Creating a Reliable Mass Spectral–Retention Time Library for All Ion Fragmentation-Based Metabolomics
Accurate metabolite identification remains one of the primary challenges in a metabolomics study. A reliable chemical spectral library increases the confidence in annotation, and the availability of raw and annotated data in public databases facilitates the transfer of Liquid chromatography coupled...
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doaj-9487100499464ceaa5f29dc4b11c867c2020-11-25T02:50:06ZengMDPI AGMetabolites2218-19892019-10-0191125110.3390/metabo9110251metabo9110251Creating a Reliable Mass Spectral–Retention Time Library for All Ion Fragmentation-Based MetabolomicsIpputa Tada0Hiroshi Tsugawa1Isabel Meister2Pei Zhang3Rie Shu4Riho Katsumi5Craig E. Wheelock6Masanori Arita7Romanas Chaleckis8Department of Genetics, SOKENDAI (Graduate University for Advanced Studies), Shizuoka 411-8540, JapanRIKEN Center for Sustainable Resource Science, Kanagawa, Yokohama 230-0045, JapanDivision of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, SwedenDivision of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, SwedenGunma University Initiative for Advanced Research (GIAR), Gunma University, Gunma 371-8510, JapanGunma University Initiative for Advanced Research (GIAR), Gunma University, Gunma 371-8510, JapanDivision of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, SwedenRIKEN Center for Sustainable Resource Science, Kanagawa, Yokohama 230-0045, JapanDivision of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, SwedenAccurate metabolite identification remains one of the primary challenges in a metabolomics study. A reliable chemical spectral library increases the confidence in annotation, and the availability of raw and annotated data in public databases facilitates the transfer of Liquid chromatography coupled to mass spectrometry (LC−MS) methods across laboratories. Here, we illustrate how the combination of MS2 spectra, accurate mass, and retention time can improve the confidence of annotation and provide techniques to create a reliable library for all ion fragmentation (AIF) data with a focus on the characterization of the retention time. The resulting spectral library incorporates information on adducts and in-source fragmentation in AIF data, while noise peaks are effectively minimized through multiple deconvolution processes. We also report the development of the Mass Spectral LIbrary MAnager (MS-LIMA) tool to accelerate library sharing and transfer across laboratories. This library construction strategy improves the confidence in annotation for AIF data in LC−MS-based metabolomics and will facilitate the sharing of retention time and mass spectral data in the metabolomics community.https://www.mdpi.com/2218-1989/9/11/251lc–msmetabolomicsmass spectral deconvolutionchemical libraryall ion fragmentation |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Ipputa Tada Hiroshi Tsugawa Isabel Meister Pei Zhang Rie Shu Riho Katsumi Craig E. Wheelock Masanori Arita Romanas Chaleckis |
spellingShingle |
Ipputa Tada Hiroshi Tsugawa Isabel Meister Pei Zhang Rie Shu Riho Katsumi Craig E. Wheelock Masanori Arita Romanas Chaleckis Creating a Reliable Mass Spectral–Retention Time Library for All Ion Fragmentation-Based Metabolomics Metabolites lc–ms metabolomics mass spectral deconvolution chemical library all ion fragmentation |
author_facet |
Ipputa Tada Hiroshi Tsugawa Isabel Meister Pei Zhang Rie Shu Riho Katsumi Craig E. Wheelock Masanori Arita Romanas Chaleckis |
author_sort |
Ipputa Tada |
title |
Creating a Reliable Mass Spectral–Retention Time Library for All Ion Fragmentation-Based Metabolomics |
title_short |
Creating a Reliable Mass Spectral–Retention Time Library for All Ion Fragmentation-Based Metabolomics |
title_full |
Creating a Reliable Mass Spectral–Retention Time Library for All Ion Fragmentation-Based Metabolomics |
title_fullStr |
Creating a Reliable Mass Spectral–Retention Time Library for All Ion Fragmentation-Based Metabolomics |
title_full_unstemmed |
Creating a Reliable Mass Spectral–Retention Time Library for All Ion Fragmentation-Based Metabolomics |
title_sort |
creating a reliable mass spectral–retention time library for all ion fragmentation-based metabolomics |
publisher |
MDPI AG |
series |
Metabolites |
issn |
2218-1989 |
publishDate |
2019-10-01 |
description |
Accurate metabolite identification remains one of the primary challenges in a metabolomics study. A reliable chemical spectral library increases the confidence in annotation, and the availability of raw and annotated data in public databases facilitates the transfer of Liquid chromatography coupled to mass spectrometry (LC−MS) methods across laboratories. Here, we illustrate how the combination of MS2 spectra, accurate mass, and retention time can improve the confidence of annotation and provide techniques to create a reliable library for all ion fragmentation (AIF) data with a focus on the characterization of the retention time. The resulting spectral library incorporates information on adducts and in-source fragmentation in AIF data, while noise peaks are effectively minimized through multiple deconvolution processes. We also report the development of the Mass Spectral LIbrary MAnager (MS-LIMA) tool to accelerate library sharing and transfer across laboratories. This library construction strategy improves the confidence in annotation for AIF data in LC−MS-based metabolomics and will facilitate the sharing of retention time and mass spectral data in the metabolomics community. |
topic |
lc–ms metabolomics mass spectral deconvolution chemical library all ion fragmentation |
url |
https://www.mdpi.com/2218-1989/9/11/251 |
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