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Open AccessArticle

Creating a Reliable Mass Spectral–Retention Time Library for All Ion Fragmentation-Based Metabolomics

1
Department of Genetics, SOKENDAI (Graduate University for Advanced Studies), Shizuoka 411-8540, Japan
2
RIKEN Center for Sustainable Resource Science, Kanagawa, Yokohama 230-0045, Japan
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RIKEN Center for Integrative Medical Sciences, Kanagawa, Yokohama 230-0045, Japan
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Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
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Gunma University Initiative for Advanced Research (GIAR), Gunma University, Gunma 371-8510, Japan
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Center for Information Biology, National Institute of Genetics, Shizuoka 411-8540, Japan
*
Author to whom correspondence should be addressed.
Metabolites 2019, 9(11), 251; https://doi.org/10.3390/metabo9110251
Received: 17 August 2019 / Revised: 21 October 2019 / Accepted: 24 October 2019 / Published: 26 October 2019
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. View Full-Text
Keywords: LC–MS; metabolomics; mass spectral deconvolution; chemical library; all ion fragmentation LC–MS; metabolomics; mass spectral deconvolution; chemical library; all ion fragmentation
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Tada, I.; Tsugawa, H.; Meister, I.; Zhang, P.; Shu, R.; Katsumi, R.; Wheelock, C.E.; Arita, M.; Chaleckis, R. Creating a Reliable Mass Spectral–Retention Time Library for All Ion Fragmentation-Based Metabolomics. Metabolites 2019, 9, 251.

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