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.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
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.
Study ID | ST003635 |
Study Title | Intracellular and supernatant metabolomes of ferroptotic Pfa1 cells using HPLC-MS/MS |
Study 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 Research Center |
Last Name | Seidel |
First Name | Eric |
Address | Joseph-Steltzmann-Str 26, 50931 Cologne, Germany |
eric.seidel@uk-koeln.de | |
Phone | +492118184372 |
Submit Date | 2024-03-25 |
Raw Data Available | Yes |
Raw Data File Type(s) | raw(Thermo) |
Analysis Type Detail | LC-MS |
Release Date | 2024-12-31 |
Release Version | 1 |
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 | Sample source |
---|---|---|---|---|
SA393778 | ES01_060_Media | 1 µM Fer 1 + 1 µM Tamoxifen | 30 h | Embryonic Fibroblasts (Pfa1) |
SA393779 | ES01_056_Media | 1 µM Fer 1 + 1 µM Tamoxifen | 30 h | Embryonic Fibroblasts (Pfa1) |
SA393780 | ES01_020_Intracell | 1 µM Fer 1 + 1 µM Tamoxifen | 30 h | Embryonic Fibroblasts (Pfa1) |
SA393781 | ES01_019_Intracell | 1 µM Fer 1 + 1 µM Tamoxifen | 30 h | Embryonic Fibroblasts (Pfa1) |
SA393782 | ES01_018_Intracell | 1 µM Fer 1 + 1 µM Tamoxifen | 30 h | Embryonic Fibroblasts (Pfa1) |
SA393783 | ES01_017_Intracell | 1 µM Fer 1 + 1 µM Tamoxifen | 30 h | Embryonic Fibroblasts (Pfa1) |
SA393784 | ES01_016_Intracell | 1 µM Fer 1 + 1 µM Tamoxifen | 30 h | Embryonic Fibroblasts (Pfa1) |
SA393785 | ES01_057_Media | 1 µM Fer 1 + 1 µM Tamoxifen | 30 h | Embryonic Fibroblasts (Pfa1) |
SA393786 | ES01_058_Media | 1 µM Fer 1 + 1 µM Tamoxifen | 30 h | Embryonic Fibroblasts (Pfa1) |
SA393787 | ES01_059_Media | 1 µM Fer 1 + 1 µM Tamoxifen | 30 h | Embryonic Fibroblasts (Pfa1) |
SA393788 | ES01_076_Media | 1 µM Fer 1 + 1 µM Tamoxifen | 48 h | Embryonic Fibroblasts (Pfa1) |
SA393789 | ES01_036_Intracell | 1 µM Fer 1 + 1 µM Tamoxifen | 48 h | Embryonic Fibroblasts (Pfa1) |
SA393790 | ES01_077_Media | 1 µM Fer 1 + 1 µM Tamoxifen | 48 h | Embryonic Fibroblasts (Pfa1) |
SA393791 | ES01_078_Media | 1 µM Fer 1 + 1 µM Tamoxifen | 48 h | Embryonic Fibroblasts (Pfa1) |
SA393792 | ES01_079_Media | 1 µM Fer 1 + 1 µM Tamoxifen | 48 h | Embryonic Fibroblasts (Pfa1) |
SA393793 | ES01_080_Media | 1 µM Fer 1 + 1 µM Tamoxifen | 48 h | Embryonic Fibroblasts (Pfa1) |
SA393794 | ES01_040_Intracell | 1 µM Fer 1 + 1 µM Tamoxifen | 48 h | Embryonic Fibroblasts (Pfa1) |
SA393795 | ES01_039_Intracell | 1 µM Fer 1 + 1 µM Tamoxifen | 48 h | Embryonic Fibroblasts (Pfa1) |
SA393796 | ES01_038_Intracell | 1 µM Fer 1 + 1 µM Tamoxifen | 48 h | Embryonic Fibroblasts (Pfa1) |
SA393797 | ES01_037_Intracell | 1 µM Fer 1 + 1 µM Tamoxifen | 48 h | Embryonic Fibroblasts (Pfa1) |
SA393798 | ES01_096_Media | 1 µM Fer 1 + 1 µM Tamoxifen | 72 h | Embryonic Fibroblasts (Pfa1) |
