Analytical Chemistry, volume 92, issue 1, pages 588-592

Deep Learning for the Precise Peak Detection in High-Resolution LC–MS Data

Melnikov Arsenty D ^{1, 2}

Tsentalovich Yuri P ^{1, 2}

Yanshole Vadim V ^{1, 2}

Hide authors affiliations Show authors affiliations: 2 affiliations

International Tomography Center SB RAS, Institutskaya 3A, Novosibirsk 630090, Russia |

Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russia |

Publication type: Journal Article

Publication date: 2019-12-16

American Chemical Society (ACS)

Journal: Analytical Chemistry

Quartile SCImago

Quartile WOS

Impact factor: 7.4

ISSN: 00032700, 15206882, 21542686

DOI: 10.1021/acs.analchem.9b04811

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Analytical Chemistry

Abstract

This letter is devoted to the application of machine learning, namely, convolutional neural networks to solve problems in the initial steps of the common pipeline for data analysis in metabolomics. These steps are the peak detection and the peak integration in raw liquid chromatography-mass spectrometry (LC-MS) data. Widely used algorithms suffer from rather poor precision for these tasks, yielding many false positive signals. In the present work, we developed an algorithm named peakonly, which has high flexibility for the detection or exclusion of low-intensity noisy peaks, and shows excellent quality in the detection of true positive peaks, approaching the highest possible precision. The current approach was developed for the analysis of high-resolution LC-MS data for the purposes of metabolomics, but potentially it can be applied with several adaptations in other fields, which utilize high-resolution GC- or LC-MS techniques. Peakonly is freely available on GitHub ( https://github.com/arseha/peakonly ) under an MIT license.

By date By citations

Citations by journals

	2 4 6 8 10 12
Analytical Chemistry	Analytical Chemistry, 12, 12.37% Analytical Chemistry 12 publications, 12.37%
Journal of Chromatography A	Journal of Chromatography A, 8, 8.25% Journal of Chromatography A 8 publications, 8.25%
Briefings in Bioinformatics	Briefings in Bioinformatics, 5, 5.15% Briefings in Bioinformatics 5 publications, 5.15%
Metabolites	Metabolites, 4, 4.12% Metabolites 4 publications, 4.12%
Molecules	Molecules, 2, 2.06% Molecules 2 publications, 2.06%
Foods	Foods, 2, 2.06% Foods 2 publications, 2.06%
Chemometrics and Intelligent Laboratory Systems	Chemometrics and Intelligent Laboratory Systems, 2, 2.06% Chemometrics and Intelligent Laboratory Systems 2 publications, 2.06%
Computational and Structural Biotechnology Journal	Computational and Structural Biotechnology Journal, 2, 2.06% Computational and Structural Biotechnology Journal 2 publications, 2.06%
Analytica Chimica Acta	Analytica Chimica Acta, 2, 2.06% Analytica Chimica Acta 2 publications, 2.06%
TrAC - Trends in Analytical Chemistry	TrAC - Trends in Analytical Chemistry, 2, 2.06% TrAC - Trends in Analytical Chemistry 2 publications, 2.06%
Environmental Science Advances	Environmental Science Advances, 2, 2.06% Environmental Science Advances 2 publications, 2.06%
Bioinformatics	Bioinformatics, 2, 2.06% Bioinformatics 2 publications, 2.06%
Artificial Intelligence Review	Artificial Intelligence Review, 1, 1.03% Artificial Intelligence Review 1 publication, 1.03%
Frontiers in Computational Neuroscience	Frontiers in Computational Neuroscience, 1, 1.03% Frontiers in Computational Neuroscience 1 publication, 1.03%
Biomolecules	Biomolecules, 1, 1.03% Biomolecules 1 publication, 1.03%
Sensors	Sensors, 1, 1.03% Sensors 1 publication, 1.03%
Frontiers in Molecular Biosciences	Frontiers in Molecular Biosciences, 1, 1.03% Frontiers in Molecular Biosciences 1 publication, 1.03%
International Journal of Molecular Sciences	International Journal of Molecular Sciences, 1, 1.03% International Journal of Molecular Sciences 1 publication, 1.03%
Experimental and Molecular Medicine	Experimental and Molecular Medicine, 1, 1.03% Experimental and Molecular Medicine 1 publication, 1.03%
Metabolomics	Metabolomics, 1, 1.03% Metabolomics 1 publication, 1.03%
Scientific Reports	Scientific Reports, 1, 1.03% Scientific Reports 1 publication, 1.03%
Stem Cell Reviews and Reports	Stem Cell Reviews and Reports, 1, 1.03% Stem Cell Reviews and Reports 1 publication, 1.03%
Journal of Hazardous Materials	Journal of Hazardous Materials, 1, 1.03% Journal of Hazardous Materials 1 publication, 1.03%
Cell Reports Physical Science	Cell Reports Physical Science, 1, 1.03% Cell Reports Physical Science 1 publication, 1.03%
Biotechnology Advances	Biotechnology Advances, 1, 1.03% Biotechnology Advances 1 publication, 1.03%
Nuclear Engineering and Technology	Nuclear Engineering and Technology, 1, 1.03% Nuclear Engineering and Technology 1 publication, 1.03%
Progress in Materials Science	Progress in Materials Science, 1, 1.03% Progress in Materials Science 1 publication, 1.03%
Journal of Instrumentation	Journal of Instrumentation, 1, 1.03% Journal of Instrumentation 1 publication, 1.03%
Metabolic Engineering	Metabolic Engineering, 1, 1.03% Metabolic Engineering 1 publication, 1.03%

