PXD000502

PXD000502 is an original dataset announced via ProteomeXchange.

Title	Mouse cerebellum (phospho)proteome LC-MSMS
Description	Cerebella from wild-type and cGKI knockout mice, on 129/Sv background, were subjected to protein digestion using trypsin o/n and chemically labeled with dimethyl labeling. After labeling the samples were mixed and subjected to both strong cation exchange and phosphopeptide enrichment. The SCX fractions and the enriched phosphopeptides were then analyzed on an Orbitrap mass spectrometer. Data analysis: For each raw data file recorded by the mass spectrometer, peak lists were generated using Proteome Discoverer (version 1.3, Thermo Scientific, Bremen, Germany) using a standardized workflow. Peak lists, generated in Proteome Discoverer, were searched against a Swiss-Prot database (version 2.3.02, taxonomy Mus musculus, 32402 protein entries) supplemented with frequently observed contaminants, using Mascot (version 2.3.02 Matrix Science, London, UK). The database search was performed by using the following paramenters: a mass tolerance of 50 ppm for the precursor masses and +/-0.6 Da for CID/ETD fragment ions and +/-0.05 Da for HCD fragments. Enzyme specificity was set to Trypsin with 2 missed cleavages allowed. Carbarmidomethylation of cysteines was set as fixed modification, oxidation of methionine and dimethyl labeling (L, I, H) of lysine residues and N termini, and phosphorylation (S, T, Y) (for the phosphoproteome analysis) were used as variable modifications. Percolator was used to filter the PSMs for <1% false discovery-rate. Phosphorylation sites were localized by applying phosphoRS (pRS) (v2.0). Triplex dimethyl labeling was used as quantification method, with a mass precision for the 2 ppm for consecutive precursor mass scan. A retention time tolerance of 0.5 min was used to account effect of deuterium on retention time. To further filter for high quality data we used the following parameters: high confidence peptide spectrum matches, minimal Mascot score of 20, minimal peptide length of 6 and only unique rank 1 peptide. For the phosphopeptides analysis, the search rank 1 peptide was added to the previous filters. For the identification and quantitation of the proteins, only the unique peptides were considered.
HostingRepository	PRIDE
AnnounceDate	2014-07-24
AnnouncementXML	Submission_2014-07-24_03:50:15.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Eleonora Corradini
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	phosphorylated residue
Instrument	Q Exactive; LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2013-10-09 01:05:19	ID requested
1	2014-06-17 06:17:57	announced
2	2014-06-17 06:25:45	announced	Updated publication reference for PubMed record(s): 24925903.
⏵ 3	2014-07-24 03:50:16	announced	Updated project metadata.

Corradini E, Vallur R, Raaijmakers LM, Feil S, Feil R, Heck AJ, Scholten A, Alterations in the cerebellar (Phospho)proteome of a cyclic guanosine monophosphate (cGMP)-dependent protein kinase knockout mouse. Mol Cell Proteomics, 13(8):2004-16(2014) [pubmed]

ProteomeXchange project tag: PRIME-XS Project

curator keyword: Biological

submitter keyword: Cerebellum, proteome, phosphoproteome, cGKI knock out, LC-MSMS

Eleonora Corradini
contact affiliation	Biomolecular and mass spectrometry group
contact email	e.corradini1@uu.nl
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/2014/06/PXD000502

PRIDE project URI

• PRIDE
  1. PXD000502
     1. Label: PRIDE project
     2. Name: Mouse cerebellum (phospho)proteome LC-MSMS