MassIVE MSV000086786

Partial Public PXD023918

BioID mass spectrometry analysis of proteins proximal to human NERCLIN

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Description

To gain insight into the function of NERCLIN in human cells, we analyzed its proximal proteins by the proximity-dependent biotin identification (BioID) approach. 143B cells were transfected with fusion constructs using jetPRIME. Following 24 h of transfection, biotin was added to each plate and allowed to biotinylate the proximal proteins for the next 24 h. The plates were washed with PBS, cells were scraped, pelleted and frozen. For each sample, four biological replicates were analyzed. Liquid chromatography mass spectrometry analysis was performed on an Orbitrap Elite ETD mass spectrometer (Thermo Scientific) using the Xcalibur version 2.7.1 coupled to a Thermo Scientific nLCII nanoflow system. The mass spec analysis was done in technical duplicates. Thermo.RAW files were searched with Proteome Discoverer 1.4 (Thermo Scientific) against SEQUEST search engine. The search parameters were taken from. All reported data were based on high confidence peptides assigned in Proteome Discoverer with a 0.01% FDR by Percolator. Control samples (GFP and AIF) and Contaminant Repository for Affinity Purification database were used to identify high confidence interactors of NERCLIN based on the spectral counts. [doi:10.25345/C5D792] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Human, 143B cells, NERCLIN, mitochondria

Contact

Principal Investigators:
(in alphabetical order) 		Markku Varjosalo, University of Helsinki, Finland
Svetlana Konovalova, University of Helsinki, Finland
Submitting User: skonoval
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Identification 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.

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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.

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Number of distinct technical replicates across all analyses (original submission and reanalyses) associated with this dataset.

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Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

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Number of distinct protein accessions reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct unmodified peptide sequences reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct peptide sequences (including modified variants or peptidoforms) reported across all analyses (original submission and reanalyses) associated with this dataset.

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Total number of peptide-spectrum matches (i.e. spectrum identifications) reported across all analyses (original submission and reanalyses) associated with this dataset.

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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.

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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.