Summary of Study ST002046

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 PR001293. The data can be accessed directly via it's Project DOI: 10.21228/M8KH6M 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.

Perform statistical analysis  |  Show all samples  |  Show named metabolites  |  Download named metabolite data  |  Perform analysis on untargeted data  
Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data files (Contains raw data)
Study IDST002046
Study TitleA Taguchi Design of Experiments Approach for Untargeted Metabolomics Sample Preparation Optimization
Study TypeDesign of Experiments - Extraction Optimization
Study SummaryMetabolomics commonly uses analytical techniques such as nuclear magnetic resonance (NMR) and liquid chromatography coupled to mass spectrometry (LC-MS) to quantify and identify metabolites associated with biological variation. Metabolome coverage from non-targeted LC-MS studies relies heavily on the pre-analytical protocols (e.g., homogenization and extraction) used. Chosen protocols impact which metabolites are successfully measured, which in turn impacts biological conclusions. Different homogenization and extraction methods produce significant variability in metabolome coverage, sample reproducibility, and extraction efficiency. Herein we describe an efficient Taguchi method design of experiments (DOE) approach to optimize the extraction solvent and volume, extraction time, and LC reconstitution solvent for a sequential non-polar and polar Caenorhabditis elegans extraction. DOE is rarely used in metabolomics yet provides a systematic approach for optimizing sample preparation while simultaneously decreasing the number of experiments required to obtain high-quality data.
Institute
University of Georgia
Last NameGarcia
First NameBrianna
Address315 Riverbend Road
Emailbrianna.garcia@uga.edu
Phone6269059945
Submit Date2021-12-16
Num Groups10
Total Subjects30
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2022-12-20
Release Version1
Brianna Garcia Brianna Garcia
https://dx.doi.org/10.21228/M8KH6M
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001293
Project DOI:doi: 10.21228/M8KH6M
Project Title:A Taguchi Design of Experiments Approach for Untargeted Metabolomics Sample Preparation Optimization
Project Type:Design of Experiments - Sample preparation optimization
Project Summary:Metabolomics commonly uses analytical techniques such as nuclear magnetic resonance (NMR) and liquid chromatography coupled to mass spectrometry (LC-MS) to quantify and identify metabolites associated with biological variation. Metabolome coverage from non-targeted LC-MS studies relies heavily on the pre-analytical protocols (e.g., homogenization and extraction) used. Chosen protocols impact which metabolites are successfully measured, which in turn impacts biological conclusions. Different homogenization and extraction methods produce significant variability in metabolome coverage, sample reproducibility, and extraction efficiency. Herein we describe an efficient Taguchi method design of experiments (DOE) approach to optimize the extraction solvent and volume, extraction time, and LC reconstitution solvent for a sequential non-polar and polar Caenorhabditis elegans extraction. DOE is rarely used in metabolomics yet provides a systematic approach for optimizing sample preparation while simultaneously decreasing the number of experiments required to obtain high-quality data.
Institute:University of Georgia
Department:Chemistry, Biochemistry, Complex Carbohydrate Research Center
Laboratory:Edison Lab
Last Name:Garcia
First Name:Brianna
Address:315 Riverbend Road, Athens, GA, 30602, USA
Email:brianna.garcia@uga.edu
Phone:6269059945
Funding Source:NIH Metabolomics Common Fund
Contributors:Goncalo J. Gouveia, Amanda O. Shaver, I. Jonathan Amster, Arthur S. Edison, Franklin E. Leach III

Subject:

Subject ID:SU002128
Subject Type:Invertebrate
Subject Species:Caenorhabditis elegans
Taxonomy ID:6239

Factors:

