Summary of Study ST001777

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 PR001131. The data can be accessed directly via it's Project DOI: 10.21228/M8HD7B This work is supported by NIH grant, U2C- DK119886.

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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 IDST001777
Study TitleComparison of High-Resolution Fourier Transform Mass Spectrometry Platforms for Metabolite Annotation - C. elegans
Study TypeMS based metabolomics
Study SummaryFourier transform ion cyclotron resonance (FT-ICR) and Orbitrap mass spectrometry (MS) are among the highest-performing analytical platforms in metabolomics. Their high mass measurement accuracy and mass resolving power enable detailed investigation of biological metabolomes. Non-targeted MS experiments, however, yield extremely complex datasets that make metabolite annotation very challenging, if not impossible. High-resolution accurate mass measurements greatly facilitate this process by reducing mass errors and spectral overlaps. When applied together with relative isotopic abundance (RIA) measurements, heuristic rules, and constraints during searches, the number of candidate elemental formula(s) can be significantly reduced. Here, we evaluate the performance of two leading analytical MS platforms, Orbitrap ID-X and 12T solariX FT-ICR mass spectrometers, in terms of mass accuracy and RIA measurements, and how these factors affect the assignment of the correct elemental formulae in metabolite annotation. Quality of the mass measurements was evaluated under various experimental conditions (resolution: 120 K, 240 K, 500 K; automatic gain control: 5e4, 1e5, 5e5) for the Orbitrap MS platform.
Institute
Georgia Institute of Technology
DepartmentChemistry
LaboratoryFernández
Last NameHuang
First NameDanning
Address901 Atlantic Dr NE
Emaildhuang74@gatech.edu
Phone4045127523
Submit Date2021-05-05
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2022-05-05
Release Version1
Danning Huang Danning Huang
https://dx.doi.org/10.21228/M8HD7B
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001131
Project DOI:doi: 10.21228/M8HD7B
Project Title:Comparison of High-Resolution Fourier Transform Mass Spectrometry Platforms for Metabolite Annotation (part I)
Project Type:MS based metabolomics
Project Summary:Fourier transform ion cyclotron resonance (FT-ICR) and Orbitrap mass spectrometry (MS) are among the highest-performing analytical platforms in metabolomics. Their high mass measurement accuracy and mass resolving power enable detailed investigation of biological metabolomes. Non-targeted MS experiments, however, yield extremely complex datasets that make metabolite annotation very challenging, if not impossible. High-resolution accurate mass measurements greatly facilitate this process by reducing mass errors and spectral overlaps. When applied together with relative isotopic abundance (RIA) measurements, heuristic rules, and constraints during searches, the number of candidate elemental formula(s) can be significantly reduced. Here, we evaluate the performance of two leading analytical MS platforms, Orbitrap ID-X and 12T solariX FT-ICR mass spectrometers, in terms of mass accuracy and RIA measurements, and how these factors affect the assignment of the correct elemental formulae in metabolite annotation. Quality of the mass measurements was evaluated under various experimental conditions (resolution: 120 K, 240 K, 500 K; automatic gain control: 5e4, 1e5, 5e5) for the Orbitrap MS platform.
Institute:Georgia Institute of Technology
Department:Chemistry
Laboratory:Fernández
Last Name:Huang
First Name:Danning
Address:901 Atlantic Dr NE, Atlanta, GA, 30332, USA
Email:dhuang74@gatech.edu
Phone:404-512-7523

Subject:

Subject ID:SU001854
Subject Type:Synthetic sample

Factors:

Subject type: Synthetic sample; Subject species: - (Factor headings shown in green)

mb_sample_id local_sample_id Experimental Condition
SA164978PD1074 C. elegans mixture 4AGC 1e5 - R 120K - neg
SA164979Model mixture 4AGC 1e5 - R 120K - neg
SA164980PD1074 C. elegans mixture 13AGC 1e5 - R 120K - pos
SA164981Model mixture 13AGC 1e5 - R 120K - pos
SA164982PD1074 C. elegans mixture 5AGC 1e5 - R 240K - neg
SA164983Model mixture 5AGC 1e5 - R 240K - neg
SA164984Model mixture 14AGC 1e5 - R 240K - pos
SA164985PD1074 C. elegans mixture 14AGC 1e5 - R 240K - pos
SA164986Model mixture 6AGC 1e5 - R 500K - neg
SA164987PD1074 C. elegans mixture 6AGC 1e5 - R 500K - neg
SA164988Model mixture 15AGC 1e5 - R 500K - pos
SA164989PD1074 C. elegans mixture 15AGC 1e5 - R 500K - pos
SA164990Model mixture 1AGC 5e4 - R 120K - neg
SA164991PD1074 C. elegans mixture 1AGC 5e4 - R 120K - neg
SA164992PD1074 C. elegans mixture 10AGC 5e4 - R 120K - pos
SA164993Model mixture 10AGC 5e4 - R 120K - pos
SA164994Model mixture 2AGC 5e4 - R 240K - neg
SA164995PD1074 C. elegans mixture 2AGC 5e4 - R 240K - neg
SA164996PD1074 C. elegans mixture 11AGC 5e4 - R 240K - pos
SA164997Model mixture 11AGC 5e4 - R 240K - pos
SA164998Model mixture 3AGC 5e4 - R 500K - neg
SA164999PD1074 C. elegans mixture 3AGC 5e4 - R 500K - neg
SA165000Model mixture 12AGC 5e4 - R 500K - pos
SA165001PD1074 C. elegans mixture 12AGC 5e4 - R 500K - pos
SA165002Model mixture 7AGC 5e5 - R 120K - neg
SA165003PD1074 C. elegans mixture 7AGC 5e5 - R 120K - neg
SA165004Model mixture 16AGC 5e5 - R 120K - pos
SA165005PD1074 C. elegans mixture 16AGC 5e5 - R 120K - pos
SA165006Model mixture 8AGC 5e5 - R 240K - neg
SA165007PD1074 C. elegans mixture 8AGC 5e5 - R 240K - neg
SA165008Model mixture 17AGC 5e5 - R 240K - pos
SA165009PD1074 C. elegans mixture 17AGC 5e5 - R 240K - pos
SA165010Model mixture 9AGC 5e5 - R 500K - neg
SA165011PD1074 C. elegans mixture 9AGC 5e5 - R 500K - neg
SA165012Model mixture 18AGC 5e5 - R 500K - pos
SA165013PD1074 C. elegans mixture 18AGC 5e5 - R 500K - pos
Showing results 1 to 36 of 36

