MassIVE MSV000088904

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Proteome Alterations during Clonal Isolation of Human Pancreatic Cancer Cell Lines

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Description

Starting from an initial cell culture (Reference), three human pancreatic cancer cell lines (MIA PaCa-2, AsPC-1 and PANC-1) were either maintained by standard cell culture (Standard) or underwent clonal isolation to obtain single-cell colonies (SCC). Emerging cell pellets of five replicates per condition were subjected to proteomic sample preparation with subsequent isobaric peptide labelling with tandem mass tags (TMTpro-16plex; leaving one channel empty). All samples of one cell line were pooled and subjected to high-pH fractionation, resulting in 12 fractions which were subsequently analyzed via explorative mass spectrometry. [doi:10.25345/C5QB9V68S] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Clonal Isolation ; Single-Cell Isolation ; Limiting Dilution ; Explorative Proteomics ; TMTpro-16plex ; FACS

Contact

Principal Investigators:
(in alphabetical order) 		Prof. Oliver Schilling, Institute for Surgical Pathology, University Medical Center Freiburg, Germany
Submitting User: PatrickBernhard

Publications

Bernhard P, Feilen T, Rogg M, Fröhlich K, Cosenza-Contreras M, Hause F, Schell C, Schilling O.
Proteome alterations during clonal isolation of established human pancreatic cancer cell lines.
Cell Mol Life Sci. 2022 Oct 22;79(11):561. Epub 2022 Oct 22.

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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.

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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.

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.

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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.