SA393799 | ES01_097_Media | 1 µM Fer 1 + 1 µM Tamoxifen | 72 h | Embryonic Fibroblasts (Pfa1) |
SA393800 | ES01_098_Media | 1 µM Fer 1 + 1 µM Tamoxifen | 72 h | Embryonic Fibroblasts (Pfa1) |
SA393801 | ES01_099_Media | 1 µM Fer 1 + 1 µM Tamoxifen | 72 h | Embryonic Fibroblasts (Pfa1) |
SA393802 | ES01_100_Media | 1 µM Fer 1 + 1 µM Tamoxifen | 72 h | Embryonic Fibroblasts (Pfa1) |
SA393803 | ES01_051_Media | 1 µM Fer 1 | 30 h | Embryonic Fibroblasts (Pfa1) |
SA393804 | ES01_052_Media | 1 µM Fer 1 | 30 h | Embryonic Fibroblasts (Pfa1) |
SA393805 | ES01_053_Media | 1 µM Fer 1 | 30 h | Embryonic Fibroblasts (Pfa1) |
SA393806 | ES01_054_Media | 1 µM Fer 1 | 30 h | Embryonic Fibroblasts (Pfa1) |
SA393807 | ES01_055_Media | 1 µM Fer 1 | 30 h | Embryonic Fibroblasts (Pfa1) |
SA393808 | ES01_015_Intracell | 1 µM Fer 1 | 30 h | Embryonic Fibroblasts (Pfa1) |
SA393809 | ES01_011_Intracell | 1 µM Fer 1 | 30 h | Embryonic Fibroblasts (Pfa1) |
SA393810 | ES01_014_Intracell | 1 µM Fer 1 | 30 h | Embryonic Fibroblasts (Pfa1) |
SA393811 | ES01_013_Intracell | 1 µM Fer 1 | 30 h | Embryonic Fibroblasts (Pfa1) |
SA393812 | ES01_012_Intracell | 1 µM Fer 1 | 30 h | Embryonic Fibroblasts (Pfa1) |
SA393813 | ES01_073_Media | 1 µM Fer 1 | 48 h | Embryonic Fibroblasts (Pfa1) |
SA393814 | ES01_075_Media | 1 µM Fer 1 | 48 h | Embryonic Fibroblasts (Pfa1) |
SA393815 | ES01_074_Media | 1 µM Fer 1 | 48 h | Embryonic Fibroblasts (Pfa1) |
SA393816 | ES01_072_Media | 1 µM Fer 1 | 48 h | Embryonic Fibroblasts (Pfa1) |
SA393817 | ES01_035_Intracell | 1 µM Fer 1 | 48 h | Embryonic Fibroblasts (Pfa1) |
SA393818 | ES01_034_Intracell | 1 µM Fer 1 | 48 h | Embryonic Fibroblasts (Pfa1) |
SA393819 | ES01_033_Intracell | 1 µM Fer 1 | 48 h | Embryonic Fibroblasts (Pfa1) |
SA393820 | ES01_032_Intracell | 1 µM Fer 1 | 48 h | Embryonic Fibroblasts (Pfa1) |
SA393821 | ES01_031_Intracell | 1 µM Fer 1 | 48 h | Embryonic Fibroblasts (Pfa1) |
SA393822 | ES01_071_Media | 1 µM Fer 1 | 48 h | Embryonic Fibroblasts (Pfa1) |
SA393823 | ES01_092_Media | 1 µM Fer 1 | 72 h | Embryonic Fibroblasts (Pfa1) |
SA393824 | ES01_093_Media | 1 µM Fer 1 | 72 h | Embryonic Fibroblasts (Pfa1) |
SA393825 | ES01_094_Media | 1 µM Fer 1 | 72 h | Embryonic Fibroblasts (Pfa1) |
SA393826 | ES01_095_Media | 1 µM Fer 1 | 72 h | Embryonic Fibroblasts (Pfa1) |
SA393827 | ES01_091_Media | 1 µM Fer 1 | 72 h | Embryonic Fibroblasts (Pfa1) |
SA393828 | ES01_046_Media | 1 µM Tamoxifen | 30 h | Embryonic Fibroblasts (Pfa1) |
SA393829 | ES01_050_Media | 1 µM Tamoxifen | 30 h | Embryonic Fibroblasts (Pfa1) |
SA393830 | ES01_049_Media | 1 µM Tamoxifen | 30 h | Embryonic Fibroblasts (Pfa1) |
SA393831 | ES01_048_Media | 1 µM Tamoxifen | 30 h | Embryonic Fibroblasts (Pfa1) |
SA393832 | ES01_047_Media | 1 µM Tamoxifen | 30 h | Embryonic Fibroblasts (Pfa1) |
