MassIVE MSV000095375

Complete Public PXD054048

Ahmed_LINC00324_timsTOFPro2_P124_VS18_VS19

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Description

This dataset consists of 12 raw MS files and associated peak lists and results files, acquired on a timsTOF Pro 2 mass spectrometer. Six files were acquired in Data Dependent Acquisition mode and six were acquired in Data Independent Acquisition mode. Samples were generated by Sameen Ahmed. Sample clean-up, digestion, and mass spectrometry acquisition were performed by Cassandra Wong. Analysis was performed by Sameen Ahmed, Philipp Maass, and Cassandra Wong. The files are associated with a manuscript submitted for publication by Sameen Ahmed et al. The main goal of this paper was to determine total protein levels in wildtype (WT) and deltaLINC00324 C-28/I2 chondrocytes. Specifically, investigated how the loss of the tRNA-overlapping lncRNA locus LINC00324 locus affected codon usage at the protein level. Philipp G. Maass is the corresponding author of the manuscript (Philipp.maass@sickkids.ca); Anne-Claude Gingras should be contacted for questions on this dataset (gingras@lunenfeld.ca) This submission is associated with 4 Supplementary Files (in addition to this README file) Table 1 describes the composition of the DDA dataset Table 2 lists all the DDA peptide identification evidence (MSFragger) Table 3 describes the composition of the DIA dataset Table 4 lists the DIA protein identifications (DIA-NN) Table 5 lists the DIA peptide identifications (DIA-NN) [doi:10.25345/C5RJ4962R] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: tROL ; LINC00324 ; codon usage

Contact

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