MassIVE MSV000097789

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Deep single cell proteomics of the model HepG2 liver cancer cell line.

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Description

The HepG2 cell line is a model for exploring hepatotoxicity, drug metabolism and cell cycle status. Single cells were isolated in this stage of the study using a Tecan UNO system with single stage lysis/digestion in microwell plates. The resulting tryptic digests were analyzed using an EvoSep One system with peptides analyzed using diaPASEF on a TIMSTOF Ultra2 system. Please note that due to the size of this study and challenges in both size and accessioning data from novel mass analyzers, each stage of the study will be accessioned separately. This repository only contains cells analyzed using the default EvoSep 40SPD zoom method and a custom EvoSep 80SPD method where separation occurs on a 10cm x 75um x `1.9um ReproSil column. [doi:10.25345/C5RB6WF2M] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Liver cancer ; Hepatocyte ; Cell cycle ; Single cell proteomics ; DatasetType:Proteomics

Contact

Principal Investigators:
(in alphabetical order) 		Ben Orsburn, University of Pittsburgh, USA
Submitting User: ben_orsburn
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Experimental Design
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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.

"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.