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

mb_sample_id local_sample_id sample_type experiment_number lc_ms_method
SA192337exp10_hilic_neg_01Sample 10 hilic_neg
SA192338exp10_hilic_neg_02Sample 10 hilic_neg
SA192339exp10_hilic_neg_03Sample 10 hilic_neg
SA192340exp10_hilic_pos_01Sample 10 hilic_pos
SA192341exp10_hilic_pos_02Sample 10 hilic_pos
SA192342exp10_hilic_pos_03Sample 10 hilic_pos
SA192343exp10_rp_neg_03Sample 10 rp_neg
SA192344exp10_rp_neg_02Sample 10 rp_neg
SA192345exp10_rp_neg_01Sample 10 rp_neg
SA192346exp10_rp_pos_03Sample 10 rp_pos
SA192347exp10_rp_pos_02Sample 10 rp_pos
SA192348exp10_rp_pos_01Sample 10 rp_pos
SA192349exp1_hilic_neg_02Sample 1 hilic_neg
SA192350exp1_hilic_neg_03Sample 1 hilic_neg
SA192351exp1_hilic_neg_01Sample 1 hilic_neg
SA192352exp1_hilic_pos_02Sample 1 hilic_pos
SA192353exp1_hilic_pos_03Sample 1 hilic_pos
SA192354exp1_hilic_pos_01Sample 1 hilic_pos
SA192355exp1_rp_neg_03Sample 1 rp_neg
SA192356exp1_rp_neg_02Sample 1 rp_neg
SA192357exp1_rp_neg_01Sample 1 rp_neg
SA192358exp1_rp_pos_01Sample 1 rp_pos
SA192359exp1_rp_pos_03Sample 1 rp_pos
SA192360exp1_rp_pos_02Sample 1 rp_pos
SA192361exp2_hilic_neg_03Sample 2 hilic_neg
SA192362exp2_hilic_neg_01Sample 2 hilic_neg
SA192363exp2_hilic_neg_02Sample 2 hilic_neg
SA192364exp2_hilic_pos_01Sample 2 hilic_pos
SA192365exp2_hilic_pos_02Sample 2 hilic_pos
SA192366exp2_hilic_pos_03Sample 2 hilic_pos
SA192367exp2_rp_neg_02Sample 2 rp_neg
SA192368exp2_rp_neg_03Sample 2 rp_neg
SA192369exp2_rp_neg_01Sample 2 rp_neg
SA192370exp2_rp_pos_01Sample 2 rp_pos
SA192371exp2_rp_pos_02Sample 2 rp_pos
SA192372exp2_rp_pos_03Sample 2 rp_pos
SA192373exp3_hilic_neg_01Sample 3 hilic_neg
SA192374exp3_hilic_neg_03Sample 3 hilic_neg
SA192375exp3_hilic_neg_02Sample 3 hilic_neg
SA192376exp3_hilic_pos_02Sample 3 hilic_pos
SA192377exp3_hilic_pos_03Sample 3 hilic_pos
SA192378exp3_hilic_pos_01Sample 3 hilic_pos
SA192379exp3_rp_neg_01Sample 3 rp_neg
SA192380exp3_rp_neg_03Sample 3 rp_neg
SA192381exp3_rp_neg_02Sample 3 rp_neg
SA192382exp3_rp_pos_02Sample 3 rp_pos
SA192383exp3_rp_pos_01Sample 3 rp_pos
SA192384exp3_rp_pos_03Sample 3 rp_pos
SA192385exp4_hilic_neg_03Sample 4 hilic_neg
SA192386exp4_hilic_neg_02Sample 4 hilic_neg
SA192387exp4_hilic_neg_01Sample 4 hilic_neg
SA192388exp4_hilic_pos_02Sample 4 hilic_pos
SA192389exp4_hilic_pos_03Sample 4 hilic_pos
SA192390exp4_hilic_pos_01Sample 4 hilic_pos
SA192391exp4_rp_neg_03Sample 4 rp_neg
SA192392exp4_rp_neg_02Sample 4 rp_neg
SA192393exp4_rp_neg_01Sample 4 rp_neg
SA192394exp4_rp_pos_01Sample 4 rp_pos
SA192395exp4_rp_pos_03Sample 4 rp_pos
SA192396exp4_rp_pos_02Sample 4 rp_pos
SA192397exp5_hilic_neg_02Sample 5 hilic_neg
SA192398exp5_hilic_neg_01Sample 5 hilic_neg
SA192399exp5_hilic_neg_03Sample 5 hilic_neg
SA192400exp5_hilic_pos_02Sample 5 hilic_pos
SA192401exp5_hilic_pos_01Sample 5 hilic_pos
SA192402exp5_hilic_pos_03Sample 5 hilic_pos
SA192403exp5_rp_neg_01Sample 5 rp_neg
SA192404exp5_rp_neg_02Sample 5 rp_neg
SA192405exp5_rp_neg_03Sample 5 rp_neg
SA192406exp5_rp_pos_03Sample 5 rp_pos
SA192407exp5_rp_pos_02Sample 5 rp_pos
SA192408exp5_rp_pos_01Sample 5 rp_pos
SA192409exp6_hilic_neg_03Sample 6 hilic_neg
SA192410exp6_hilic_neg_01Sample 6 hilic_neg
SA192411exp6_hilic_neg_02Sample 6 hilic_neg
SA192412exp6_hilic_pos_03Sample 6 hilic_pos
SA192413exp6_hilic_pos_02Sample 6 hilic_pos
SA192414exp6_hilic_pos_01Sample 6 hilic_pos
SA192415exp6_rp_neg_01Sample 6 rp_neg
SA192416exp6_rp_neg_02Sample 6 rp_neg
SA192417exp6_rp_neg_03Sample 6 rp_neg
SA192418exp6_rp_pos_01Sample 6 rp_pos
SA192419exp6_rp_pos_03Sample 6 rp_pos
SA192420exp6_rp_pos_02Sample 6 rp_pos
SA192421exp7_hilic_neg_03Sample 7 hilic_neg
SA192422exp7_hilic_neg_01Sample 7 hilic_neg
SA192423exp7_hilic_neg_02Sample 7 hilic_neg
SA192424exp7_hilic_pos_02Sample 7 hilic_pos
SA192425exp7_hilic_pos_03Sample 7 hilic_pos
SA192426exp7_hilic_pos_01Sample 7 hilic_pos
SA192427exp7_rp_neg_02Sample 7 rp_neg
SA192428exp7_rp_neg_01Sample 7 rp_neg
SA192429exp7_rp_neg_03Sample 7 rp_neg
SA192430exp7_rp_pos_02Sample 7 rp_pos
SA192431exp7_rp_pos_01Sample 7 rp_pos
SA192432exp7_rp_pos_03Sample 7 rp_pos
SA192433exp8_hilic_neg_01Sample 8 hilic_neg
SA192434exp8_hilic_neg_02Sample 8 hilic_neg
SA192435exp8_hilic_neg_03Sample 8 hilic_neg
SA192436exp8_hilic_pos_01Sample 8 hilic_pos
Showing page 1 of 2     Results:    1  2  Next     Showing results 1 to 100 of 120

