Summary of Study ST001385

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 PR000949. The data can be accessed directly via it's Project DOI: 10.21228/M8198B 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 IDST001385
Study TitleMicrobial and metabolic variations mediate the influence of childhood and adolescent EDC and trace element exposure on breast density.
Study SummaryOur CHEAR project builds on the longitudinal Growth and Obesity Cohort Study in Santiago, Chile, which includes approximately 500 girls born in 2002-2003. Participants were recruited in 2006 from public nursery schools of six counties in Santiago representative of low to middle income families. Children were included if they were singletons with birthweight between 2500 and 4500g, and had no physical, medical or endocrine diseases that may alter the growth and/or onset of puberty. Semi-annual collection of participant anthropometric and pubertal development data by trained dietitians has continued since 2009. The overall objectives of our CHEAR study are to assess how exposure to endocrine-disrupting chemicals (phenols and phthalates), and trace elements (metals) measured in urine samples at Tanner stages 1 and 4 and 1 year post-menarche influence the pubertal microbiome and metabolome, and the potential impact on adolescent breast composition measured by DXA at Tanner stage 4 and 2 years post-menarche.
Institute
Icahn School of Medicine at Mount Sinai
Last NamePetrick
First NameLauren
AddressDepartment of Environmental Medicine and Public Health, Atran Building 3rd floor, 101st St. between Madison and 5th Ave, New York, New York, 10029, USA
Emaillauren.petrick@mssm.edu
Phone212 241 7351
Submit Date2020-05-22
Raw Data AvailableYes
Raw Data File Type(s)d
Chear StudyYes
Analysis Type DetailLC-MS
Release Date2022-03-01
Release Version1
Lauren Petrick Lauren Petrick
https://dx.doi.org/10.21228/M8198B
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000949
Project DOI:doi: 10.21228/M8198B
Project Title:CHEAR_2017_1977 Urine Metabolomics
Project Summary:To perform an untargeted metabolomics analysis of urine samples, matrix blanks and quality control samples. The metabolomics approach will be performed using both reverse phase (RP) and HILIC chromatography (ZHP) separations coupled to high-resolution mass spectrometry.
Institute:Icahn School of Medicine at Mount Sinai
Last Name:Petrick
First Name:Lauren
Address:Department of Environmental Medicine and Public Health, Atran Building 3rd floor, 101st St. between Madison and 5th Ave, New York, New York, 10029, USA
Email:lauren.petrick@mssm.edu
Phone:212 241 7351

Subject:

Subject ID:SU001459
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606

Factors:

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

mb_sample_id local_sample_id Factor
SA101195matrix_19S065_25matrix
SA101196matrix_19S065_2matrix
SA101197matrix_19S065_24matrix
SA101198matrix_19S065_26matrix
SA101199matrix_19S065_27matrix
SA101200matrix_19S065_11matrix
SA101201matrix_19S065_15matrix
SA101202matrix_19S065_23matrix
SA101203matrix_19S065_22matrix
SA101204matrix_19S065_12matrix
SA101205matrix_19S065_3matrix
SA101206matrix_19S065_30matrix
SA101207matrix_19S065_29matrix
SA101208matrix_19S065_8matrix
SA101209matrix_19S065_28matrix
SA101210matrix_19S065_13matrix
SA101211matrix_19S065_10matrix
SA101212matrix_19S065_5matrix
SA101213matrix_19S065_4matrix
SA101214matrix_19S065_6matrix
SA101215matrix_19S065_7matrix
SA101216matrix_19S065_9matrix
SA101217matrix_19S065_1matrix
SA101218matrix_19S065_20matrix
SA101219matrix_19S065_21matrix
SA101220matrix_19S065_14matrix
SA101221matrix_19S065_17matrix
SA101222matrix_19S065_16matrix
SA101223matrix_19S065_19matrix
SA101224matrix_19S065_18matrix
SA101102NIST3672_15NIST
SA101103NIST3672_14NIST
SA101104NIST3672_4NIST
SA101105NIST3672_8NIST
SA101106NIST3672_5NIST
SA101107NIST3672_6NIST
SA101108NIST3672_9NIST
SA101109NIST3672_10NIST
SA101110NIST3672_11NIST
SA101111NIST3672_12NIST
SA101112NIST3672_13NIST
SA101113NIST3672_2NIST
SA101114NIST3672_3NIST
SA101115NIST3672_7NIST
SA101116NIST3672_1NIST
SA101117LQC_19S065_31PooledQC
SA101118LQC_19S065_28PooledQC
SA101119LQC_19S065_41PooledQC
SA101120LQC_19S065_10PooledQC
SA101121LQC_19S065_11PooledQC
SA101122LQC_19S065_30PooledQC
SA101123LQC_19S065_29PooledQC
SA101124LQC_19S065_15PooledQC
SA101125LQC_19S065_5PooledQC
SA101126LQC_19S065_6PooledQC
SA101127LQC_19S065_18PooledQC
SA101128LQC_19S065_9PooledQC
SA101129LQC_19S065_40PooledQC
SA101130LQC_19S065_21PooledQC
SA101131LQC_19S065_42PooledQC
SA101132LQC_19S065_22PooledQC
SA101133LQC_19S065_7PooledQC
SA101134LQC_19S065_33PooledQC
SA101135LQC_19S065_8PooledQC
SA101136LQC_19S065_34PooledQC
SA101137LQC_19S065_23PooledQC
SA101138LQC_19S065_24PooledQC
SA101139LQC_19S065_44PooledQC
SA101140LQC_19S065_13PooledQC
SA101141LQC_19S065_3PooledQC
SA101142LQC_19S065_26PooledQC
SA101143LQC_19S065_39PooledQC
SA101144LQC_19S065_25PooledQC
SA101145LQC_19S065_36PooledQC
SA101146LQC_19S065_2PooledQC
SA101147LQC_19S065_20PooledQC
SA101148LQC_19S065_35PooledQC
SA101149LQC_19S065_19PooledQC
SA101150LQC_19S065_14PooledQC
SA101151LQC_19S065_1PooledQC
SA101152LQC_19S065_43PooledQC
SA101153LQC_19S065_17PooledQC
SA101154LQC_19S065_32PooledQC
SA101155LQC_19S065_37PooledQC
SA101156LQC_19S065_4PooledQC
SA101157LQC_19S065_38PooledQC
SA101158LQC_19S065_27PooledQC
SA101159LQC_19S065_16PooledQC
SA101160LQC_19S065_12PooledQC
SA101225C-1SJH4-U-00sample
SA101226C-1SK39-U-00sample
SA101227C-1SJT7-U-00sample
SA101228C-1SJW1-U-00sample
SA101229C-1SKG5-U-00sample
SA101230C-1SKE9-U-00sample
SA101231C-1SJM3-U-00sample
SA101232C-1SGT0-U-00sample
SA101233C-1SF83-U-00sample
SA101234C-1SF26-U-00sample
SA101235C-1SET2-U-00sample
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Collection:

Collection ID:CO001454
Collection Summary:Samples were received and stored at -80°C until processing. In total, 315 samples had sufficient sample volume for metabolomics analysis.
Collection Protocol Filename:Report_Michels_ 2017_1977.docx
Sample Type:Urine
Storage Conditions:-80℃

Treatment:

Treatment ID:TR001474
Treatment Summary:See report
Treatment Protocol Filename:Report_Michels_ 2017_1977.docx

Sample Preparation:

Sampleprep ID:SP001467
Sampleprep Summary:Aliquoting was initially performed for all CHEAR assays, and included an aliquot of each sample for metabolomics and specific gravity measurements. Specific gravity measurements were made first, to determine dilution factors required for pre-acquisition normalization. Specific gravity and dilution factors are included in the “Meta_2019_Michels2017_1977.csv” Urine samples were thawed on ice in batches of approximately 65 samples, and vortexed. The sample was diluted with water down to a specific gravity of 1.002 for pre-acquisition normalization. A 20 L aliquot of the diluted sample was prepared for metabolomics analysis. In addition, a 20 L aliquot from each diluted sample was combined for use as a pooled quality control sample and re-aliquoted into 20L samples. Samples were then returned to -80°C until analysis. Extraction was performed in batches of approximately 65 samples, immediately prior to LC-HRMS analysis. All samples in a batch were thawed on ice, combined with 180L of acetonitrile containing internal standards, and vortexed for 30sec. Samples were then centrifuged (13000 g, 15 min, °C), and 60 L of supernatant transferred to two LC vials for RP and HILIC analysis. Extract remainder was returned to -80°C. Following the same protocol 20 L aliquots each of a matrix blank (replacing the urine with H2O, “matrix”), a CHEAR Reference urine sample (global quality control, “UT”), a NIST 3672 sample (global quality control, “NIST”), and multiple pooledQC samples (local quality control, “LQC”) were extracted.
Sampleprep Protocol Filename:Report_Michels_ 2017_1977.docx

