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
Email	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

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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.

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.