Summary of Study ST004421

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 PR002792. The data can be accessed directly via it's Project DOI: 10.21228/M8RV8C This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php

Study ID	ST004421
Study Title	Comparative lipidomics of iPSC-derived microglia protocols reveal lipid droplet and immune differences mediated by media composition
Study Summary	In this study, we have compared the lipid composition of iPSC-derived microglia generated using a classical EB-based method and an iTF-based method. TG are strongly increased in iTF microglia due to the absence of a media supplement (B-27). Supplementing iTF microglia with B-27, or its component L-carnitine, reduces TG and promotes a homeostatic state. B-27 also renders iTF microglia metabolically responsive to immune stimuli. Overall, our data show that iMGL differentiation methods have a major impact on microglial lipidomes and warrant attention when studying AD and neuroinflammatory processes involving lipids.
Institute	VU Amsterdam
Department	Department of Functional Genomics, CNCR
Laboratory	Dementia discovery group
Last Name	van der Kant
First Name	Rik
Address	De Boelelaan 1100, Amsterdam, North-Holland, 1081HZ, Netherlands
Email	r.h.n.vander.kant@vu.nl
Phone	+31205981809
Submit Date	2025-12-03
Raw Data Available	Yes
Raw Data File Type(s)	mzML
Analysis Type Detail	MS(Dir. Inf.)
Release Date	2026-01-08
Release Version	1

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Project:

Project ID:	PR002792
Project DOI:	doi: 10.21228/M8RV8C
Project Title:	Lipidomic analysis of iPSC-derived microglia models
Project Summary:	Altered microglial lipid metabolism is heavily implicated in Alzheimer’s disease (AD) and ageing. Recently, protocols were developed to generate human induced pluripotent stem cell-derived microglia-like cells (iMGL) to study microglial function in vitro, including embryoid body-based methods and transcription factor-dependent (iTF) approaches. Here, we performed comparative lipidomics on iMGL from these methods and report major differences in multiple lipid classes including triglycerides (TG), a storage form of fatty acids implicated in microglial reactivity. We compared the lipid composition of iPSC-derived microglia generated using a classical EB-based method and an iTF-based method.
Institute:	VU Amsterdam
Department:	Department of Functional Genomics, CNCR
Laboratory:	Dementia discovery group
Last Name:	van der Kant
First Name:	Rik
Address:	De Boelelaan 1100, Amsterdam, North-Holland, 1081HZ, Netherlands
Email:	r.h.n.vander.kant@vu.nl
Phone:	+31205981809

Subject:

Subject ID:	SU004581
Subject Type:	Cultured cells
Subject Species:	Homo sapiens
Taxonomy ID:	9606

Factors:

Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id	local_sample_id	Genotype	Sample source
SA522382	NLA_2023_007 - Blank2	N/A	Blank
SA522383	NB_2025_015 - Blank_3	N/A	Blank
SA522384	NB_2025_015 - Blank_2	N/A	Blank
SA522385	NB_2025_015 - Blank_1	N/A	Blank
SA522386	NB_2024_039 - Blank_4	N/A	Blank
SA522387	NB_2024_039 - Blank_3	N/A	Blank
SA522388	NB_2024_039 - Blank_2	N/A	Blank
SA522389	NB_2024_039 - Blank_1	N/A	Blank
SA522390	NLA_2023_007 - Blank1	N/A	Blank
SA522391	NB_2025_015 - Blank_5	N/A	Blank
SA522392	NB_2024_029 - Blank_4_2	N/A	Blank
SA522393	NB_2024_029 - Blank_3_2	N/A	Blank
SA522394	NB_2024_029 - Blank_2_2	N/A	Blank
SA522395	NB_2024_029 - Blank_1_2	N/A	Blank
SA522396	NB_2024_029 - Blank_3_1	N/A	Blank
SA522397	NB_2024_029 - Blank_2_1	N/A	Blank
SA522398	NB_2024_029 - Blank_1_1	N/A	Blank
SA522399	NB_2025_015 - Blank_4	N/A	Blank
SA522400	NB_2024_029 - Blank_4_1	N/A	Blank
SA522401	NB_2025_058 - Blank_4	N/A	Blank
SA522402	NB_2025_058 - Blank_3	N/A	Blank
SA522403	NB_2025_058 - Blank_2	N/A	Blank
SA522404	NB_2025_058 - Blank_1	N/A	Blank
SA522405	NB_2025_058 - QC_Ams_3	N/A	K-562 line
SA522406	NB_2024_029 - QC_C_3_2	N/A	K-562 line
SA522407	NB_2024_029 - QC_C_2_2	N/A	K-562 line
SA522408	NB_2024_029 - QC_C_1_2	N/A	K-562 line
SA522409	NB_2025_058 - QC_Ams_2	N/A	K-562 line
SA522410	NB_2025_015 - QC_Ams_4	N/A	K-562 line
SA522411	NB_2024_029 - QC_C_4_2	N/A	K-562 line
SA522412	NB_2025_058 - QC_C1_1	N/A	K-562 line
SA522413	NB_2024_029 - QC_C_4_1	N/A	K-562 line
SA522414	NB_2024_029 - QC_C_2_1	N/A	K-562 line
SA522415	NB_2024_029 - QC_C_1_1	N/A	K-562 line
SA522416	NB_2025_058 - QC_C1_2	N/A	K-562 line
SA522417	NB_2025_058 - QC_C1_3	N/A	K-562 line
SA522418	NB_2025_058 - QC_C1_4	N/A	K-562 line
SA522419	NB_2025_015 - QC_Ams_3	N/A	K-562 line
SA522420	NB_2025_058 - QC_Ams_4	N/A	K-562 line
SA522421	NB_2024_029 - QC_C_3_1	N/A	K-562 line
SA522422	NB_2025_058 - QC_Ams_1	N/A	K-562 line
SA522423	NB_2025_015 - QC_C_3	N/A	K-562 line
SA522424	NB_2025_015 - QC_Ams_2	N/A	K-562 line
SA522425	NLA_2023_007 - QCC1	N/A	K-562 line
SA522426	NB_2025_015 - QC_Ams_1	N/A	K-562 line
SA522427	NB_2025_015 - QC_Ams_5	N/A	K-562 line
SA522428	NB_2025_015 - QC_C_2	N/A	K-562 line
SA522429	NB_2025_015 - QC_C_1	N/A	K-562 line
SA522430	NB_2025_015 - QC_C_4	N/A	K-562 line
SA522431	NB_2025_015 - QC_C_5	N/A	K-562 line
SA522432	NB_2024_039 - QCC_4	N/A	K-562 line
SA522433	NB_2024_039 - QCC_3	N/A	K-562 line
SA522434	NB_2024_039 - QCC_2	N/A	K-562 line
SA522435	NB_2024_039 - QCC_1	N/A	K-562 line
SA522436	NLA_2023_007 - QCC2	N/A	K-562 line
SA522437	NB_2025_015 - 040	Wild-type	iPSC-derived microglia
SA522438	NB_2025_015 - 041	Wild-type	iPSC-derived microglia
SA522439	NB_2025_015 - 042	Wild-type	iPSC-derived microglia
SA522440	NB_2025_015 - 043	Wild-type	iPSC-derived microglia
SA522441	NB_2025_015 - 045	Wild-type	iPSC-derived microglia
SA522442	NB_2025_015 - 044	Wild-type	iPSC-derived microglia
SA522443	NB_2025_058 - 003	Wild-type	iPSC-derived microglia
SA522444	NB_2025_058 - 001	Wild-type	iPSC-derived microglia
SA522445	NB_2025_015 - 038	Wild-type	iPSC-derived microglia
SA522446	NB_2025_058 - 002	Wild-type	iPSC-derived microglia
SA522447	NB_2025_015 - 039	Wild-type	iPSC-derived microglia
SA522448	NB_2025_015 - 028	Wild-type	iPSC-derived microglia
SA522449	NB_2025_015 - 037	Wild-type	iPSC-derived microglia
SA522450	NB_2025_015 - 036	Wild-type	iPSC-derived microglia
SA522451	NB_2025_015 - 035	Wild-type	iPSC-derived microglia
SA522452	NB_2025_015 - 034	Wild-type	iPSC-derived microglia
SA522453	NB_2025_015 - 030	Wild-type	iPSC-derived microglia
SA522454	NB_2025_015 - 029	Wild-type	iPSC-derived microglia
SA522455	NB_2025_015 - 027	Wild-type	iPSC-derived microglia
SA522456	NB_2025_015 - 026	Wild-type	iPSC-derived microglia
SA522457	NB_2025_015 - 025	Wild-type	iPSC-derived microglia
SA522458	NB_2025_015 - 024	Wild-type	iPSC-derived microglia
SA522459	NB_2025_058 - 005	Wild-type	iPSC-derived microglia
SA522460	NB_2025_058 - 004	Wild-type	iPSC-derived microglia
SA522461	NB_2025_058 - 024	Wild-type	iPSC-derived microglia
SA522462	NB_2025_058 - 006	Wild-type	iPSC-derived microglia
SA522463	NB_2025_058 - 019	Wild-type	iPSC-derived microglia
SA522464	NB_2025_015 - 022	Wild-type	iPSC-derived microglia
SA522465	NB_2025_058 - 027	Wild-type	iPSC-derived microglia
SA522466	NB_2024_039 - 042	Wild-type	iPSC-derived microglia
SA522467	NB_2024_039 - 041	Wild-type	iPSC-derived microglia
SA522468	NB_2024_039 - 040	Wild-type	iPSC-derived microglia
SA522469	NB_2025_058 - 026	Wild-type	iPSC-derived microglia
SA522470	NB_2025_058 - 025	Wild-type	iPSC-derived microglia
SA522471	NB_2025_058 - 023	Wild-type	iPSC-derived microglia
SA522472	NB_2025_058 - 022	Wild-type	iPSC-derived microglia
SA522473	NB_2025_058 - 020	Wild-type	iPSC-derived microglia
SA522474	NB_2025_058 - 018	Wild-type	iPSC-derived microglia
SA522475	NB_2025_058 - 007	Wild-type	iPSC-derived microglia
SA522476	NB_2025_058 - 017	Wild-type	iPSC-derived microglia
SA522477	NB_2025_058 - 016	Wild-type	iPSC-derived microglia
SA522478	NB_2025_058 - 015	Wild-type	iPSC-derived microglia
SA522479	NB_2025_058 - 014	Wild-type	iPSC-derived microglia
SA522480	NB_2025_058 - 013	Wild-type	iPSC-derived microglia
SA522481	NB_2025_058 - 012	Wild-type	iPSC-derived microglia

