MetaMOPE: A web service for mobile phase determination and fast chromatography peaks evaluation for metabolomics

Dong Ming Tsai; Ching Yao Chang; Shih Ming Lin; Tien Chueh Kuo; San Yuan Wang; Guan Yuan Chen; Ching Hua Kuo; Yufeng Jane Tseng

doi:10.1093/bioadv/vbad061

MetaMOPE: A web service for mobile phase determination and fast chromatography peaks evaluation for metabolomics

Dong Ming Tsai, Ching Yao Chang, Shih Ming Lin, Tien Chueh Kuo, San Yuan Wang, Guan Yuan Chen, Ching Hua Kuo, Yufeng Jane Tseng

Research output: Contribution to journal › Article › peer-review

Abstract

Motivation: Liquid chromatography coupled with mass spectrometry (LC-MS) is widely used in metabolomics studies, while HILIC LC-MS is particularly suited for polar metabolites. Determining an optimized mobile phase and developing a proper liquid chromatography method tend to be laborious, time-consuming and empirical. Results: We developed a containerized web tool providing a workflow to quickly determine the optimized mobile phase by batch-evaluating chromatography peaks for metabolomics LC-MS studies. A mass chromatographic quality value, an asymmetric factor, and the local maximum intensity of the extracted ion chromatogram were calculated to determine the number of peaks and peak retention time. The optimal mobile phase can be quickly determined by selecting the mobile phase that produces the largest number of resolved peaks. Moreover, the workflow enables one to automatically process the repeats by evaluating chromatography peaks and determining the retention time of large standards. This workflow was validated with 20 chemical standards and successfully constructed a reference library of 571 metabolites for the HILIC LC-MS platform.

Original language	English
Article number	vbad061
Journal	Bioinformatics Advances
Volume	3
Issue number	1
DOIs	https://doi.org/10.1093/bioadv/vbad061
Publication status	Published - 2023

ASJC Scopus subject areas

Structural Biology
Molecular Biology
Genetics
Computer Science Applications

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10.1093/bioadv/vbad061

Cite this

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title = "MetaMOPE: A web service for mobile phase determination and fast chromatography peaks evaluation for metabolomics",

abstract = "Motivation: Liquid chromatography coupled with mass spectrometry (LC-MS) is widely used in metabolomics studies, while HILIC LC-MS is particularly suited for polar metabolites. Determining an optimized mobile phase and developing a proper liquid chromatography method tend to be laborious, time-consuming and empirical. Results: We developed a containerized web tool providing a workflow to quickly determine the optimized mobile phase by batch-evaluating chromatography peaks for metabolomics LC-MS studies. A mass chromatographic quality value, an asymmetric factor, and the local maximum intensity of the extracted ion chromatogram were calculated to determine the number of peaks and peak retention time. The optimal mobile phase can be quickly determined by selecting the mobile phase that produces the largest number of resolved peaks. Moreover, the workflow enables one to automatically process the repeats by evaluating chromatography peaks and determining the retention time of large standards. This workflow was validated with 20 chemical standards and successfully constructed a reference library of 571 metabolites for the HILIC LC-MS platform.",

author = "Tsai, {Dong Ming} and Chang, {Ching Yao} and Lin, {Shih Ming} and Kuo, {Tien Chueh} and Wang, {San Yuan} and Chen, {Guan Yuan} and Kuo, {Ching Hua} and Tseng, {Yufeng Jane}",

note = "Funding Information: This work was supported by the Ministry of Science and Technology [MOST 107-2627-E-002-002-, MOST 108-2321-B-038-003-, MOST 111-2320-B-002-043-MY2]; and the Taiwan Food and Drug Administration, Ministry of Health and Welfare [MOHW109-FDA-D-114-000611, MOHW112-FDA-D-114-000611]; and National Taiwan University [NTU-CC-109L892703]. We thank the Computational Molecular Design and Metabolomics Laboratory, Department of Computer Science and Information Engineering, Metabolomics Core Laboratory, Centers of Genomics and Precision Medicine, National Taiwan University, the “Center of Precision Medicine” from The Featured Areas Research Center Program within the framework of the Higher Education Sprout Project by the Ministry of Education (MOE), and Physics Division, National Center for Theoretical Sciences for their resources. Publisher Copyright: {\textcopyright} 2023 The Author(s). Published by Oxford University Press.",

year = "2023",

doi = "10.1093/bioadv/vbad061",

language = "English",

volume = "3",

journal = "Bioinformatics Advances",

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publisher = "Oxford University Press",

