MassIVE MSV000084658

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Gonatopoulos-Pournatzis _eIF4Gmicroexon_P105_Lumos

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Description

A This dataset consists of 24 raw MS files, acquired on Orbitrap Fusion Lumos Tribrid mass spectrometer operated in Data Dependent Acquisition mode. B Mouse samples were generated by Thomas Gonatopoulos-Pournatzis. Proteomics sample preparation and mass spectrometric acquisition was performed by Shen Zhang. Analysis was performed by Shen Zhang and Robert J. Weatheritt. C The files are associated with a manuscript submitted for publication by Thomas Gonatopoulos-Pournatzis et al. The main goal of this paper was to reveal a critical role for alternative splicing in the functional specialization of the translational machinery, and further uncover an autism-disrupted mechanism by which microexons reprogram the synaptic proteome to control neuronal activity and higher-order cognitive functions. D Benjamin J. Blencowe (b.blencowe@utoronto.ca), Sabine P. Cordes (cordes@lunenfeld.ca) and Thomas Gonatopoulos-Pournatzis (thomas.gonatopoulos@utoronto.ca) are the corresponding authors of the manuscript; Anne-Claude Gingras should be contacted for questions on this dataset (gingras@lunenfeld.ca). This submission is associated with 2 Supplementary Files (in addition to this README file) Table 1 describes the composition of this dataset Table 2 lists all the protein and peptide identification evidence [doi:10.25345/C57T1B] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: iTRAQ ; eIF4G ; microexon ; Autism ; global proteomics

Contact

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

Publications

Thomas Gonatopoulos-Pournatzis 1, Rieko Niibori 2, Eric W Salter 3, Robert J Weatheritt 4, Brian Tsang 5, Shaghayegh Farhangmehr 6, Xinyi Liang 7, Ulrich Braunschweig 8, Jonathan Roth 9, Shen Zhang 2, Tyler Henderson 10, Eesha Sharma 6, Mathieu Quesnel-Vallières 6, Jon Permanyer 11, Stefan Maier 2, John Georgiou 2, Manuel Irimia 12, Nahum Sonenberg 13, Julie D Forman-Kay 5, Anne-Claude Gingras 10, Graham L Collingridge 14, Melanie A Woodin 7, Sabine P Cordes 15, Benjamin J Blencowe 16.
Autism-Misregulated eIF4G Microexons Control Synaptic Translation and Higher Order Cognitive Functions.
Mol Cell . 2020 Mar 19;77(6):1176-1192.e16. doi: 10.1016/j.molcel.2020.01.006. Epub 2020 Jan 29.

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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.

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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.