Summary of Study ST003616

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 PR002235. The data can be accessed directly via it's Project DOI: 10.21228/M8QR7N 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.

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Study ID	ST003616
Study Title	Non-Targeted Analysis of the Chemical Exposome During Pregnancy Using High-Resolution Mass Spectrometry
Study Type	Research
Study Summary	The widespread use of human-made chemicals in daily life leads to chronic exposure to complex mixtures of potentially harmful substances. To investigate chemical exposures among pregnant women in New York City, we applied a non-targeted analysis (NTA) workflow to 83 paired prenatal placenta and serum samples (including 30 preterm birth pairs) collected through the New York University Children’s Health and Environment Study. Our objectives were to: i) characterize chemical exposures in this population, ii) compare chemical profiles between placenta and serum samples as well as between preterm and term births, and iii) examine potential associations between exogenous chemicals and endogenous metabolites.
Institute	NYU Grossman School of Medicine
Department	Division of Environmental Pediatrics, Department of Pediatrics
Last Name	Xiaowen
First Name	Ji
Address	NYU Medical Science Building, 6th Floor, 540 1st Ave., New York, NY 10016
Email	jix01@nyu.edu; xiaowen.ji@nyulangone.org
Phone	3476227357
Submit Date	2024-09-26
Total Subjects	83
Num Females	83
Raw Data Available	Yes
Raw Data File Type(s)	mzML
Analysis Type Detail	LC-MS
Release Date	2024-12-30
Release Version	1

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Project:

Project ID:	PR002235
Project DOI:	doi: 10.21228/M8QR7N
Project Title:	An insight into the chemical exposome during pregnancy
Project Type:	Research
Project Summary:	This project focuses on the non-targeted analysis of serum and placenta samples from pregnant women to identify exogenous chemicals.
Institute:	NYU Grossman School of Medicine
Department:	Department of Pediatrics
Laboratory:	MS6 98
Last Name:	Xiaowen
First Name:	Ji
Address:	550 1st Ave
Email:	jix01@nyu.edu; Xiaowen.Ji@nyulangone.org
Phone:	3476227357
Funding Source:	K99/R00 ES032892-01
Contributors:	Xiaowen Ji, Mathusa Lakuleswaran, Dimitri Abrahamsson

Subject:

Subject ID:	SU003745
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606
Gender:	Female
Human Ethnicity:	hispanic, asian, white, other

Factors:

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

mb_sample_id	local_sample_id	Gestation term	Sample source
SA392878	P-Batch-1-Preterm-1	Preterm	placenta
SA392879	P-Batch-4-Preterm-22	Preterm	placenta
SA392880	P-Batch-3-Preterm-17	Preterm	placenta
SA392881	P-Batch-4-Preterm-3	Preterm	placenta
SA392882	P-Batch-4-Preterm-13	Preterm	placenta
SA392883	P-Batch-4-Preterm-17	Preterm	placenta
SA392884	P-Batch-4-Preterm-18	Preterm	placenta
SA392885	P-Batch-4-Preterm-19	Preterm	placenta
SA392886	P-Batch-4-Preterm-21	Preterm	placenta
SA392887	P-Batch-1-Preterm-2	Preterm	placenta
SA392888	P-Batch-3-Preterm-15	Preterm	placenta
SA392889	P-Batch-2-Preterm-10	Preterm	placenta
SA392890	P-Batch-2-Preterm-8	Preterm	placenta
SA392891	P-Batch-2-Preterm-4	Preterm	placenta
SA392892	P-Batch-1-Preterm-17	Preterm	placenta
SA392893	P-Batch-1-Preterm-16	Preterm	placenta
SA392894	P-Batch-1-Preterm-12	Preterm	placenta
SA392895	P-Batch-1-Preterm-7	Preterm	placenta
SA392896	P-Batch-1-Preterm-6	Preterm	placenta
SA392897	P-Batch-3-Preterm-16	Preterm	placenta
SA392898	P-Batch-2-Preterm-6	Preterm	placenta
SA392899	P-Batch-2-Preterm-16	Preterm	placenta
SA392900	P-Batch-2-Preterm-17	Preterm	placenta
SA392901	P-Batch-3-Preterm-10	Preterm	placenta
SA392902	P-Batch-2-Preterm-20	Preterm	placenta
SA392903	P-Batch-2-Preterm-19	Preterm	placenta
SA392904	P-Batch-2-Preterm-14	Preterm	placenta
SA392905	P-Batch-2-Preterm-15	Preterm	placenta
SA392906	P-Batch-3-Preterm-3	Preterm	placenta
SA392907	P-Batch-3-Preterm-4	Preterm	placenta
SA392848	S-Batch-2-Preterm-19	Preterm	Serum
SA392849	S-Batch-1-Preterm-7	Preterm	Serum
SA392850	S-Batch-1-Preterm-12	Preterm	Serum
SA392851	S-Batch-1-Preterm-16	Preterm	Serum
SA392852	S-Batch-1-Preterm-17	Preterm	Serum
SA392853	S-Batch-2-Preterm-4	Preterm	Serum
SA392854	S-Batch-2-Preterm-6	Preterm	Serum
SA392855	S-Batch-2-Preterm-8	Preterm	Serum
SA392856	S-Batch-2-Preterm-10	Preterm	Serum
SA392857	S-Batch-2-Preterm-14	Preterm	Serum
SA392858	S-Batch-2-Preterm-15	Preterm	Serum
SA392859	S-Batch-2-Preterm-16	Preterm	Serum
SA392860	S-Batch-2-Preterm-17	Preterm	Serum
SA392861	S-Batch-2-Preterm-20	Preterm	Serum
SA392862	S-Batch-1-Preterm-2	Preterm	Serum
SA392863	S-Batch-3-Preterm-3	Preterm	Serum
SA392864	S-Batch-3-Preterm-4	Preterm	Serum
SA392865	S-Batch-3-Preterm-10	Preterm	Serum
SA392866	S-Batch-3-Preterm-15	Preterm	Serum
SA392867	S-Batch-3-Preterm-16	Preterm	Serum
SA392868	S-Batch-3-Preterm-17	Preterm	Serum
SA392869	S-Batch-4-Preterm-3	Preterm	Serum
SA392870	S-Batch-4-Preterm-13	Preterm	Serum
SA392871	S-Batch-4-Preterm-17	Preterm	Serum
SA392872	S-Batch-4-Preterm-18	Preterm	Serum
SA392873	S-Batch-4-Preterm-19	Preterm	Serum
SA392874	S-Batch-4-Preterm-21	Preterm	Serum
SA392875	S-Batch-4-Preterm-22	Preterm	Serum
SA392876	S-Batch-1-Preterm-6	Preterm	Serum
SA392877	S-Batch-1-Preterm-1	Preterm	Serum
SA392961	P-Batch-1-Term-13	Term	placenta
SA392962	P-Batch-1-Term-8	Term	placenta
SA392963	P-Batch-1-Term-11	Term	placenta
SA392964	P-Batch-1-Term-5	Term	placenta
SA392965	P-Batch-1-Term-4	Term	placenta
SA392966	P-Batch-1-Term-14	Term	placenta
SA392967	P-Batch-1-Term-3	Term	placenta
SA392968	P-Batch-1-Term-15	Term	placenta
SA392969	P-Batch-1-Term-9	Term	placenta
SA392970	P-Batch-1-Term-10	Term	placenta
SA392971	P-Batch-3-Term-13	Term	placenta
SA392972	P-Batch-2-Term-18	Term	placenta
SA392973	P-Batch-4-Term-5	Term	placenta
SA392974	P-Batch-4-Term-12	Term	placenta
SA392975	P-Batch-4-Term-11	Term	placenta
SA392976	P-Batch-4-Term-10	Term	placenta
SA392977	P-Batch-4-Term-9	Term	placenta
SA392978	P-Batch-4-Term-8	Term	placenta
SA392979	P-Batch-4-Term-7	Term	placenta
SA392980	P-Batch-4-Term-6	Term	placenta
SA392981	P-Batch-4-Term-4	Term	placenta
SA392982	P-Batch-4-Term-14	Term	placenta
SA392983	P-Batch-3-Term-9	Term	placenta
SA392984	P-Batch-4-Term-2	Term	placenta
SA392985	P-Batch-4-Term-1	Term	placenta
SA392986	P-Batch-3-Term-20	Term	placenta
SA392987	P-Batch-3-Term-19	Term	placenta
SA392988	P-Batch-3-Term-18	Term	placenta
SA392989	P-Batch-3-Term-11	Term	placenta
SA392990	P-Batch-3-Term-12	Term	placenta
SA392991	P-Batch-3-Term-8	Term	placenta
SA392992	P-Batch-4-Term-15	Term	placenta
SA392993	P-Batch-1-Term-18	Term	placenta
SA392994	P-Batch-2-Term-7	Term	placenta
SA392995	P-Batch-1-Term-19	Term	placenta
SA392996	P-Batch-1-Term-20	Term	placenta
SA392997	P-Batch-2-Term-1	Term	placenta
SA392998	P-Batch-2-Term-2	Term	placenta
SA392999	P-Batch-2-Term-3	Term	placenta
SA393000	P-Batch-3-Term-14	Term	placenta

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Collection:

Collection ID:	CO003738
Collection Summary:	The NYU CHES is an ongoing pregnancy and birth cohort study that began in March 2016. It enrolls pregnant participants over 18 years old and under 18 weeks of gestation from hospitals like NYU Brooklyn, Bellevue, and NYU Manhattan. Placenta samples were collected immediately after birth, and third-trimester serum samples were obtained. Placental cores (1.1–4.8 g, with one at 15 g) were excised from the umbilical cord by CHES staff following hospital protocols.
Sample Type:	Placenta; Blood (serum)
Collection Location:	NYU Brooklyn, Bellevue, and NYU Manhattan
Collection Duration:	The placenta was collected immediately after birth, and serum samples were obtained during the third trimester of pregnancy
Storage Conditions:	-80℃
Additives:	None

Treatment:

Treatment ID:	TR003754
Treatment Summary:	No Treatment

Sample Preparation:

Sampleprep ID:	SP003752
Sampleprep Summary:	The preparation of placental tissues and serum for LC-MS analysis involved a series of precise steps. Thawed placental tissues were homogenized with anhydrous Na₂SO₄ using a Tissuemiser Homogenizer. Extraction was performed with 100% methanol, employing ultrasound treatment for 10 minutes. The samples underwent three extraction cycles, with centrifugation at 14,000 rpm for 10 minutes after each step, and the combined supernatants were collected. Serum samples, after thorough vortexing, were processed by adding methanol (400 µL to 100 µL of serum), followed by centrifugation at 13,400 rpm for 5 minutes to remove lipoprotein precipitates. Both placental and serum extracts were cleaned using Oasis HLB solid-phase extraction (SPE) cartridges. The extracts were diluted (placenta: 300 mL, serum: 6 mL) and loaded onto preconditioned cartridges at a flow rate of ≤1 mL/min. After washing with water and 5% methanol, the cartridges were vacuum-dried and eluted with methanol. The eluates were evaporated under nitrogen at 35°C and reconstituted in a 1:1 methanol-water mixture. Prior to LC-MS analysis, the reconstituted samples were filtered through PTFE syringe filters to ensure removal of particulate matter. This method provides clean, concentrated extracts suitable for small molecule analysis.
Processing Storage Conditions:	-80℃
Extract Storage:	-20℃

Combined analysis:

Analysis ID	AN005941	AN005942
Analysis type	MS	MS
Chromatography type	Reversed phase	Reversed phase
Chromatography system	Thermo Vanquish	Thermo Vanquish
Column	Ascentis C18 HPLC (150 × 2.1 mm, 3um)	Ascentis C18 HPLC (150 × 2.1 mm, 3um)
MS Type	ESI	ESI
MS instrument type	Orbitrap	Orbitrap
MS instrument name	Thermo Orbitrap Exploris 240	Thermo Orbitrap Exploris 240
Ion Mode	POSITIVE	NEGATIVE
Units	Abundance	Abundance

Chromatography:

Chromatography ID:	CH004516
Instrument Name:	Thermo Vanquish
Column Name:	Ascentis C18 HPLC (150 × 2.1 mm, 3um)
Column Temperature:	45
Flow Gradient:	The gradient increased from 5% to 100% B over 15 minutes, held for 5 minutes, and returned to initial conditions for re-equilibration from 20.1 to 25 minutes.
Flow Rate:	0.2 mL/min
Solvent A:	5% methanol/95% water; 0.1% Formic acid
Solvent B:	100% methanol; 0.1% Formic acid
Chromatography Type:	Reversed phase

MS:

MS ID:	MS005658
Analysis ID:	AN005941
Instrument Name:	Thermo Orbitrap Exploris 240
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	sheath gas flow 35, auxiliary gas flow 10, sweep gas flow 1, vaporizer temperature 400 °C, spray voltage 3300 V , S-lens RF level 70%, and ion transfer tube temperature 350 °C. Full MS and data-dependent MS² (ddMS²) spectra were acquired with a resolution of 90,000 for Full MS and 12,000 for ddMS², normalized AGC target (standard), auto maximum injection time, normalized HCD collision energy of 30%, 50%, and 70%, Full MS scan range of 100–1000 m/z, and a ddMS² isolation window of 0.7 m/z with 10 scans.
Ion Mode:	POSITIVE

MS ID:	MS005659
Analysis ID:	AN005942
Instrument Name:	Thermo Orbitrap Exploris 240
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	sheath gas flow 35, auxiliary gas flow 10, sweep gas flow 1, vaporizer temperature 400 °C, spray voltage 2000 V, S-lens RF level 70%, and ion transfer tube temperature 350 °C. Full MS and data-dependent MS² (ddMS²) spectra were acquired with a resolution of 90,000 for Full MS and 12,000 for ddMS², normalized AGC target (standard), auto maximum injection time, normalized HCD collision energy of 30%, 50%, and 70%, Full MS scan range of 100–1000 m/z, and a ddMS² isolation window of 0.7 m/z with 10 scans.
Ion Mode:	NEGATIVE