MassIVE MSV000090947

Complete Public PXD039042

Kuzmin_Park_c4orf19_BioID_P88_2022

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Description

This dataset consists of 6 raw MS files and associated peak lists and result files, acquired on a SCIEX TripleTOF 6600 mass spectrometer operated in Data Dependent Acquisition mode. Samples were generated by Elena Kuzmin and affinity purification and mass spectrometric acquisition was performed by Kento Abe. Analysis was performed by Kento Abe and Anne-Claude Gingras. The files are associated with a manuscript submitted for publication by Kuzmin et al. This study identifies chromosome 4p as a frequently deleted region in basal breast cancer, associated with poor prognosis, evolves early during cancer progression and confers onto cells a proliferative state. Context-specific dosage sensitivity revealed genetic network rewiring maintaining large chromosomal deletions revealing a novel member of the STRIPAK complex, c4orf19. Morag Park is the corresponding author of the manuscript (morag.park@mcgill.ca); Anne-Claude Gingras should be contacted for questions on this dataset (gingras@lunenfeld.ca). [doi:10.25345/C5CJ87R1Q] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: BioID ; Proximity-dependent biotinylation ; Affinity purification ; c4orf19

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.

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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.

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.

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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.

"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.

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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.

"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.