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metID: A R package for automatable compound annotation for LC−MS-based data

View ORCID ProfileXiaotao Shen, Si Wu, Liang Liang, Songjie Chen, View ORCID ProfileKévin Contrepois, Zheng-Jiang Zhu, Michael Snyder
doi: https://doi.org/10.1101/2021.05.08.443258
Xiaotao Shen
1Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94304, USA
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Si Wu
1Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94304, USA
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Liang Liang
1Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94304, USA
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Songjie Chen
1Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94304, USA
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Kévin Contrepois
1Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94304, USA
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Zheng-Jiang Zhu
2Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
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  • For correspondence: mpsnyder@stanford.edu
Michael Snyder
1Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94304, USA
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  • For correspondence: mpsnyder@stanford.edu
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Abstract

Summary Accurate and efficient compound annotation is a long-standing challenge for LC−MS-based data (e.g. untargeted metabolomics and exposomics). Substantial efforts have been devoted to overcoming this obstacle, whereas current tools are limited by the sources of spectral information used (in-house and public databases) and are not automated and streamlined. Therefore, we developed metID, an R package that combines information from all major databases for comprehensive and streamlined compound annotation. metID is a flexible, simple, and powerful tool that can be installed on all platforms, allowing the compound annotation process to be fully automatic and reproducible. A detailed tutorial and a case study are provided in Supplementary Materials.

Availability and implementation https://jaspershen.github.io/metID/.

Contact jiangzhu{at}sioc.ac.cn and mpsnyder{at}stanford.edu

Competing Interest Statement

M.S. is a co-founder and member of the scientific advisory boards of the following: Personalis, SensOmics, Filtricine, Qbio, January, Mirvie, and Oralome.

Footnotes

  • https://jaspershen.github.io/metID/index.html

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted May 10, 2021.
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metID: A R package for automatable compound annotation for LC−MS-based data
Xiaotao Shen, Si Wu, Liang Liang, Songjie Chen, Kévin Contrepois, Zheng-Jiang Zhu, Michael Snyder
bioRxiv 2021.05.08.443258; doi: https://doi.org/10.1101/2021.05.08.443258
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metID: A R package for automatable compound annotation for LC−MS-based data
Xiaotao Shen, Si Wu, Liang Liang, Songjie Chen, Kévin Contrepois, Zheng-Jiang Zhu, Michael Snyder
bioRxiv 2021.05.08.443258; doi: https://doi.org/10.1101/2021.05.08.443258

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