SA393833 | ES01_010_Intracell | 1 µM Tamoxifen | 30 h | Embryonic Fibroblasts (Pfa1) |
SA393834 | ES01_009_Intracell | 1 µM Tamoxifen | 30 h | Embryonic Fibroblasts (Pfa1) |
SA393835 | ES01_008_Intracell | 1 µM Tamoxifen | 30 h | Embryonic Fibroblasts (Pfa1) |
SA393836 | ES01_007_Intracell | 1 µM Tamoxifen | 30 h | Embryonic Fibroblasts (Pfa1) |
SA393837 | ES01_006_Intracell | 1 µM Tamoxifen | 30 h | Embryonic Fibroblasts (Pfa1) |
SA393838 | ES01_067_Media | 1 µM Tamoxifen | 48 h | Embryonic Fibroblasts (Pfa1) |
SA393839 | ES01_070_Media | 1 µM Tamoxifen | 48 h | Embryonic Fibroblasts (Pfa1) |
SA393840 | ES01_069_Media | 1 µM Tamoxifen | 48 h | Embryonic Fibroblasts (Pfa1) |
SA393841 | ES01_068_Media | 1 µM Tamoxifen | 48 h | Embryonic Fibroblasts (Pfa1) |
SA393842 | ES01_027_Intracell | 1 µM Tamoxifen | 48 h | Embryonic Fibroblasts (Pfa1) |
SA393843 | ES01_066_Media | 1 µM Tamoxifen | 48 h | Embryonic Fibroblasts (Pfa1) |
SA393844 | ES01_029_Intracell | 1 µM Tamoxifen | 48 h | Embryonic Fibroblasts (Pfa1) |
SA393845 | ES01_030_Intracell | 1 µM Tamoxifen | 48 h | Embryonic Fibroblasts (Pfa1) |
SA393846 | ES01_026_Intracell | 1 µM Tamoxifen | 48 h | Embryonic Fibroblasts (Pfa1) |
SA393847 | ES01_028_Intracell | 1 µM Tamoxifen | 48 h | Embryonic Fibroblasts (Pfa1) |
SA393848 | ES01_090_Media | 1 µM Tamoxifen | 72 h | Embryonic Fibroblasts (Pfa1) |
SA393849 | ES01_089_Media | 1 µM Tamoxifen | 72 h | Embryonic Fibroblasts (Pfa1) |
SA393850 | ES01_088_Media | 1 µM Tamoxifen | 72 h | Embryonic Fibroblasts (Pfa1) |
SA393851 | ES01_087_Media | 1 µM Tamoxifen | 72 h | Embryonic Fibroblasts (Pfa1) |
SA393852 | ES01_086_Media | 1 µM Tamoxifen | 72 h | Embryonic Fibroblasts (Pfa1) |
SA393853 | ES01_PoolB10_Media | Pooled Samples | Pooled Samples | Embryonic Fibroblasts (Pfa1) |
SA393854 | ES01_PoolB9_Media | Pooled Samples | Pooled Samples | Embryonic Fibroblasts (Pfa1) |
SA393855 | ES01_PoolB11_Media | Pooled Samples | Pooled Samples | Embryonic Fibroblasts (Pfa1) |
SA393856 | ES01_PoolA1_Intracell | Pooled Samples | Pooled Samples | Embryonic Fibroblasts (Pfa1) |
SA393857 | ES01_PoolB4_Media | Pooled Samples | Pooled Samples | Embryonic Fibroblasts (Pfa1) |
SA393858 | ES01_PoolB5_Media | Pooled Samples | Pooled Samples | Embryonic Fibroblasts (Pfa1) |
SA393859 | ES01_PoolB6_Media | Pooled Samples | Pooled Samples | Embryonic Fibroblasts (Pfa1) |
SA393860 | ES01_PoolA2_Intracell | Pooled Samples | Pooled Samples | Embryonic Fibroblasts (Pfa1) |
SA393861 | ES01_PoolA6_Intracell | Pooled Samples | Pooled Samples | Embryonic Fibroblasts (Pfa1) |
SA393862 | ES01_PoolA3_Intracell | Pooled Samples | Pooled Samples | Embryonic Fibroblasts (Pfa1) |
SA393863 | ES01_PoolA4_Intracell | Pooled Samples | Pooled Samples | Embryonic Fibroblasts (Pfa1) |