Collection:

Collection ID:CO002121
Collection Summary:C. elegans were grown on large-scale culture plates (LSCPs), manually counted, aliquoted into 50,000 worm tubes, lyophilized and weighed. See detailed protocol for worm growth at: Shaver, A. O., Gouveia, G. J., Kirby, P. S., Andersen, E. C., Edison, A. S. Culture and Assay of Large-Scale Mixed-Stage Caenorhabditis elegans Populations. J. Vis. Exp. (171), e61453, doi:10.3791/61453 (2021).
Sample Type:Worms
Volumeoramount Collected:50,000 worms
Storage Conditions:-80℃
Storage Vials:2.0 mL screwcap tubes

Treatment:

Treatment ID:TR002140
Treatment Summary:The compared groups are different extraction protocols using a Taguchi Design of Experiments (DOE) approach. 3 different types of: solvent, volume, extraction time, and reconstitution solvent were investigated. Solvents included: IPA, MeOH, and 1:1 1-Butanol:MeOH for non-polar extractions followed by an 80:20 MeOH/H2O sequential polar extraction. Volumes of 0.5, 1.0, and 3.0 mL were used; Times: 0.5, 2.0, or 12.0 hours, and reconstitution solvents: IPA, 60/40 H2O/ACN, or 50/50 IPA/ACN (non-polar), and H2O, MeOH, or 80/20 MeOH/H2O (polar). Detailed information on the 9 different experimental conditions can be found in the attached manuscript or methods.