	2 4 6 8 10 12

Citations by publishers

	5 10 15 20 25 30
Elsevier	Elsevier, 26, 26.8% Elsevier 26 publications, 26.8%
American Chemical Society (ACS)	American Chemical Society (ACS), 14, 14.43% American Chemical Society (ACS) 14 publications, 14.43%
Multidisciplinary Digital Publishing Institute (MDPI)	Multidisciplinary Digital Publishing Institute (MDPI), 11, 11.34% Multidisciplinary Digital Publishing Institute (MDPI) 11 publications, 11.34%
Springer Nature	Springer Nature, 9, 9.28% Springer Nature 9 publications, 9.28%
Oxford University Press	Oxford University Press, 7, 7.22% Oxford University Press 7 publications, 7.22%
Royal Society of Chemistry (RSC)	Royal Society of Chemistry (RSC), 6, 6.19% Royal Society of Chemistry (RSC) 6 publications, 6.19%
Frontiers Media S.A.	Frontiers Media S.A., 3, 3.09% Frontiers Media S.A. 3 publications, 3.09%
Wiley	Wiley, 3, 3.09% Wiley 3 publications, 3.09%
Taylor & Francis	Taylor & Francis, 2, 2.06% Taylor & Francis 2 publications, 2.06%
IOP Publishing	IOP Publishing, 1, 1.03% IOP Publishing 1 publication, 1.03%
International Union of Crystallography (IUCr)	International Union of Crystallography (IUCr), 1, 1.03% International Union of Crystallography (IUCr) 1 publication, 1.03%
American Association for Clinical Chemistry	American Association for Clinical Chemistry, 1, 1.03% American Association for Clinical Chemistry 1 publication, 1.03%
Optical Society of America	Optical Society of America, 1, 1.03% Optical Society of America 1 publication, 1.03%
	5 10 15 20 25 30

We do not take into account publications that without a DOI.
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Melnikov A. D. et al. Deep Learning for the Precise Peak Detection in High-Resolution LC–MS Data // Analytical Chemistry. 2019. Vol. 92. No. 1. pp. 588-592.

GOST all authors (up to 50) Copy

Melnikov A. D., Tsentalovich Y. P., Yanshole V. V. Deep Learning for the Precise Peak Detection in High-Resolution LC–MS Data // Analytical Chemistry. 2019. Vol. 92. No. 1. pp. 588-592.

RIS |

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RIS Copy

TY - JOUR

DO - 10.1021/acs.analchem.9b04811

UR - https://doi.org/10.1021%2Facs.analchem.9b04811

TI - Deep Learning for the Precise Peak Detection in High-Resolution LC–MS Data

T2 - Analytical Chemistry

AU - Melnikov, Arsenty D

AU - Tsentalovich, Yuri P

AU - Yanshole, Vadim V

PY - 2019

DA - 2019/12/16 00:00:00

PB - American Chemical Society (ACS)

SP - 588-592

IS - 1

VL - 92

SN - 0003-2700

SN - 1520-6882

SN - 2154-2686

ER -

BibTex |

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BibTex Copy

@article{2019_Melnikov,

author = {Arsenty D Melnikov and Yuri P Tsentalovich and Vadim V Yanshole},

title = {Deep Learning for the Precise Peak Detection in High-Resolution LC–MS Data},

journal = {Analytical Chemistry},

year = {2019},

volume = {92},

publisher = {American Chemical Society (ACS)},

month = {dec},

url = {https://doi.org/10.1021%2Facs.analchem.9b04811},

number = {1},

pages = {588--592},

doi = {10.1021/acs.analchem.9b04811}

}

MLA

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MLA Copy

Melnikov, Arsenty D., et al. “Deep Learning for the Precise Peak Detection in High-Resolution LC–MS Data.” Analytical Chemistry, vol. 92, no. 1, Dec. 2019, pp. 588-592. https://doi.org/10.1021%2Facs.analchem.9b04811.

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Publisher

American Chemical Society (ACS)

Journal

Analytical Chemistry

Quartile SCImago

Quartile WOS

Impact factor

7.4

ISSN

00032700 (Print)
15206882 (Electronic)
21542686 (Print)

Labs

Laboratory of Proteomics and Metabolomics

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