MassIVE MSV000096677

Partial Public

An X-linked long non-coding RNA, PTCHD1-AS regulates autistic behaviors in humans and in mice

Subscribe Comment Convert Spectra Add Reanalysis

Description

Adult mouse dorsal striatum and frontal cortex samples (Wk 8 to 12) were processed by the Network Biology Collaborative Centre (NBCC) at the Lunenfeld Tanenbaum Research Institute (Toronto, Canada). Samples of 100 ug protein in RIPA lysis buffer (20 188, MilliporeSigma) were resuspended in 5 percent SDS, and 50 mM triethylammonium bicarbonate. 25 ug of protein was reduced (20mM DTT) and alkylated (40mM iodoacetamide in dark). Samples were processed with the standard S-trap micro spin column (C02 micro, Protifi) digestion protocol. 10 ug per sample was resuspended in 10 uL of 100 mM HEPES pH8 and labelled with 80 ug of a unique tandem mass tag (TMT) 16 plex channel (A44520, Thermo Fisher Scientific) in 4 uL of acetonitrile for 1 hour at RT. The reaction was quenched with 1 percent hydroxylamine. 5 percent of each sample was pooled and acquired with data dependent acquisition using nano high performance liquid chromatography tandem mass spectrometry. A Vanquish Neo UHPLC system was coupled to an Orbitrap Fusion Lumos Tribrid mass spectrometer (FETD2 10002, Thermo Fisher Scientific) and peptides were eluted off a nano-spray emitter generated from fused silica capillary tubing ( 75 um i.d., 365 um o.d. and 5 to 8 um tip opening, and packed to 15 cm with C18 reversed phase material (Reprosil Pur 120 C18 AQ, 3 um)) with a 120 min gradient. Flowrate was maintained at 400 nL per min with a consistent 0.1 percent formic acid background. There were 3 acetonitrile ramps: (1) 3.2 percent to 16.8percent over 72 minutes, (2) 16.8 percent to 24.8 percent over 28 minutes, and (3) 24.8 percent to 35.2 percent over 20 minutes. The first mass spectrometry scan ran for with accumulated time of 50 ms, a mass range of 400 to 16000 mz, orbitrap resolution of 120000, 30 percent radio frequency lens, 200 percent automatic gain control, and 1800 volts. The subsequent tandem mass spectrometry scan had cycle times of 2 s, 35 ms accumulation time, 33 percent higher-energy collisional dissociation collision energy and a first mass to charge ratio of 120 to 1800 mz. All candidate ions had a charge state from 2 to 7, and automatic gain control target of 400 percent isolated using an orbitrap resolution of 50000. [doi:10.25345/C5474740C] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Dorsal striatum, frontal cortex, Mouse ; DatasetType:Proteomics

Contact

Principal Investigators:
(in alphabetical order) 		Stephen Scherer, The Hospital for Sick Children, Canada
Submitting User: jmacdonald
Number of Files:
Total Size:
Spectra:
Subscribers:
 
Owner Reanalyses
Experimental Design
    Conditions:
    Biological Replicates:
    Technical Replicates:
 
Identification Results
    Proteins (Human, Remapped):
    Proteins (Reported):
    Peptides:
    Variant Peptides:
    PSMs:
 
Quantification Results
    Differential Proteins:
    Quantified Proteins:
 
Browse Dataset Files
 
FTP Download Link (click to copy):

Species

Instrument

Modifications

- Dataset Reanalyses

+ Dataset History

Click here to queue conversion of this dataset's submitted spectrum files to open formats (e.g. mzML). This process may take some time.

When complete, the converted files will be available in the "ccms_peak" subdirectory of the dataset's FTP space (accessible via the "FTP Download" link to the right).
Number of distinct conditions across all analyses (original submission and reanalyses) associated with this dataset.

Distinct condition labels are counted across all files submitted in the "Metadata" category having a "Condition" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct biological replicates across all analyses (original submission and reanalyses) associated with this dataset.

Distinct replicate labels are counted across all files submitted in the "Metadata" category having a "BioReplicate" or "Replicate" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct technical replicates across all analyses (original submission and reanalyses) associated with this dataset.

The technical replicate count is defined as the maximum number of times any one distinct combination of condition and biological replicate was analyzed across all files submitted in the "Metadata" category. In the case of fractionated experiments, only the first fraction is considered.

"N/A" means no results of this type were submitted.
Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

"N/A" means no results of this type were submitted.
Number of distinct protein accessions reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct unmodified peptide sequences reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct peptide sequences (including modified variants or peptidoforms) reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Total number of peptide-spectrum matches (i.e. spectrum identifications) reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct proteins quantified across all analyses (original submission and reanalyses) associated with this dataset.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct proteins found to be differentially abundant in at least one comparison across all analyses (original submission and reanalyses) associated with this dataset.

A protein is differentially abundant if its change in abundance across conditions is found to be statistically significant with an adjusted p-value <= 0.05 and lists no issues associated with statistical tests for differential abundance.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
This dataset may not contain all raw spectra data as originally deposited in PRIDE. It has been imported to MassIVE for reanalysis purposes, so its spectra data here may consist solely of processed peak lists suitable for reanalysis with most software.