Collection:

Collection ID:CO001847
Collection Summary:PD1074 C. elegans samples (~10 mg) were collected and lyophilized.
Sample Type:Worms
Storage Conditions:-80℃

Treatment:

Treatment ID:TR001867
Treatment Summary:standard PD1047 C.elegans treatment

Sample Preparation:

Sampleprep ID:SP001860
Sampleprep Summary:Model Mixture Sample Preparation One hundred and four selected chemical standard compounds were purchased from Sigma-Aldrich (St. Louis, MO, USA) and used to prepare stock solutions at a concentration of 0.001 M in LC-MS grade methanol (Fisher Scientific, Pittsburgh, PA, USA). These standards were selected because they map to key metabolic pathways, some involved in cancer. If a chemical could not be completely dissolved in methanol, LC-MS grade water (Fisher Scientific, Pittsburgh, PA, USA) was added to increase solubility. A pooled sample of 104 standard compounds was diluted with methanol at a final concentration of 5 μM. PD1074 C. elegans Bio-mixture Sample Preparation Three 2.0 mm zirconium oxide beads and ~75 μL volume of 0.5 mm glass beads were added to each lyophilized PD1074 C. elegans sample (~10 mg). Samples were placed in a TissueLyser II (QIAGEN, Hilden, Germany) and homogenized at 1,800 rpm, -80 °C for 3 min. One and a half mL of 80% methanol (in water) was added to each homogenized sample. Samples were then shaken using an Isotemp high speed shaker (Fisher Scientific, Pittsburgh, PA, USA) at 1,500 rpm for 30 min, and centrifuged at 22,100 g for 5 min. The supernatant was collected, dried and stored at -80 °C. Prior to MS analysis, dried C. elegans matrices were resuspended with 1 mL LC-MS grade methanol containing the 104 standard compounds at a 5 μM concentration.

Combined analysis:

Analysis ID AN002884 AN002885
Analysis type MS MS
Chromatography type HILIC HILIC
Chromatography system Thermo Vanquish Thermo Vanquish
Column Waters Acquity BEH Amide (150 x 2.1mm, 1.7um) Waters Acquity BEH Amide (150 x 2.1mm, 1.7um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Orbitrap ID-X Tribrid Thermo Orbitrap ID-X Tribrid
Ion Mode POSITIVE NEGATIVE
Units Da Da

Chromatography:

Chromatography ID:CH002139
Chromatography Summary:HILIC method
Instrument Name:Thermo Vanquish
Column Name:Waters Acquity BEH Amide (150 x 2.1mm, 1.7um)
Column Temperature:40
Flow Rate:0.4 ml/min
Sample Injection:2μL
Solvent A:water/acetonitrile (80:20 v/v), with 10 mM formate and 0.1% formic acid
Solvent B:acetonitrile with 0.1% formic acid
Chromatography Type:HILIC

MS:

MS ID:MS002677
Analysis ID:AN002884
Instrument Name:Thermo Orbitrap ID-X Tribrid
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Samples were analyzed in positive and negative ion modes for HILIC chromatography. Spectral features were extracted from the raw data using MZmine 2.51.
Ion Mode:POSITIVE
Spray Voltage:3.5 kV
Automatic Gain Control:5e4, 1e5, 5e5
  
MS ID:MS002678
Analysis ID:AN002885
Instrument Name:Thermo Orbitrap ID-X Tribrid
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Samples were analyzed in positive and negative ion modes for HILIC chromatography. Spectral features were extracted from the raw data using MZmine 2.51.
Ion Mode:NEGATIVE
Spray Voltage:-2.5 kV
Automatic Gain Control:5e4, 1e5, 5e5
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