Combined analysis:

Analysis ID AN002312 AN002313
Analysis type MS MS
Chromatography type Reversed phase HILIC
Chromatography system Agilent 1290 Infinity II Agilent 1290 Infinity II
Column Agilent Zorbax Eclipse Plus C18 RRHD column (50 x 2.1mm, 1.8um) SeQuant ZIC-HILIC (100 x 2.1mm, 3.5um)
MS Type ESI ESI
MS instrument type QTOF QTOF
MS instrument name Agilent 6550 QTOF Agilent 6545 QTOF
Ion Mode NEGATIVE POSITIVE
Units area area

Chromatography:

Chromatography ID:CH001699
Chromatography Summary:Reverse Phase Gradient separation
Instrument Name:Agilent 1290 Infinity II
Column Name:Agilent Zorbax Eclipse Plus C18 RRHD column (50 x 2.1mm, 1.8um)
Column Temperature:25°C
Flow Rate:0.4 mL/min
Sample Injection:2uL
Chromatography Type:Reversed phase
  
Chromatography ID:CH001700
Chromatography Summary:HILIC Gradient separation
Instrument Name:Agilent 1290 Infinity II
Column Name:SeQuant ZIC-HILIC (100 x 2.1mm, 3.5um)
Column Temperature:25°C
Flow Rate:0.3 mL/min
Sample Injection:2uL
Chromatography Type:HILIC

MS:

MS ID:MS002155
Analysis ID:AN002312
Instrument Name:Agilent 6550 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:Database dependent targeted identification: Metabolites were identified based upon in-house database matching considering retention time, accurate mass, and MSMS matching (when available) matching with pure standards analyzed under the same conditions. Untargeted metabolomics analysis: Parameters for peak picking grouping, and alignment with ‘XCMS’ included centwave feature detection, orbiwarp retention time correction, minimum fraction of samples in one group to be a valid group = 0.25, isotopic ppm error = 10. Width of overlapping m/z slices (mzwid) = 0.003 or 0.015, and retention time window (bw) = 12.4 s and 22 s for ZHP and RPN, respectively. Minimum and maximum peak width were 5 and 20 s for reverse phase and 10 and 60 s for HILIC. The resulting peak table of retention times, m/z values, and peak areas was exported for data processing. Annotation of the untargeted data was facilitated by xMSannotator using the annotation scheme of Schymanski et al. (Environmental Science & Technology, 2014). Level 1 and 2 annotations were those that were confirmed with database dependent annotation. Lower confidence annotations (level 4) are those from the HMDB and T3DB online databases that were highly ranking by xMSannotator. Level 5 annotations were named by “mz_rt”. Metadata for the analysis including the batch and run order of each injection are provided in the Metafile, “Meta_2019_Michels2017_1977.csv”. We also included the Specific gravity measurements and dilution factor performed for each sample prior to data acquisition.
Ion Mode:NEGATIVE
  
MS ID:MS002156
Analysis ID:AN002313
Instrument Name:Agilent 6545 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:Database dependent targeted identification: Metabolites were identified based upon in-house database matching considering retention time, accurate mass, and MSMS matching (when available) matching with pure standards analyzed under the same conditions. Untargeted metabolomics analysis: Parameters for peak picking grouping, and alignment with ‘XCMS’ included centwave feature detection, orbiwarp retention time correction, minimum fraction of samples in one group to be a valid group = 0.25, isotopic ppm error = 10. Width of overlapping m/z slices (mzwid) = 0.003 or 0.015, and retention time window (bw) = 12.4 s and 22 s for ZHP and RPN, respectively. Minimum and maximum peak width were 5 and 20 s for reverse phase and 10 and 60 s for HILIC. The resulting peak table of retention times, m/z values, and peak areas was exported for data processing. Annotation of the untargeted data was facilitated by xMSannotator using the annotation scheme of Schymanski et al. (Environmental Science & Technology, 2014). Level 1 and 2 annotations were those that were confirmed with database dependent annotation. Lower confidence annotations (level 4) are those from the HMDB and T3DB online databases that were highly ranking by xMSannotator. Level 5 annotations were named by “mz_rt”. Metadata for the analysis including the batch and run order of each injection are provided in the Metafile, “Meta_2019_Michels2017_1977.csv”. We also included the Specific gravity measurements and dilution factor performed for each sample prior to data acquisition.
Ion Mode:POSITIVE
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