MassIVE MSV000086277

Partial Public

MDCK cell line adaptation to suspension growth

Description

Dataset submission for journal publication: Label-free quantification was performed using the software Progenesis LC-MS 3.0 (Nonlinear Dynamics, Germany). LC-MS runs were aligned to an automatically selected reference run. After peak picking, a list of the features was exported and analyzed using SearchGUI (Vaudel et al. 2011). Therefore, the list was divided 15 times and analyzed using the OMSSA and X!tandem search algorithm through the Uniprot/Trembel database (2013/07) of Canis familiaris entries. Established search parameters: tryptic digest with a maximum of one missed cleavage; fixed modification: carbamidomethylation of cysteine, variable modification: oxidation of methionine; peptide charge 2plus to 4plus; monoisotopic peptide masses; peptide tolerance of 0.3 Da; MS/MS tolerance of 0.5 Da. Data were imported into Peptide-Shaker (Version 0.22.5) and corrected with a false discovery rate of 0.05 (Barsnes et al. 2011; Vaudel et al. 2011). Afterwards, result files were imported to Progenesis and protein lists with calculated protein quantities were exported to Excel. For statistical analysis of the data a Students t-Test with a p-value less then 0.05 was performed with R (Team 2008). [doi:10.25345/C5R193] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: MDCK cell ; suspension growth

Contact

Principal Investigators:
(in alphabetical order)
Sabine Pech, MPI for dynamics of complex technical systems, Germany
Submitting User: SPech
Number of Files:
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Spectra:
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Owner Reanalyses
Experimental Design
    Conditions:
    Biological Replicates:
    Technical Replicates:
 
Identification Results
    Proteins (Human, Remapped):
    Proteins (Reported):
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Quantification Results
    Differential Proteins:
    Quantified Proteins:
 
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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.

"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.