MassIVE MSV000092988

Partial Public

Cunjie_SLC3A2_Agilent6550_FigS3

Subscribe Comment Convert Spectra Add Reanalysis

Description

This dataset consists of 8 raw MS files, acquired on Agilent 6550 iFunnel Q-TOF MS (Agilent Inc., Santa Clara, CA) mass spectrometer operated in Data dependent acquisition (DDA) and target MS/MS mode. Code for variants with additional NXS/T sites: 255I WTseq: (N365, N381, N424, N506) 256G N273A (+1 site) 257A N273A; N355D (+2 sites) 258F N355D; N492D (+2 sites) 259J N273A; N355D; N492D (+3 sites) CJ1 D365N (-1 site) CJ2 D381N (-1 site) Cunjie Zhang did all the sample preparation, mass spectrometric acquisition and data analysis. The files are associated with a manuscript submitted for publication by Cunjie Zhang et al. SLC3A2 (4F2hc, CD98) is a single-pass transmembrane glycoprotein and acts as a disulfide-linked adaptor to the SLC7A5 and SLC7A11 exchangers which import essential amino acids and cystine while exporting Gln and Glu, respectively. Cancer cells often over-express SLC3A2, SLC7A5, SLC7A11 and the N-glycans branching, which support tumor progression by increasing mTOR signaling and mitigation of oxidative stress (ox-stress). Branched chain amino acids and mitigation of oxidative stress are also central to aging. Furthermore, the evolution of N-glycosylation sites on SLC3A adaptors and SLC7A transporters suggests a critical but poorly understood role for N-glycans. We have profiled the N-glycan structures at each site SLC3A2 (4F2hc, CD98) and analyzed their impact on trafficking, protein interactions, cellular AA balance and sensitivity to ox-stress.] James W. Dennis is the corresponding author of the manuscript; James W. Dennis should be contacted for questions on this dataset DENNIS@lunenfeld.ca This submission is associated with: Figure S3 Table S2: Site-specific N-glycan SLC3A2 endogenous Figure S3 in the paper (in addition to this README file) [doi:10.25345/C5XG9FN20] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: SLC3A2 ; N-glycan ; Cancer

Contact

Principal Investigators:
(in alphabetical order) 		Anne-Claude Gingras, LTRI, Canada
Submitting User: gingraslab
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.