MassIVE MSV000089872

Partial Public PXD035277

Volpatti_Myopathy_P124_Lumos_VS8

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Description

This dataset consists of 9 raw MS files, acquired on Orbitrap Fusion Lumos Tribrid mass spectrometer operated in Data Dependent Acquisition mode. Cells and lysates were generated by Jonathan Volpatti. Sample processing and mass spectrometry acquisition was performed by Cassandra Wong. Data analysis was performed by Cassandra Wong and Jonathan Volpatti. The files are associated with a manuscript submitted for publication by Jonathan Volpatti et al. The main goal of this paper was to understand underlying X-linked myotubular myopathies (XLMTM) disease pathomechanisms and identify potential therapies. James J. Dowling is the corresponding author of the manuscript (james.dowling@sickkids.ca); Karen Colwill should be contacted for questions on this dataset (colwill@lunenfeld.ca) This submission is associated with 3 Supplementary Files (in addition to this README file) Table 1 describes the composition of this dataset Table 2 describes all protein, peptide and PSM (peptide spectral match) evidence Table 3 describes only protein level analysis [doi:10.25345/C5416T371] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: X-linked myotubular myopathy ; Mtm1 ; VPA

Contact

Principal Investigators:
(in alphabetical order) 		Karen Colwill, LTRI, Canada
Submitting User: LTRI_proteomics

Publications

Jonathan R Volpatti 1 2, Mehdi M Ghahramani-Seno 2, Mélanie Mansat 3, Nesrin Sabha 2, Ege Sarikaya 1 2, Sarah J Goodman 2 4, Eric Chater-Diehl 2, Alper Celik 2, Emanuela Pannia 2, Carine Froment 5, Lucie Combes-Soia 5, Nika Maani 1 2, Kyoko E Yuki 2, Gaëtan Chicanne 3, Liis Uusküla-Reimand 2, Simon Monis 1 2, Sana Akhtar Alvi 2, Casie A Genetti 6, Bernard Payrastre 3 7, Alan H Beggs 6, Carsten G Bonnemann 8, Francesco Muntoni 9, Michael D Wilson 1 2 10, Rosanna Weksberg 1 2 11 12, Julien Viaud 3, James J Dowling 13 14 15 16.
X-linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition.
Acta Neuropathol . 2022 Sep;144(3):537-563. doi: 10.1007/s00401-022-02468-7. Epub 2022 Jul 17.

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Experimental Design
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Identification Results
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Quantification Results
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Species

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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.