MassIVE MSV000080694

Imported Reanalysis Dataset Public PXD003562

Global analysis of protein degradation rates in wildtype, Atg5-/- and Atg7-/- primary human fibroblasts

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Description

In this project, we employed a dynamic mass spectrometry-based proteomic approach to obtain global maps of basal autophagic flux in human primary fibroblasts (HCA2-hTert). The data provide a comparison of protein degradation rates between wildtype and autophagy deficient (Atg5-/- and Atg7-/-) cells. The media utilized for isotopic labeling was Eagle’s Minimum Essential Medium (ATCC) supplemented with 15% dialyzed fetal bovine serum (Thermo Scientific), 100U/mL penicillin, 100U/mL streptomycin. Prior to labeling, cells were gradually adapted to unlabeled media over the course of multiple passages. Cells were then plated at a density of 500,000 cells per 10 cm plate. 8 days after plating, the confluent quiescent cultures were switched to MEM labeling media for SILAC (Thermo Scientific) supplemented with L-Arginine:HCl (13C6, 99%) and L-Lysine:2HCl (13C6, 99%)(Cambridge Isotope Laboratories) at concentrations of 0.1264 g/L and 0.087 g/L and 15% dialyzed fetal bovine serum (Thermo scientific). Cells were collected after 0d, 2d, 4d, 6d of labeling, washed with PBS and cell pellets were frozen prior to further analysis. In order to assess the precision of our measurements, biological replicate experiments were conducted for WT+vector and Atg5-/- experiments and cells were collected after 4d for analysis [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: autophagy ; Atg5 ; Atg7 ; human primary fibroblasts ; protein degradation rates

Contact

Principal Investigators:
(in alphabetical order) 		Sina Ghaemmaghami, Department of Biology, University of Rochester, NY, USA, N/A
Submitting User: ccms

Publications

Zhang T, Shen S, Qu J, Ghaemmaghami S.
Global Analysis of Cellular Protein Flux Quantifies the Selectivity of Basal Autophagy.
Cell Rep. 2016 Mar 15;14(10):2426-39. Epub 2016 Mar 3.

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Identification Results
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When complete, the converted files will be available in the "ccms_peak" subdirectory of the dataset's FTP space (accessible via the "FTP Download" link to the right).
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.