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T1 - MetaMOPE

T2 - A web service for mobile phase determination and fast chromatography peaks evaluation for metabolomics

AU - Tsai, Dong Ming

AU - Chang, Ching Yao

AU - Lin, Shih Ming

AU - Kuo, Tien Chueh

AU - Wang, San Yuan

AU - Chen, Guan Yuan

AU - Kuo, Ching Hua

AU - Tseng, Yufeng Jane

N1 - Funding Information: This work was supported by the Ministry of Science and Technology [MOST 107-2627-E-002-002-, MOST 108-2321-B-038-003-, MOST 111-2320-B-002-043-MY2]; and the Taiwan Food and Drug Administration, Ministry of Health and Welfare [MOHW109-FDA-D-114-000611, MOHW112-FDA-D-114-000611]; and National Taiwan University [NTU-CC-109L892703]. We thank the Computational Molecular Design and Metabolomics Laboratory, Department of Computer Science and Information Engineering, Metabolomics Core Laboratory, Centers of Genomics and Precision Medicine, National Taiwan University, the “Center of Precision Medicine” from The Featured Areas Research Center Program within the framework of the Higher Education Sprout Project by the Ministry of Education (MOE), and Physics Division, National Center for Theoretical Sciences for their resources. Publisher Copyright: © 2023 The Author(s). Published by Oxford University Press.

PY - 2023

Y1 - 2023

N2 - Motivation: Liquid chromatography coupled with mass spectrometry (LC-MS) is widely used in metabolomics studies, while HILIC LC-MS is particularly suited for polar metabolites. Determining an optimized mobile phase and developing a proper liquid chromatography method tend to be laborious, time-consuming and empirical. Results: We developed a containerized web tool providing a workflow to quickly determine the optimized mobile phase by batch-evaluating chromatography peaks for metabolomics LC-MS studies. A mass chromatographic quality value, an asymmetric factor, and the local maximum intensity of the extracted ion chromatogram were calculated to determine the number of peaks and peak retention time. The optimal mobile phase can be quickly determined by selecting the mobile phase that produces the largest number of resolved peaks. Moreover, the workflow enables one to automatically process the repeats by evaluating chromatography peaks and determining the retention time of large standards. This workflow was validated with 20 chemical standards and successfully constructed a reference library of 571 metabolites for the HILIC LC-MS platform.

AB - Motivation: Liquid chromatography coupled with mass spectrometry (LC-MS) is widely used in metabolomics studies, while HILIC LC-MS is particularly suited for polar metabolites. Determining an optimized mobile phase and developing a proper liquid chromatography method tend to be laborious, time-consuming and empirical. Results: We developed a containerized web tool providing a workflow to quickly determine the optimized mobile phase by batch-evaluating chromatography peaks for metabolomics LC-MS studies. A mass chromatographic quality value, an asymmetric factor, and the local maximum intensity of the extracted ion chromatogram were calculated to determine the number of peaks and peak retention time. The optimal mobile phase can be quickly determined by selecting the mobile phase that produces the largest number of resolved peaks. Moreover, the workflow enables one to automatically process the repeats by evaluating chromatography peaks and determining the retention time of large standards. This workflow was validated with 20 chemical standards and successfully constructed a reference library of 571 metabolites for the HILIC LC-MS platform.

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MetaMOPE: A web service for mobile phase determination and fast chromatography peaks evaluation for metabolomics

Abstract

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