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Collection:

Collection ID:	CO004574
Collection Summary:	Human iPSC-derived microglia-like cells (iMGL) were harvested as follows: cells were washed in DPBS and incubated with Accutase for 7 min before centrifugation at 300g for 5 min. Cell pellets were resuspended in ADF12 and 0.5-1.5 million cells transferred to a conical tube and centrifuged at 300g for 5 min. Cells were resuspended in 1 mL DPBS and transferred into 1.5 mL tubes before centrifugation at 300g for 5 min at 4°C. The supernatant was aspirated, and the cell pellet snap-frozen in liquid nitrogen and stored at -80°C until further processing.
Sample Type:	iPSC-derived microglia

Treatment:

Treatment ID:	TR004590
Treatment Summary:	Not applicable

Sample Preparation:

Sampleprep ID:	SP004587
Sampleprep Summary:	Lipidomic analysis was performed following standardized, quantitative protocols, as previously described (Feringa et al., 2025; Ghorasaini et al., 2021). Briefly, 25 µL of the Lipidyzer internal standard mix containing 54 deuterated standards, was added to the cell pellet. Extraction was performed using a methyl tert-butyl ether-based method. After drying under a gentle stream of nitrogen, samples were dissolved in running buffer consisting of methanol:dichloromethane (1:1) containing 10 mM ammonium acetate, before injection into the Lipidyzer platform consisting of a SCIEX QTRAP 5500 mass spectrometer equipped with an SelexION DMS interface and a Nexera X3 UHPLCsystem. SLA software was used to process data files and report lipid class, species concentration and composition values (Su et al., 2021). Lipidyzer data analysis was carried out on SODA-light, a built-in data browser for the Neurolipid Atlas repository.

