MassIVE MSV000093705

Complete Public PXD048043

Schreiber_2023_VS1_Exploring options for proximity-dependent biotinylation experiments

Description

This dataset consists of 52 raw mass spectrometry files and associated peak lists and results files, acquired on a Thermo Orbitrap Exploris 480 operated in Data-Dependent Acquisition mode. Samples were generated by Karl Schreiber (clones were generated by Eileigh Kadijk and Karl Schreiber) and affinity purification and mass spectrometric acquisition were performed by Karl Schreiber. Analysis was performed by Karl Schreiber and Ji-Young Youn. The files are associated with a manuscript by Karl Schreiber et al. that evaluates different labeling enzymes and affinity resins for proximity-dependent biotinylation experiments. Ji-Young Youn is the corresponding author for the manuscript and should be contacted for questions regarding this dataset (jiyoung.youn@sickkids.ca). This submission is associated with three Supplementary Files (in addition to this README file): Table I describes the composition of this dataset (sample information) Table II lists all the peptide identification evidence (per MSFragger) Table III lists the SAINTexpress interactions for all analyses performed [doi:10.25345/C5CV4C30Z] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: proximity-dependent biotinylation, BioID, miniTurbo, APEX2, TDP-43, TARDBP, Streptavidin Sepharose, MagResyn MS, SAINTexpress, proximal interactions

Contact

Principal Investigators:
(in alphabetical order)
Ji-Young Youn, Hospital for Sick Children, Canada
Submitting User: Younlab_Toronto
Number of Files:
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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:
 
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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.