassXport 3.0 (Bruker) and searched with X!Tandem. The X!Tandem scores were then converted to pepXML, modeled and translated to probabilities for each peptide-spectral match by PeptideProphet. The X!Tandem search was here performed allowing a random error ±0.5 Da, +1 or +2 Da isotopic error, carbamidomethylation as fixed and oxidation as variable modification and the k-score plug-in.
HostingRepository	PRIDE
AnnounceDate	2012-12-18Z
AnnouncementXML	Submission_2012-12-18_07:57:28.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Anthonius A.M. Heemskerk
SpeciesList	scientific name: Danio rerio (Zebrafish) (Brachydanio rerio); NCBI TaxID: 7955;
ModificationList	iodoacetamide derivatized residue
Instrument	Bruker Daltonics amaZon series

Dataset History

Revision	Datetime	Status
0	2012-12-18 07:33:33	ID requested
⏵ 1	2012-12-18 07:57:28	announced
⏵ 1	2014-07-25 00:48:24	announced

Publication List

no publication

no publication

Keyword List

submitter keyword: Danio Rerio, CE-MS/MS, LC-MS/MS

submitter keyword: Danio Rerio, CE-MS/MS, LC-MS/MS

Contact List

Anthonius A.M. Heemskerk
contact affiliation	Leiden University Medical Center
contact email	a.a.m.heemskerk@lumc.nl

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/2012/12/PXD000112

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/2012/12/PXD000112