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.
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.
| Study ID | ST001777 |
| Study Title | Comparison of High-Resolution Fourier Transform Mass Spectrometry Platforms for Metabolite Annotation - C. elegans |
| Study Type | MS based metabolomics |
| Study 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 |
| dhuang74@gatech.edu | |
| Phone | 4045127523 |
| Submit Date | 2021-05-05 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2022-05-05 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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 |
|---|---|---|
| SA164978 | PD1074 C. elegans mixture 4 | AGC 1e5 - R 120K - neg |
| SA164979 | Model mixture 4 | AGC 1e5 - R 120K - neg |
| SA164980 | PD1074 C. elegans mixture 13 | AGC 1e5 - R 120K - pos |
| SA164981 | Model mixture 13 | AGC 1e5 - R 120K - pos |
| SA164982 | PD1074 C. elegans mixture 5 | AGC 1e5 - R 240K - neg |
| SA164983 | Model mixture 5 | AGC 1e5 - R 240K - neg |
| SA164984 | Model mixture 14 | AGC 1e5 - R 240K - pos |
| SA164985 | PD1074 C. elegans mixture 14 | AGC 1e5 - R 240K - pos |
| SA164986 | Model mixture 6 | AGC 1e5 - R 500K - neg |
| SA164987 | PD1074 C. elegans mixture 6 | AGC 1e5 - R 500K - neg |
| SA164988 | Model mixture 15 | AGC 1e5 - R 500K - pos |
| SA164989 | PD1074 C. elegans mixture 15 | AGC 1e5 - R 500K - pos |
| SA164990 | Model mixture 1 | AGC 5e4 - R 120K - neg |
| SA164991 | PD1074 C. elegans mixture 1 | AGC 5e4 - R 120K - neg |
| SA164992 | PD1074 C. elegans mixture 10 | AGC 5e4 - R 120K - pos |
| SA164993 | Model mixture 10 | AGC 5e4 - R 120K - pos |
| SA164994 | Model mixture 2 | AGC 5e4 - R 240K - neg |
| SA164995 | PD1074 C. elegans mixture 2 | AGC 5e4 - R 240K - neg |
| SA164996 | PD1074 C. elegans mixture 11 | AGC 5e4 - R 240K - pos |
| SA164997 | Model mixture 11 | AGC 5e4 - R 240K - pos |
| SA164998 | Model mixture 3 | AGC 5e4 - R 500K - neg |
| SA164999 | PD1074 C. elegans mixture 3 | AGC 5e4 - R 500K - neg |
| SA165000 | Model mixture 12 | AGC 5e4 - R 500K - pos |
| SA165001 | PD1074 C. elegans mixture 12 | AGC 5e4 - R 500K - pos |
| SA165002 | Model mixture 7 | AGC 5e5 - R 120K - neg |
| SA165003 | PD1074 C. elegans mixture 7 | AGC 5e5 - R 120K - neg |
| SA165004 | Model mixture 16 | AGC 5e5 - R 120K - pos |
| SA165005 | PD1074 C. elegans mixture 16 | AGC 5e5 - R 120K - pos |
| SA165006 | Model mixture 8 | AGC 5e5 - R 240K - neg |
| SA165007 | PD1074 C. elegans mixture 8 | AGC 5e5 - R 240K - neg |
| SA165008 | Model mixture 17 | AGC 5e5 - R 240K - pos |
| SA165009 | PD1074 C. elegans mixture 17 | AGC 5e5 - R 240K - pos |
| SA165010 | Model mixture 9 | AGC 5e5 - R 500K - neg |
| SA165011 | PD1074 C. elegans mixture 9 | AGC 5e5 - R 500K - neg |
| SA165012 | Model mixture 18 | AGC 5e5 - R 500K - pos |
| SA165013 | PD1074 C. elegans mixture 18 | AGC 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: | 80% water/20% acetonitrile; 0.1% formic acid; 10 mM ammonium acetate |
| Solvent B: | 100% acetonitrile; 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 |