Sample Preparation:

Sampleprep ID:SP002134
Sampleprep Summary:Samples were extracted according to the L9 orthogonal array described in the manuscript. Details are shown in the attached methods, but for full context refer to the manuscript.

Combined analysis:

Analysis ID AN003330 AN003331 AN003332 AN003333
Analysis type MS MS MS MS
Chromatography type Reversed phase Reversed phase HILIC HILIC
Chromatography system Thermo Vanquish 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) Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
MS Type ESI ESI ESI ESI
MS instrument type Orbitrap Orbitrap Orbitrap Orbitrap
MS instrument name Thermo Q Exactive HF-X Orbitrap Thermo Q Exactive HF-X Orbitrap Thermo Q Exactive HF-X Orbitrap Thermo Q Exactive HF-X Orbitrap
Ion Mode POSITIVE NEGATIVE POSITIVE NEGATIVE
Units Peak height Peak height Peak height Peak height

Chromatography:

Chromatography ID:CH002467
Chromatography Summary:The following gradient program was used: -5.0 20% B; 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 -5.0 and 0.0 minutes, and a curve 6 for the remainder of the gradient.
Instrument Name:Thermo Vanquish
Column Name:Thermo Scientific Accucore C30 (150 x 2.1mm,2.6um)
Column Temperature:55
Flow Rate:0.400 mL/min
Sample Injection:2.0 uL
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:CH002468
Chromatography Summary:The following gradient program was used: -5.0 min 95% B; 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 -5.0 and 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.
Instrument Name:Thermo Vanquish
Column Name:Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
Column Temperature:40
Flow Rate:0.400 mL/min
Sample Injection:2.0 uL
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:MS003100
Analysis ID:AN003330
Instrument Name:Thermo Q Exactive HF-X Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Scan range 150-2000 m/z. Details in attached methods. MZmine 2.53 was used for data processing.
Ion Mode:POSITIVE
Capillary Temperature:262.50
Dry Gas Flow:50
Dry Gas Temp:425.0
Source Temperature:425.0
Spray Voltage:3500
Dataformat:.raw Profile
  
MS ID:MS003101
Analysis ID:AN003331
Instrument Name:Thermo Q Exactive HF-X Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Scan range 150-2000 m/z. Details in attached methods. MZmine 2.53 was used for data processing.
Ion Mode:NEGATIVE
Capillary Temperature:262.50
Dry Gas Flow:50
Dry Gas Temp:425.0
Source Temperature:425.0
Spray Voltage:2500
Dataformat:.raw Profile
  
MS ID:MS003102
Analysis ID:AN003332
Instrument Name:Thermo Q Exactive HF-X Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Scan range 70-1050 m/z. Details in attached methods. MZmine 2.53 was used for data processing.
Ion Mode:POSITIVE
Capillary Temperature:262.50
Dry Gas Flow:50
Dry Gas Temp:425.0
Source Temperature:425.0
Spray Voltage:3500
Dataformat:.raw Profile
  
MS ID:MS003103
Analysis ID:AN003333
Instrument Name:Thermo Q Exactive HF-X Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Scan range 70-1050 m/z. Details in attached methods. MZmine 2.53 was used for data processing.
Ion Mode:NEGATIVE
Capillary Temperature:262.50
Dry Gas Flow:50
Dry Gas Temp:425.0
Source Temperature:425.0
Spray Voltage:2500
Dataformat:.raw Profile
  logo