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Lipid Annotator: Towards Accurate Annotation in Non-Targeted Liquid Chromatography High-Resolution Tandem Mass Spectrometry (LC-HRMS/MS) Lipidomics Using a Rapid and User-Friendly Software

Lipidomics has great promise in various applications; however, a major bottleneck in lipidomics is the accurate and comprehensive annotation of high-resolution tandem mass spectral data. While the number of available lipidomics software has drastically increased over the past five years, the reducti...

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Autores principales: Koelmel, Jeremy P., Li, Xiangdong, Stow, Sarah M., Sartain, Mark J., Murali, Adithya, Kemperman, Robin, Tsugawa, Hiroshi, Takahashi, Mikiko, Vasiliou, Vasilis, Bowden, John A., Yost, Richard A., Garrett, Timothy J., Kitagawa, Norton
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7142889/
https://www.ncbi.nlm.nih.gov/pubmed/32178227
http://dx.doi.org/10.3390/metabo10030101
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author Koelmel, Jeremy P.
Li, Xiangdong
Stow, Sarah M.
Sartain, Mark J.
Murali, Adithya
Kemperman, Robin
Tsugawa, Hiroshi
Takahashi, Mikiko
Vasiliou, Vasilis
Bowden, John A.
Yost, Richard A.
Garrett, Timothy J.
Kitagawa, Norton
author_facet Koelmel, Jeremy P.
Li, Xiangdong
Stow, Sarah M.
Sartain, Mark J.
Murali, Adithya
Kemperman, Robin
Tsugawa, Hiroshi
Takahashi, Mikiko
Vasiliou, Vasilis
Bowden, John A.
Yost, Richard A.
Garrett, Timothy J.
Kitagawa, Norton
author_sort Koelmel, Jeremy P.
collection PubMed
description Lipidomics has great promise in various applications; however, a major bottleneck in lipidomics is the accurate and comprehensive annotation of high-resolution tandem mass spectral data. While the number of available lipidomics software has drastically increased over the past five years, the reduction of false positives and the realization of obtaining structurally accurate annotations remains a significant challenge. We introduce Lipid Annotator, which is a user-friendly software for lipidomic analysis of data collected by liquid chromatography high-resolution tandem mass spectrometry (LC-HRMS/MS). We validate annotation accuracy against lipid standards and other lipidomics software. Lipid Annotator was integrated into a workflow applying an iterative exclusion MS/MS acquisition strategy to National Institute of Standards and Technology (NIST) SRM 1950 Metabolites in Frozen Human Plasma using reverse phase LC-HRMS/MS. Lipid Annotator, LipidMatch, and MS-DIAL produced consensus annotations at the level of lipid class for 98% and 96% of features detected in positive and negative mode, respectively. Lipid Annotator provides percentages of fatty acyl constituent species and employs scoring algorithms based on probability theory, which is less subjective than the tolerance and weighted match scores commonly used by available software. Lipid Annotator enables analysis of large sample cohorts and improves data-processing throughput as compared to previous lipidomics software.
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spelling pubmed-71428892020-04-14 Lipid Annotator: Towards Accurate Annotation in Non-Targeted Liquid Chromatography High-Resolution Tandem Mass Spectrometry (LC-HRMS/MS) Lipidomics Using a Rapid and User-Friendly Software Koelmel, Jeremy P. Li, Xiangdong Stow, Sarah M. Sartain, Mark J. Murali, Adithya Kemperman, Robin Tsugawa, Hiroshi Takahashi, Mikiko Vasiliou, Vasilis Bowden, John A. Yost, Richard A. Garrett, Timothy J. Kitagawa, Norton Metabolites Article Lipidomics has great promise in various applications; however, a major bottleneck in lipidomics is the accurate and comprehensive annotation of high-resolution tandem mass spectral data. While the number of available lipidomics software has drastically increased over the past five years, the reduction of false positives and the realization of obtaining structurally accurate annotations remains a significant challenge. We introduce Lipid Annotator, which is a user-friendly software for lipidomic analysis of data collected by liquid chromatography high-resolution tandem mass spectrometry (LC-HRMS/MS). We validate annotation accuracy against lipid standards and other lipidomics software. Lipid Annotator was integrated into a workflow applying an iterative exclusion MS/MS acquisition strategy to National Institute of Standards and Technology (NIST) SRM 1950 Metabolites in Frozen Human Plasma using reverse phase LC-HRMS/MS. Lipid Annotator, LipidMatch, and MS-DIAL produced consensus annotations at the level of lipid class for 98% and 96% of features detected in positive and negative mode, respectively. Lipid Annotator provides percentages of fatty acyl constituent species and employs scoring algorithms based on probability theory, which is less subjective than the tolerance and weighted match scores commonly used by available software. Lipid Annotator enables analysis of large sample cohorts and improves data-processing throughput as compared to previous lipidomics software. MDPI 2020-03-12 /pmc/articles/PMC7142889/ /pubmed/32178227 http://dx.doi.org/10.3390/metabo10030101 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Koelmel, Jeremy P.
Li, Xiangdong
Stow, Sarah M.
Sartain, Mark J.
Murali, Adithya
Kemperman, Robin
Tsugawa, Hiroshi
Takahashi, Mikiko
Vasiliou, Vasilis
Bowden, John A.
Yost, Richard A.
Garrett, Timothy J.
Kitagawa, Norton
Lipid Annotator: Towards Accurate Annotation in Non-Targeted Liquid Chromatography High-Resolution Tandem Mass Spectrometry (LC-HRMS/MS) Lipidomics Using a Rapid and User-Friendly Software
title Lipid Annotator: Towards Accurate Annotation in Non-Targeted Liquid Chromatography High-Resolution Tandem Mass Spectrometry (LC-HRMS/MS) Lipidomics Using a Rapid and User-Friendly Software
title_full Lipid Annotator: Towards Accurate Annotation in Non-Targeted Liquid Chromatography High-Resolution Tandem Mass Spectrometry (LC-HRMS/MS) Lipidomics Using a Rapid and User-Friendly Software
title_fullStr Lipid Annotator: Towards Accurate Annotation in Non-Targeted Liquid Chromatography High-Resolution Tandem Mass Spectrometry (LC-HRMS/MS) Lipidomics Using a Rapid and User-Friendly Software
title_full_unstemmed Lipid Annotator: Towards Accurate Annotation in Non-Targeted Liquid Chromatography High-Resolution Tandem Mass Spectrometry (LC-HRMS/MS) Lipidomics Using a Rapid and User-Friendly Software
title_short Lipid Annotator: Towards Accurate Annotation in Non-Targeted Liquid Chromatography High-Resolution Tandem Mass Spectrometry (LC-HRMS/MS) Lipidomics Using a Rapid and User-Friendly Software
title_sort lipid annotator: towards accurate annotation in non-targeted liquid chromatography high-resolution tandem mass spectrometry (lc-hrms/ms) lipidomics using a rapid and user-friendly software
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7142889/
https://www.ncbi.nlm.nih.gov/pubmed/32178227
http://dx.doi.org/10.3390/metabo10030101
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