Sampleprep ID:

SP004587

Sampleprep Summary:

Lipidomic analysis was performed following standardized, quantitative protocols, as previously described (Feringa et al., 2025; Ghorasaini et al., 2021). Briefly, 25 µL of the Lipidyzer internal standard mix containing 54 deuterated standards, was added to the cell pellet. Extraction was performed using a methyl tert-butyl ether-based method. After drying under a gentle stream of nitrogen, samples were dissolved in running buffer consisting of methanol:dichloromethane (1:1) containing 10 mM ammonium acetate, before injection into the Lipidyzer platform consisting of a SCIEX QTRAP 5500 mass spectrometer equipped with an SelexION DMS interface and a Nexera X3 UHPLCsystem. SLA software was used to process data files and report lipid class, species concentration and composition values (Su et al., 2021). Lipidyzer data analysis was carried out on SODA-light, a built-in data browser for the Neurolipid Atlas repository.

Combined analysis:

Analysis ID	AN007397	AN007398
Chromatography ID	CH005605	CH005605
MS ID	MS007090	MS007091
Analysis type	MS	MS
Chromatography type	None (Direct infusion)	None (Direct infusion)
Chromatography system	none	none
Column	none	none
MS Type	ESI	ESI
MS instrument type	Triple quadrupole	Triple quadrupole
MS instrument name	ABI Sciex 5500 QTrap	ABI Sciex 5500 QTrap
Ion Mode	UNSPECIFIED	UNSPECIFIED
Units	nmol/g	nmol/g

Chromatography:

Chromatography ID:	CH005605
Instrument Name:	none
Column Name:	none
Column Temperature:	N/A
Flow Gradient:	N/A
Flow Rate:	N/A
Solvent A:	N/A
Solvent B:	N/A
Chromatography Type:	None (Direct infusion)

MS:

MS ID:	MS007090
Analysis ID:	AN007397
Instrument Name:	ABI Sciex 5500 QTrap
Instrument Type:	Triple quadrupole
MS Type:	ESI
MS Comments:	Method 1: Lipidomics measurements are ran on a Sciex Qtrap 6500+ mounted with a Differential Mobility Separation (DMS) cell. As the sensitivity of the mass spectrometer is affected by the DMS cell, each sample is injected twice into the mass spectrometer, once for a measurement with DMS separation (method 1) and once without DMS separation (method 2). The mass spectrometer and DMS cell are operated by Analyst 1.7.3, which runs separate method files for both methods to measure a corresponding panel of lipids in Multiple Reaction Monitoring (MRM) across 20 cycles in both positive mode and negative mode. Shotgun Lipidomics Assistant (SLA) utilizes this dictionary combined with the standard_dict and ISOcorrectlist to quantify lipid concentrations in mzmL files based on the ratio of the analyte to the defined internal standard and applies isotopic correction, resulting in excel file outputs for each method which we have uploaded.
Ion Mode:	UNSPECIFIED

MS ID:	MS007091
Analysis ID:	AN007398
Instrument Name:	ABI Sciex 5500 QTrap
Instrument Type:	Triple quadrupole
MS Type:	ESI
MS Comments:	Method 2: Lipidomics measurements are ran on a Sciex Qtrap 6500+ mounted with a Differential Mobility Separation (DMS) cell. As the sensitivity of the mass spectrometer is affected by the DMS cell, each sample is injected twice into the mass spectrometer, once for a measurement with DMS separation (method 1) and once without DMS separation (method 2). The mass spectrometer and DMS cell are operated by Analyst 1.7.3, which runs separate method files for both methods to measure a corresponding panel of lipids in Multiple Reaction Monitoring (MRM) across 20 cycles in both positive mode and negative mode. Shotgun Lipidomics Assistant (SLA) utilizes this dictionary combined with the standard_dict and ISOcorrectlist to quantify lipid concentrations in mzmL files based on the ratio of the analyte to the defined internal standard and applies isotopic correction, resulting in excel file outputs for each method which we have uploaded.
Ion Mode:	UNSPECIFIED