Proteomics

Dataset Information

0

MDCK cell line adaptation to suspension growth


ABSTRACT: 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).

INSTRUMENT(S): Q-Exactive

SUBMITTER: Sabine Pech  

PROVIDER: MSV000086277 | MassIVE | Tue Oct 13 12:54:00 BST 2020

REPOSITORIES: MassIVE

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