Summary of Study ST002092

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 PR001328. The data can be accessed directly via it's Project DOI: 10.21228/M82978 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 IDST002092
Study TitleAddressing batch effects in large-scale metabolomics with augmented experimental design and meta-analysis
Study SummaryUntargeted LC-MS study conducted using RP and HILIC chromatography on three groups of C. elegans: natural isolates, central metabolism mutants, and UDP-glucuronosyltransferase mutants. An augmented study design, rank transformation of the raw data, strict QA/QC followed by a meta-analysis was used for data analysis.
Institute
University of Georgia - Complex Carbohydrate Research Center
LaboratoryEdison Lab
Last NameGarcia
First NameBrianna
Address315 Riverbend Road
Emailbrianna.garcia@uga.edu
Phone7065424401
Submit Date2022-02-14
Num Groups3
Total Subjects119
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2022-04-04
Release Version1
Brianna Garcia Brianna Garcia
https://dx.doi.org/10.21228/M82978
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001328
Project DOI:doi: 10.21228/M82978
Project Title:Addressing batch effects in large-scale metabolomics with augmented experimental design and meta-analysis
Project Summary:Untargeted LC-MS study conducted using RP and HILIC chromatography on three groups of C. elegans: natural isolates, central metabolism mutants, and UDP-glucuronosyltransferase mutants. An augmented study design, rank transformation of the raw data, strict QA/QC followed by a meta-analysis was used for data analysis.
Institute:University of Georgia - Complex Carbohydrate Research Center
Laboratory:Edison Lab
Last Name:Garcia
First Name:Brianna
Address:315 Riverbend Road, Athens, GA 30602
Email:brianna.garcia@uga.edu
Phone:7065424401
Funding Source:U2CES030167
Contributors:Amanda O. Shaver, Goncalo J. Gouveia, Alison M. Morse, Zihao Liu, Carter K. Asef, Ricardo M. Borges, Franklin E. Leach III, Erik C. Andersen, I. Jonathan Amster, Facundo M. Fernández, Arthur S. Edison, and Lauren M. McIntyre

Subject:

Subject ID:SU002176
Subject Type:Invertebrate
Subject Species:Caenorhabditis elegans
Taxonomy ID:6239
Gender:Hermaphrodite

Factors:

Subject type: Invertebrate; Subject species: Caenorhabditis elegans (Factor headings shown in green)

mb_sample_id local_sample_id Strain Sample type
SA200809b6_aos_120AUM2073 sample
SA200810b6_aos_135AUM2073 sample
SA200811b5_aos_51AUM2073 sample
SA200812b6_aos_169AUM2073 sample
SA200813b5_aos_91AUM2073 sample
SA200814b5_aos_79AUM2073 sample
SA200815b1_aos_142CB4856 sample
SA200816b1_aos_145CB4856 sample
SA200817b2_aos_130CB4856 sample
SA200818b2_aos_170CB4856 sample
SA200819b2_aos_199CX11314 sample
SA200820b2_aos_103CX11314 sample
SA200821b2_aos_175CX11314 sample
SA200822b1_aos_76CX11314 sample
SA200823b1_aos_25CX11314 sample
SA200824b1_aos_127CX11314 sample
SA200825b1_aos_65DL238 sample
SA200826b1_aos_50DL238 sample
SA200827b2_aos_174DL238 sample
SA200828b1_aos_46DL238 sample
SA200829b2_aos_165DL238 sample
SA200830b2_aos_192DL238 sample
SA200831b3_aos_86KJ550 sample
SA200832b4_aos_134KJ550 sample
SA200833b4_aos_109KJ550 sample
SA200834b4_aos_100KJ550 sample
SA200835b3_aos_28KJ550 sample
SA200836b2_aos_56N2 sample
SA200837b2_aos_106N2 sample
SA200838b1_aos_48N2 sample
SA200839b1_aos_67N2 sample
SA200840b1_aos_58N2 sample
SA200841b2_aos_188PD1074 sample
SA200842b2_aos_200PD1074 sample
SA200843b6_aos_102PD1074 sample
SA200844b4_aos_92PD1074 sample
SA200845b4_aos_180PD1074 sample
SA200846b1_aos_54PD1074 sample
SA200847b4_aos_87PD1074 sample
SA200848b6_aos_107PD1074 sample
SA200849b2_aos_167PD1074 sample
SA200850b5_aos_43PD1074 sample
SA200851b5_aos_41PD1074 sample
SA200852b2_aos_124PD1074 sample
SA200853b5_aos_54PD1074 sample
SA200854b5_aos_78PD1074 sample
SA200855b5_aos_87PD1074 sample
SA200856b2_aos_107PD1074 sample
SA200857b1_aos_78PD1074 sample
SA200858b5_aos_181PD1074 sample
SA200859b2_aos_102PD1074 sample
SA200860b5_aos_196PD1074 sample
SA200861b5_aos_75PD1074 sample
SA200862b6_aos_140PD1074 sample
SA200863b3_aos_78PD1074 sample
SA200864b1_aos_43PD1074 sample
SA200865b6_aos_90PD1074 sample
SA200866b3_aos_90PD1074 sample
SA200867b6_aos_198PD1074 sample
SA200868b3_aos_54PD1074 sample
SA200869b3_aos_43PD1074 sample
SA200870b1_aos_129PD1074 sample
SA200871b3_aos_38PD1074 sample
SA200872b1_aos_149PD1074 sample
SA200873b1_aos_27PD1074 sample
SA200874b4_aos_140PD1074 sample
SA200875b3_aos_99PD1074 sample
SA200876b2_aos_53PD1074 sample
SA200877b6_aos_167PD1074 sample
SA200878b4_aos_124PD1074 sample
SA200879b4_aos_107PD1074 sample
SA200880b3_aos_27PD1074 sample
SA200881b6_aos_188PD1074 sample
SA200882b3_aos_185PD1074 sample
SA200883b2_aos_108RB2011 sample
SA200884b2_aos_173RB2011 sample
SA200885b1_aos_122RB2011 sample
SA200886b1_aos_32RB2011 sample
SA200887b6_aos_118RB2055 sample
SA200888b6_aos_186RB2055 sample
SA200889b6_aos_114RB2055 sample
SA200890b5_aos_83RB2055 sample
SA200891b5_aos_26RB2055 sample
SA200892b5_aos_45RB2055 sample
SA200893b3_aos_36RB2347 sample
SA200894b4_aos_116RB2347 sample
SA200895b4_aos_95RB2347 sample
SA200896b3_aos_74RB2347 sample
SA200897b4_aos_171RB2347 sample
SA200898b3_aos_37RB2347 sample
SA200899b4_aos_82RB2347 sample
SA200900b4_aos_111RB2550 sample
SA200901b3_aos_35RB2550 sample
SA200902b3_aos_40RB2550 sample
SA200903b3_aos_71RB2550 sample
SA200904b4_aos_81RB2550 sample
SA200905b4_aos_96RB2550 sample
SA200906b6_aos_88RB2607 sample
SA200907b6_aos_166RB2607 sample
SA200908b6_aos_133RB2607 sample
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Collection:

