Summary of Study ST003635

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR002248. The data can be accessed directly via it's Project DOI: 10.21228/M8224Q This work is supported by NIH grant, U2C- DK119886.

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This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST003635
Study TitleIntracellular and supernatant metabolomes of ferroptotic Pfa1 cells using HPLC-MS/MS
Study SummaryIn order to investigate metabolites both secreted from and enriched in cells upon ferroptotic cell death, we compared metabolomes from supernatants and lysates of ferroptotic to nonferroptotic Pfa1 cells after 24 h(cells are alive), 30 h (ferroptosis is present) as well as supernatants after 72 h (no cells left). In Pfa1 cells, ferroptosis is induced upon treatment with tamoxifen which induces knock-out of GPX4, causing massive ferroptosis. Ferroptosis, in turn, was rescued using lipid ros scavenger FER-1 (Ferrostatin1).
Institute
CECAD Research Center
Last NameSeidel
First NameEric
AddressJoseph-Steltzmann-Str 26, 50931 Cologne, Germany
Emaileric.seidel@uk-koeln.de
Phone+492118184372
Submit Date2024-03-25
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2024-12-31
Release Version1
Eric Seidel Eric Seidel
https://dx.doi.org/10.21228/M8224Q
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR002248
Project DOI:doi: 10.21228/M8224Q
Project Title:Intracellular and supernatant metabolomes of ferroptotic Pfa1 cells using HPLC-MS/MS
Project Summary:In order to investigate metabolites both secreted from and enriched in cells upon ferroptotic cell death, we compared metabolomes from supernatants and lysates of ferroptotic to nonferroptotic Pfa1 cells after 24 h(cells are alive), 30 h (ferroptosis is present) as well as supernatants after 72 h (no cells left). In Pfa1 cells, ferroptosis is induced upon treatment with tamoxifen which induces knock-out of GPX4, causing massive ferroptosis. Ferroptosis, in turn, was rescued using lipid ros scavenger FER-1 (Ferrostatin1).
Institute:Cecad
Last Name:Seidel
First Name:Eric
Address:Joseph-Stelzmann-Str. 26, Cologne, NRW, D-50931, Germany
Email:eric.seidel@uk-koeln.de
Phone:+4902118184372

Subject:

Subject ID:SU003765
Subject Type:Cultured cells
Subject Species:Mus musculus
Taxonomy ID:10090

Factors:

Subject type: Cultured cells; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Treatment Time point
SA393778ES01_060_Media1 µM Fer 1 + 1 µM Tamoxifen 30 h
SA393779ES01_056_Media1 µM Fer 1 + 1 µM Tamoxifen 30 h
SA393780ES01_020_Intracell1 µM Fer 1 + 1 µM Tamoxifen 30 h
SA393781ES01_019_Intracell1 µM Fer 1 + 1 µM Tamoxifen 30 h
SA393782ES01_018_Intracell1 µM Fer 1 + 1 µM Tamoxifen 30 h
SA393783ES01_017_Intracell1 µM Fer 1 + 1 µM Tamoxifen 30 h
SA393784ES01_016_Intracell1 µM Fer 1 + 1 µM Tamoxifen 30 h
SA393785ES01_057_Media1 µM Fer 1 + 1 µM Tamoxifen 30 h
SA393786ES01_058_Media1 µM Fer 1 + 1 µM Tamoxifen 30 h
SA393787ES01_059_Media1 µM Fer 1 + 1 µM Tamoxifen 30 h
SA393788ES01_076_Media1 µM Fer 1 + 1 µM Tamoxifen 48 h
SA393789ES01_036_Intracell1 µM Fer 1 + 1 µM Tamoxifen 48 h
SA393790ES01_077_Media1 µM Fer 1 + 1 µM Tamoxifen 48 h
SA393791ES01_078_Media1 µM Fer 1 + 1 µM Tamoxifen 48 h
SA393792ES01_079_Media1 µM Fer 1 + 1 µM Tamoxifen 48 h
SA393793ES01_080_Media1 µM Fer 1 + 1 µM Tamoxifen 48 h
SA393794ES01_040_Intracell1 µM Fer 1 + 1 µM Tamoxifen 48 h
SA393795ES01_039_Intracell1 µM Fer 1 + 1 µM Tamoxifen 48 h
SA393796ES01_038_Intracell1 µM Fer 1 + 1 µM Tamoxifen 48 h
SA393797ES01_037_Intracell1 µM Fer 1 + 1 µM Tamoxifen 48 h
SA393798ES01_096_Media1 µM Fer 1 + 1 µM Tamoxifen 72 h
SA393799ES01_097_Media1 µM Fer 1 + 1 µM Tamoxifen 72 h
SA393800ES01_098_Media1 µM Fer 1 + 1 µM Tamoxifen 72 h
SA393801ES01_099_Media1 µM Fer 1 + 1 µM Tamoxifen 72 h
SA393802ES01_100_Media1 µM Fer 1 + 1 µM Tamoxifen 72 h
SA393803ES01_051_Media1 µM Fer 1 30 h
SA393804ES01_052_Media1 µM Fer 1 30 h
SA393805ES01_053_Media1 µM Fer 1 30 h
SA393806ES01_054_Media1 µM Fer 1 30 h
SA393807ES01_055_Media1 µM Fer 1 30 h
SA393808ES01_015_Intracell1 µM Fer 1 30 h
SA393809ES01_011_Intracell1 µM Fer 1 30 h
SA393810ES01_014_Intracell1 µM Fer 1 30 h
SA393811ES01_013_Intracell1 µM Fer 1 30 h
SA393812ES01_012_Intracell1 µM Fer 1 30 h
SA393813ES01_073_Media1 µM Fer 1 48 h
SA393814ES01_075_Media1 µM Fer 1 48 h
SA393815ES01_074_Media1 µM Fer 1 48 h
SA393816ES01_072_Media1 µM Fer 1 48 h
SA393817ES01_035_Intracell1 µM Fer 1 48 h
SA393818ES01_034_Intracell1 µM Fer 1 48 h
SA393819ES01_033_Intracell1 µM Fer 1 48 h
SA393820ES01_032_Intracell1 µM Fer 1 48 h
SA393821ES01_031_Intracell1 µM Fer 1 48 h
SA393822ES01_071_Media1 µM Fer 1 48 h
SA393823ES01_092_Media1 µM Fer 1 72 h
SA393824ES01_093_Media1 µM Fer 1 72 h
SA393825ES01_094_Media1 µM Fer 1 72 h
SA393826ES01_095_Media1 µM Fer 1 72 h
SA393827ES01_091_Media1 µM Fer 1 72 h
SA393828ES01_046_Media1 µM Tamoxifen 30 h
SA393829ES01_050_Media1 µM Tamoxifen 30 h
SA393830ES01_049_Media1 µM Tamoxifen 30 h
SA393831ES01_048_Media1 µM Tamoxifen 30 h
SA393832ES01_047_Media1 µM Tamoxifen 30 h
SA393833ES01_010_Intracell1 µM Tamoxifen 30 h
SA393834ES01_009_Intracell1 µM Tamoxifen 30 h
SA393835ES01_008_Intracell1 µM Tamoxifen 30 h
SA393836ES01_007_Intracell1 µM Tamoxifen 30 h
SA393837ES01_006_Intracell1 µM Tamoxifen 30 h
SA393838ES01_067_Media1 µM Tamoxifen 48 h
SA393839ES01_070_Media1 µM Tamoxifen 48 h
SA393840ES01_069_Media1 µM Tamoxifen 48 h
SA393841ES01_068_Media1 µM Tamoxifen 48 h
SA393842ES01_027_Intracell1 µM Tamoxifen 48 h
SA393843ES01_066_Media1 µM Tamoxifen 48 h
SA393844ES01_029_Intracell1 µM Tamoxifen 48 h
SA393845ES01_030_Intracell1 µM Tamoxifen 48 h
SA393846ES01_026_Intracell1 µM Tamoxifen 48 h
SA393847ES01_028_Intracell1 µM Tamoxifen 48 h
SA393848ES01_090_Media1 µM Tamoxifen 72 h
SA393849ES01_089_Media1 µM Tamoxifen 72 h
SA393850ES01_088_Media1 µM Tamoxifen 72 h
SA393851ES01_087_Media1 µM Tamoxifen 72 h
SA393852ES01_086_Media1 µM Tamoxifen 72 h
SA393853ES01_PoolB10_MediaPooled Samples Pooled Samples
SA393854ES01_PoolB9_MediaPooled Samples Pooled Samples
SA393855ES01_PoolB11_MediaPooled Samples Pooled Samples
SA393856ES01_PoolA1_IntracellPooled Samples Pooled Samples
SA393857ES01_PoolB4_MediaPooled Samples Pooled Samples
SA393858ES01_PoolB5_MediaPooled Samples Pooled Samples
SA393859ES01_PoolB6_MediaPooled Samples Pooled Samples
SA393860ES01_PoolA2_IntracellPooled Samples Pooled Samples
SA393861ES01_PoolA6_IntracellPooled Samples Pooled Samples
SA393862ES01_PoolA3_IntracellPooled Samples Pooled Samples
SA393863ES01_PoolA4_IntracellPooled Samples Pooled Samples
SA393864ES01_PoolA5_IntracellPooled Samples Pooled Samples
SA393865ES01_PoolB7_MediaPooled Samples Pooled Samples
SA393866ES01_PoolB3_MediaPooled Samples Pooled Samples
SA393867ES01_PoolB2_MediaPooled Samples Pooled Samples
SA393868ES01_PoolB1_MediaPooled Samples Pooled Samples
SA393869ES01_PoolB0_MediaPooled Samples Pooled Samples
SA393870ES01_PoolA11_IntracellPooled Samples Pooled Samples
SA393871ES01_PoolA0_IntracellPooled Samples Pooled Samples
SA393872ES01_PoolB8_MediaPooled Samples Pooled Samples
SA393873ES01_PoolA10_IntracellPooled Samples Pooled Samples
SA393874ES01_PoolA9_IntracellPooled Samples Pooled Samples
SA393875ES01_PoolA8_IntracellPooled Samples Pooled Samples
SA393876ES01_PoolA7_IntracellPooled Samples Pooled Samples
SA393877ES01_001_IntracellUntreated 30 h
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Collection:

Collection ID:CO003758
Collection Summary:Cells and supernatants after treatment as described in the treatment summary were collected after 24 h (cells + supernatant), 48 h (cells + supernatant) and 72 h (supernatant only). For collection, supernatant samples were centrifuged at full speed and 4°C for 5 min, in order to clear supernatants. Cells were washed twice with ice-cold PBS. Directly after collection, samples were prepared as described in the sample prep summary.
Sample Type:Mouse Embryonic Fibroblasts

Treatment:

Treatment ID:TR003774
Treatment Summary:For metabolomics analysis of ferroptotic supernatants, Pfa1 cells were seeded on 6 well plates in presence of DMSO, 1 µM tamoxifen, 1 µM Fer1 or 1 µM Tamoxifen and 1 µM Fer1(25.000 cells per well; pentaplicates per condition) for 24, 48 and 72 h.

Sample Preparation:

Sampleprep ID:SP003772
Sampleprep Summary:Cleared supernatants (50 µL) were added to 350 µL ice-cold extraction solution (50% methanol, 30% acetonitrile (both from Fisher Scientific), 20% ultrapure water, 5 µM valine-d8 (CK isotopes) on dry ice. Cells were incubated in 100 µL extraction solution for 20 min in a dry ice/methanol bath followed by scraping. Afterwards, supernatants and cell samples were then stirred vigorously in a thermomixer at full speed and 4°C followed by 20 min centrifugation at 4°C and full speed.

Chromatography:

Chromatography ID:CH004534
Instrument Name:Vanquish Horizon UHPLC
Column Name:Merck SeQuant ZIC-HILIC (150 x 2.1mm,5um)
Column Temperature:40°C
Flow Gradient:0–2 min: 80% B; 2-17 min: linear gradient from 80% B to 20% B; 17-17.1 min: linear gradient from 20% B to 80% B; 17.1-23 min: hold at 80% B
Flow Rate:0.2 mL/min
Solvent A:100% Water; 20 mM ammonium carbonate, 0.05% ammonium hydroxide
Solvent B:100% Acetonitrile
Chromatography Type:HILIC

Analysis:

Analysis ID:AN005968
Analysis Type:MS
Chromatography ID:CH004534
Num Factors:13
Num Metabolites:127
Units:Peak area
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