Summary of Study ST001778

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	ST001778
Study Title	Comparison of High-Resolution Fourier Transform Mass Spectrometry Platforms for Metabolite Annotation
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.
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)	mzML
Analysis Type Detail	ICR-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:	SU001855
Subject Type:	Synthetic sample

Factors:

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

mb_sample_id	local_sample_id	Experimental Condition
SA165014	PD1074 C. elegans mixture 2	8M - neg
SA165015	PD1074 C. elegans mixture 3	8M - neg
SA165016	Model mixture 1	8M - neg
SA165017	PD1074 C. elegans mixture 1	8M - neg
SA165018	Model mixture 2	8M - neg
SA165019	PD1074 C. elegans mixture 6	8M - pos
SA165020	PD1074 C. elegans mixture 5	8M - pos
SA165021	PD1074 C. elegans mixture 4	8M - pos
SA165022	Model mixture 4	8M - pos
SA165023	Model mixture 3	8M - pos
SA165024	Model mixture 5	8M - pos

Showing results 1 to 11 of 11

Showing results 1 to 11 of 11

Collection:

Collection ID:	CO001848
Collection Summary:	PD1074 C. elegans samples (~10 mg) were collected and lyophilized.
Sample Type:	Worms
Storage Conditions:	-80℃

Treatment:

Treatment ID:	TR001868
Treatment Summary:	standard PD1047 C.elegans treatment

Sample Preparation:

Sampleprep ID:	SP001861
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:

SP001861

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	AN002886	AN002887
Analysis type	MS	MS
Chromatography type	None (Direct infusion)	None (Direct infusion)
Chromatography system	none	none
Column	none	none
MS Type	ESI	ESI
MS instrument type	FT-ICR	FT-ICR
MS instrument name	Bruker Solarix FT-ICR-MS	Bruker Solarix FT-ICR-MS
Ion Mode	POSITIVE	NEGATIVE
Units	Da	Da

Chromatography:

Chromatography ID:	CH002140
Instrument Name:	none
Column Name:	none
Chromatography Type:	None (Direct infusion)

MS:

MS ID:	MS002679
Analysis ID:	AN002886
Instrument Name:	Bruker Solarix FT-ICR-MS
Instrument Type:	FT-ICR
MS Type:	ESI
MS Comments:	Samples were analyzed in positive and negative ion modes with direct infusion FT-ICR MS. A spectral size of 8 M was used for data acquisition with an ion accumulation time of 0.025 s and a scan range of 73.71 – 1000.00 m/z. Average scans were set to 200. Raw data files were converted into mzML format using MSConvert. Spectral features were extracted using MZmine 2.51.
Ion Mode:	POSITIVE
Capillary Voltage:	5.0kV
Dry Gas Flow:	4.0 L/min
Dry Gas Temp:	180 °C
Nebulizer:	0.5bar

MS ID:	MS002680
Analysis ID:	AN002887
Instrument Name:	Bruker Solarix FT-ICR-MS
Instrument Type:	FT-ICR
MS Type:	ESI
MS Comments:	Samples were analyzed in positive and negative ion modes with direct infusion FT-ICR MS. A spectral size of 8 M was used for data acquisition with an ion accumulation time of 0.025 s and a scan range of 73.71 – 1000.00 m/z. Average scans were set to 200. Raw data files were converted into mzML format using MSConvert. Spectral features were extracted using MZmine 2.51.
Ion Mode:	NEGATIVE
Capillary Voltage:	-4.5kV
Dry Gas Flow:	4.0 L/min
Dry Gas Temp:	180 °C
Nebulizer:	0.5bar