Collection ID:CO002169
Collection Summary:Escherichia coli (E. coli) IBAT (iterative batch average method) reference material and food source used throughout this experiment. Briefly, for each biological sample, a large-scale culture plate (LSCP) was used to generate a large mixed-stage population of worms (four to seven LSCP replicates per test strain). For each LSCP, worms were collected, population size estimated, and subsequently divided into at least 12 identical aliquots of 200,000 worms in ddH2O and flash-frozen in liquid nitrogen and stored at -80°C 8. As a quality control sample, C. elegans IBAT reference material was generated and saved in 200,000 worm aliquots.
Sample Type:Worms
Volumeoramount Collected:200,000 worms
Storage Conditions:-80℃

Treatment:

Treatment ID:TR002188
Treatment Summary:No treatments.

Sample Preparation:

Sampleprep ID:SP002182
Sampleprep Summary:Frozen aliquots of 200,000 C. elegans worms were retrieved from -80°C and lyophilized in a VirTis® BenchTop™ “K” Series Freeze Dryer (SP Industries, Inc.). After lyophilization, each aliquot was weighed and stored at -80°C until homogenization. Aliquots were homogenized for three minutes in a Qiagen Tissuelyser 2, using glass beads. Homogenized worms were extracted with 1.5 mL of isopropanol (IPA) at -20°C overnight (approximately 12 hours), then pelleted and the supernatant transferred to separate 2 mL centrifuge tubes. Supernatants were then dried down to completion in a Labconco Centrivap and stored at -80°C for non-polar LC-MS analysis. The pellet was extracted a second time using 80:20 methanol:water (MeOH:H2O) (v:v) for 20 minutes at room temperature (RT) while shaking at 1500 rpm. Samples were again pelleted to separate proteins, and the supernatant was transferred to separate 2 mL centrifuge tubes, dried down to completion, and stored at -80°C for polar LC-MS analysis
Sampleprep Protocol Filename:lcms_sequential_extraction_method.pdf
Processing Storage Conditions:-80℃
Extraction Method:IPA for non-polar; 80/20 MeOH/H2O for polar
Extract Storage:-80℃
Sample Resuspension:75 µL of IPA containing isotopically labeled lipid standards; 75 µL of 80:20 MeOH: H2O containing isotopically labeled arginine, hypoxanthine, hippuric acid, and methionine

Combined analysis:

