Dataset Information

Quantitative proteomic profiling reveals novel region-specific markers in the adult mouse brain

ABSTRACT: Here we present the data obtained from a high precision 18O-labeling strategy used to quantitatively map membrane proteins isolated from myelin-enriched fractions purified from distinct brain regions of an adult mouse. To this end, we present an updated catalog of myelin-associated proteins found in the vertebrate CNS with relevance for investigations of myelin disorders. We also present a number of regiospecific protein markers of the brain, many of which remain unannotated in current online brain mapping databases. Data analysis: Tandem mass spectra were extracted from .RAW files and searched using the SEQUEST- PVM v.27 (rev.9) database program against a Mouse protein database downloaded as FASTA-formatted sequences from EBI-IPI (database version 3.72) which contains 56957 entries where priority was given to UniProt identifiers, as well as reverse decoy sequences to empirically assess the false identification rate. Mass tolerances for precursor (MS) and product ions (MS/MS) were set to 3 and 0 m/z, respectively. Two SEQUEST searches were performed per labeling experiment setting the enzyme selectivity to trypsin while allowing one missed cleavage. In both searches, protein modifications included fixed cysteine carbamidomethylation (57 Da) whilst the 18O-specific search included a static C-terminal modification mass of 4 Da (to account for tryptic peptides fully incorporating two 18O atoms). This improved the identification of unlabeled/labeled peptide pairs without exceeding the individual search mass tolerances. Following the database searches, the utility program DTASelect was invoked to assemble SEQUEST identifications and in each case, create an exhaustive list of the most significant peptide matches to the MS/MS spectra.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Mus Musculus (mouse)

SUBMITTER: L Dagley

LAB HEAD: L Dagley

PROVIDER: PXD000327 | Pride | 2013-11-22

REPOSITORIES: Pride

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			Action	DRS
	Dagley_ProteomeXchange_Database_search_myelin.docx	Other
	Dagleyetal2013_Proteomics__supptables_final.xlsx	Xlsx
	LG100813_BS4_vs_BrH7_WT_DDA10_01.raw	Raw
	LG100813_BS4_vs_BrH7_WT_DDA10_01_dta.tar.bz2	Other
	LG100813_BS4_vs_BrH7_WT_DDA10_01_out.tar.bz2	Other

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Quantitative proteomic profiling reveals novel region-specific markers in the adult mouse brain.

Dagley Laura F LF White Carl A CA Liao Yang Y Shi Wei W Smyth Gordon K GK Orian Jacqueline M JM Emili Andrew A Purcell Anthony W AW

Proteomics 20140106 2-3

Despite major advances in neuroscience, a comprehensive understanding of the structural and functional components of the adult brain compartments remains to be fully elucidated at a quantitative molecular level. Indeed, over half of the soluble- and membrane-annotated proteins are currently unmapped within online digital brain atlases. In this study, two complementary approaches were used to assess the unique repertoire of proteins enriched within select regions of the adult mouse CNS, including ...[more]

PMID: 24259518

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