Dataset Information

Mouse cerebellum (phospho)proteome LC-MSMS

ABSTRACT: 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.

INSTRUMENT(S): LTQ Orbitrap Elite, Q Exactive

ORGANISM(S): Mus Musculus (mouse)

SUBMITTER: Eleonora Corradini

PROVIDER: PXD000502 | Pride | 2014-06-17

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	AnnotatedMassLabeledSpectraMultiConsensus.zip	Other
	OR5_120619_EC_SCX_MIX1_mouse_cerebellum_19.raw	Raw
	OR5_120619_EC_SCX_MIX1_mouse_cerebellum_20.raw	Raw
	OR5_120619_EC_SCX_MIX1_mouse_cerebellum_21.raw	Raw
	OR5_120619_EC_SCX_MIX1_mouse_cerebellum_22.raw	Raw

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Publications

Alterations in the cerebellar (Phospho)proteome of a cyclic guanosine monophosphate (cGMP)-dependent protein kinase knockout mouse.

Corradini Eleonora E Vallur Raghavan R Raaijmakers Linsey M LM Feil Susanne S Feil Robert R Heck Albert J R AJ Scholten Arjen A

Molecular & cellular proteomics : MCP 20140612 8

The cyclic nucleotide cyclic guanosine monophosphate (cGMP) plays an important role in learning and memory, but its signaling mechanisms in the mammalian brain are not fully understood. Using mass-spectrometry-based proteomics, we evaluated how the cerebellum adapts its (phospho)proteome in a knockout mouse model of cGMP-dependent protein kinase type I (cGKI). Our data reveal that a small subset of proteins in the cerebellum (∼3% of the quantified proteins) became substantially differentially ex ...[more]

PMID: 24925903

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