PXD000327

PXD000327 is an original dataset announced via ProteomeXchange.

Title	Quantitative proteomic profiling reveals novel region-specific markers in the adult mouse brain
Description	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.
HostingRepository	PRIDE
AnnounceDate	2014-08-08
AnnouncementXML	Submission_2014-08-08_01:53:33.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	L Dagley
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue; (18)O label at both C-terminal oxygens
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2013-07-08 02:27:47	ID requested
1	2013-11-22 03:28:25	announced
1	2013-11-22 05:19:36	announced
2	2014-07-25 01:20:48	announced	Updated project metadata.
⏵ 3	2014-08-08 01:53:34	announced	Updated project metadata.

Dagley LF, White CA, Liao Y, Shi W, Smyth GK, Orian JM, Emili A, Purcell AW, Quantitative proteomic profiling reveals novel region-specific markers in the adult mouse brain. Proteomics, 14(2-3):241-61(2014) [pubmed]

curator keyword: Biomedical, Biological

submitter keyword: 18O-based stable isotope labeling, mass spectrometry, membrane proteins, myelin interactome, quantitative proteomics

L Dagley
contact affiliation	Department of Biochemistry and Molecular Biology
contact email	l.gianni@student.unimelb.edu.au
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD000327
     1. Label: PRIDE project
     2. Name: Quantitative proteomic profiling reveals novel region-specific markers in the adult mouse brain