SA393864 | ES01_PoolA5_Intracell | Pooled Samples | Pooled Samples | Embryonic Fibroblasts (Pfa1) |
SA393865 | ES01_PoolB7_Media | Pooled Samples | Pooled Samples | Embryonic Fibroblasts (Pfa1) |
SA393866 | ES01_PoolB3_Media | Pooled Samples | Pooled Samples | Embryonic Fibroblasts (Pfa1) |
SA393867 | ES01_PoolB2_Media | Pooled Samples | Pooled Samples | Embryonic Fibroblasts (Pfa1) |
SA393868 | ES01_PoolB1_Media | Pooled Samples | Pooled Samples | Embryonic Fibroblasts (Pfa1) |
SA393869 | ES01_PoolB0_Media | Pooled Samples | Pooled Samples | Embryonic Fibroblasts (Pfa1) |
SA393870 | ES01_PoolA11_Intracell | Pooled Samples | Pooled Samples | Embryonic Fibroblasts (Pfa1) |
SA393871 | ES01_PoolA0_Intracell | Pooled Samples | Pooled Samples | Embryonic Fibroblasts (Pfa1) |
SA393872 | ES01_PoolB8_Media | Pooled Samples | Pooled Samples | Embryonic Fibroblasts (Pfa1) |
SA393873 | ES01_PoolA10_Intracell | Pooled Samples | Pooled Samples | Embryonic Fibroblasts (Pfa1) |
SA393874 | ES01_PoolA9_Intracell | Pooled Samples | Pooled Samples | Embryonic Fibroblasts (Pfa1) |
SA393875 | ES01_PoolA8_Intracell | Pooled Samples | Pooled Samples | Embryonic Fibroblasts (Pfa1) |
SA393876 | ES01_PoolA7_Intracell | Pooled Samples | Pooled Samples | Embryonic Fibroblasts (Pfa1) |
SA393877 | ES01_001_Intracell | Untreated | 30 h | Embryonic Fibroblasts (Pfa1) |
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. |
Combined analysis:
Analysis ID | AN005968 |
---|---|
Analysis type | MS |
Chromatography type | HILIC |
Chromatography system | Vanquish Horizon UHPLC |
Column | Merck SeQuant ZIC-HILIC (150 x 2.1mm,5um) |
MS Type | ESI |
MS instrument type | Orbitrap |
MS instrument name | Thermo Orbitrap Exploris 240 |
Ion Mode | UNSPECIFIED |
Units | Peak area |
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 |
MS:
MS ID: | MS005681 |
Analysis ID: | AN005968 |
Instrument Name: | Thermo Orbitrap Exploris 240 |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | Data acquisition of experimental samples was performed in full scan mode with polarity switching. The spray voltages were set to +3.5kV/-2.8 kV, RF lens value at 70, the heated capillary held at 320°C, and the auxiliary gas heater held at 280 °C. The flow rate for sheath gas, aux gas and sweep gas were set to 40, 15 and 0, respectively. For MS1 scans, mass range was set to m/z=70-900, AGC target set to standard and maximum injection time (IT) set to auto. Data acquisition for experimental samples used full scan mode with polarity switching at an Orbitrap resolution of 120000. Data acquisition for untargeted metabolite identification was performed using the AcquireX Deep Scan workflow, an iterative data-dependent acquisition (DDA) strategy using multiple injections of the pooled sample. |
Ion Mode: | UNSPECIFIED |