MassIVE MSV000093178

Complete Public PXD046334

AlMismar_extracellularTurboID_VS2_VS3_2023

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Description

This dataset consists of 102 raw MS files and associated peak lists and result files, 24 acquired on a TripleTOF 6600 and 78 acquired on a TimsTOF pro mass spectrometer operated in Data Dependent Acquisition mode. Additionally, there are 6 raw files acquired on a TimsTOF pro mass spectrometer operated in Data Independent Acquisition. Sample generation, affinity purification and data analysis were done by Rasha Al Mismar. Sample acquisition was done by Rasha Al Mismar and Brendon Seale. Clones were generated by Payman Samavarchi-Tehrani and Rasha Al Mismar. The files are associated with a manuscript in Science Signaling by Al Mismar et al. that optimizes an extracellular BioID approach and identifies LDLR as an extracellular proximity partner of EGFR upon ligand stimulation. Anne-Claude Gingras is the corresponding author of the manuscript and should be contacted for questions on this dataset (gingras@lunenfeld.ca) [doi:10.25345/C5M32NM6Q] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: affinity purification ; BioID ; TurboID ; proximity dependent biotinylation ; proximal protein interaction ; plasma membrane ; extracellular space

Contact

Principal Investigators:
(in alphabetical order) 		Anne-Claude Gingras, LTRI, Canada
Submitting User: gingraslab
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Experimental Design
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Identification Results
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Quantification Results
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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.