Analysis ID AN003416 AN003417 AN003418
Analysis type MS MS MS
Chromatography type Reversed phase Reversed phase HILIC
Chromatography system Thermo Vanquish Thermo Vanquish Thermo Vanquish
Column Thermo Scientific Accucore C30 (150 x 2.1mm,2.6um) Thermo Scientific Accucore C30 (150 x 2.1mm,2.6um) Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
MS Type ESI ESI ESI
MS instrument type Orbitrap Orbitrap Orbitrap
MS instrument name Thermo Orbitrap ID-X Tribrid Thermo Orbitrap ID-X Tribrid Thermo Orbitrap ID-X Tribrid
Ion Mode POSITIVE NEGATIVE POSITIVE
Units Ranked Peak Height Ranked Peak Height Ranked Peak Height

Chromatography:

Chromatography ID:CH002527
Chromatography Summary:Non-polar extracts were separated using a Vanquish (ThermoFisher Scientific), fitted with a ThermoFisher Scientific Accucore™ C30 UPLC RP column (2.1 x 150 mm, 2.6 µm particle size). The compounds were eluted with the following gradient: 60:40 acetonitrile:water (ACN:H2O) with 10 mM ammonium formate and 0.1% formic acid (mobile phase A) and 90:10 isopropanol:acetonitrile with 10 mM ammonium formate and 0.1% formic acid (mobile phase B) using the following gradient program: 0.0 min 20% B; 1.0 min 60% B; 5.0 min 70% B; 5.5 min 85% B; 8.0 min 90% B; 8.2-10.5 min 100% B; 10.7-12.0 min 20% B. A curve 5 value was set for 0.0 minutes, and a curve 6 for the remainder of the gradient. The flow rate was set at 0.400 mL min-1. The column temperature was set to 50°C, and the injection volume was 2 µL.
Instrument Name:Thermo Vanquish
Column Name:Thermo Scientific Accucore C30 (150 x 2.1mm,2.6um)
Column Temperature:50
Solvent A:40% water/60% acetonitrile; 0.1% formic acid; 10 mM ammonium formate
Solvent B:90% isopropanol/10% acetonitrile; 0.1% formic acid; 10 mM ammonium formate
Chromatography Type:Reversed phase
  
Chromatography ID:CH002528
Chromatography Summary:Polar extracts were separated using a Vanquish (ThermoFisher Scientific), fitted with a Waters Acquity UPLC BEH Amide column (2.1 x 150 mm, 1.7 µm particle size). The compounds were eluted with the following gradient: 80:20 water:acetonitrile (H2O:ACN) with 10 mM ammonium formate and 0.1% formic acid (mobile phase A) and 100% ACN with 0.1% formic acid (mobile phase B) using the following gradient program: 0.0-0.5 min 95% B; 8.0-9.4 min 40% B; 9.5-11.0 min 95% B. A curve 5 value was set for 0.0 minutes, a curve 6 at 0.5 min, curve 7 at 8.0 min, and a curve 6 for the remainder of the gradient. The flow rate was set at 0.400 mL min-1. The column temperature was set to 40°C, and the injection volume was 2 µL.
Instrument Name:Thermo Vanquish
Column Name:Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
Column Temperature:40
Solvent A:80% water/20% acetonitrile; 0.1% formic acid; 10 mM ammonium formate
Solvent B:100% acetonitrile; 0.1% formic acid
Chromatography Type:HILIC

MS:

MS ID:MS003181
Analysis ID:AN003416
Instrument Name:Thermo Orbitrap ID-X Tribrid
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:LC-MS data was collected using a Thermo Orbitrap ID-X tribrid in full profile mode at 240,000 resolution. A m/z range of 150-2000 was used. Data was centroided using Proteowizard and processed using open source software SLAW for peak picking, alignment, and feature assignment.
Ion Mode:POSITIVE
Capillary Temperature:275
Dry Gas Flow:40
Dry Gas Temp:320
Spray Voltage:3500
Dataformat:.raw Profile
  
MS ID:MS003182
Analysis ID:AN003417
Instrument Name:Thermo Orbitrap ID-X Tribrid
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:LC-MS data was collected using a Thermo Orbitrap ID-X tribrid in full profile mode at 240,000 resolution. A m/z range of 150-2000 was used. Data was centroided using Proteowizard and processed using open source software SLAW for peak picking, alignment, and feature assignment.
Ion Mode:NEGATIVE
Capillary Temperature:275
Dry Gas Flow:40
Dry Gas Temp:320
Spray Voltage:2500
Dataformat:.raw Profile
  
MS ID:MS003183
Analysis ID:AN003418
Instrument Name:Thermo Orbitrap ID-X Tribrid
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:LC-MS data was collected using a Thermo Orbitrap ID-X tribrid in full profile mode at 240,000 resolution. A m/z range of 70-1050 was used. Data was centroided using Proteowizard and processed using open source software SLAW for peak picking, alignment, and feature assignment.
Ion Mode:POSITIVE
Capillary Temperature:275
Dry Gas Flow:40
Dry Gas Temp:320
Spray Voltage:3500
Dataformat:.raw Profile
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