MassIVE MSV000092459

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GNPS - The role of norepinephrine and other metabolites on fallopian tube epithelial metastasis of ovarian cancer

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Description

DMEM, MOE SCRshRNA, MOE PTENshRNA, MOE PTENshRNAKRAS, MOE PTENshRNAp53shRNA, OVCAR8, OVCAR4 and SKOV3 conditioned media (cell-free media after 4 day incubation of cells with ovary) were collected. These conditioned media samples were lyophilized and metabolites were resuspended with 60:40 ACN:MeOH to obtain 1 mg/mL solution normalized to the dry weight of the extract. An internal standard (rifampicin, 1 uM/mL) was added to samples. Reverse-phase LC was performed on an Elute UHPLC (Bruker Daltonics) using a Phenomonex Kinetex C18 HPLC column (1.7 µm, 2.1 mm x 50 mm, 100 Å) with a sample injection volume of 2 µL. The mobile phase consisted of A (H2O with 0.1% formic acid) and B (ACN with 0.1% formic acid) with a flow rate of 0.5 mL/min. The gradient began with 5% B for 0.3 minutes and was linearly increased to 80% B over 6 minutes. The column was washed using 98% B for 1 minute, and re-equilibrated using 5% B for 1 minute. The temperature of the column oven was 40?. MS spectra were collected using a timsTOF fleX mass spectrometer (Bruker Daltonics) in positive ion mode with a mass range of 50-1000 Da and a spectra rate of 6 Hz. Prior to analysis the instrument was calibrated using 0.5 mM sodium formate. The instrument conditions were set to acquire MS and MS/MS data in separate runs, with 5 MS/MS scans for every 1 MS scan, utilizing a collision energy of 20-50 eV. DMEM, MOE SCRshRNA, MOE PTENshRNA, MOE PTENshRNAKRASG12V, MOE PTENshRNAp53R273H, OVCAR8, OVCAR4 and SKOV3 samples were analyzed in three biological replicates (N=3). [doi:10.25345/C5D795M9J] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Metabolomics ; high grade serous ovarian cancer ; cell lines

Contact

Principal Investigators:
(in alphabetical order) 		Joanna Burdette, University of Illinois at Chicago, USA
Laura Sanchez, University of California, Santa Cruz, USA
Submitting User: l2sanchez
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GNPS content goes here (MSV000092459 [task=ad54fd046e9c41afb0c4bbd28fad24b6])
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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.

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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.

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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.