MassIVE MSV000099901

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Proteomic analysis (limited proteolysis and abundance based) of human coronavirus 229E infected immortalized human lung fibroblasts (MRC5) at 8, 16, and 24 hours post infection (whole cell lysate)

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Description

LiP assays performed on mock-infected and human coronavirus 229E-infected immortalized human lung fibroblasts (MRC5) cells (BTOL0001590). Samples were harvested at 8, 16, and 24 hours post infection (HCoV-299E). Samples are derived from human whole cell lysates (BTO:0004304). Mock-infected and human coronavirus 229E-infected immortalized human lung fibroblasts (MRC5) cells were collected at 8, 16, and 24 hours post infection (HCoV-299E). Cells were lysed by freeze thaw cycles and each replicate was split in half and treated for 1 minute with proteinase K and then trypsin and the other half just treated with trypsin prior to processing for proteomic analysis. The database searching was performed using FragPipe equipped with MSFragger, following the label-free quantification and match between runs (LFQ-MBR) workflow. The database search results were further processed using in-house codes which filtered and normalized the data, and added statistical parameters. [doi:10.25345/C5NP1WX8D] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: MRC5 ; LiP ; DatasetType:Proteomics

Contact

Principal Investigators:
(in alphabetical order) 		Amy Sims, Pacific Northwest National Laboratory, United States
John T. Melchior, Pacific Northwest National Laboratory, USA
Submitting User: alchemistmatt
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Number of distinct conditions across all analyses (original submission and reanalyses) associated with 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.

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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.

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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.

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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.