QSRR Automator: A Tool for Automating Retention Time Prediction in Lipidomics and Metabolomics.

Metabolites
Bradley C NaylorJames E Cox

Abstract

The use of retention time is often critical for the identification of compounds in metabolomic and lipidomic studies. Standards are frequently unavailable for the retention time measurement of many metabolites, thus the ability to predict retention time for these compounds is highly valuable. A number of studies have applied machine learning to predict retention times, but applying a published machine learning model to different lab conditions is difficult. This is due to variation between chromatographic equipment, methods, and columns used for analysis. Recreating a machine learning model is likewise difficult without a dedicated bioinformatician. Herein we present QSRR Automator, a software package to automate retention time prediction model creation and demonstrate its utility by testing data from multiple chromatography columns from previous publications and in-house work. Analysis of these data sets shows similar accuracy to published models, demonstrating the software's utility in metabolomic and lipidomic studies.

References

Jun 23, 2007·Nucleic Acids Research·Eoin FahyShankar Subramaniam
Feb 19, 2008·Journal of Lipid Research·Vitali MatyashDominik Schwudke
May 6, 2015·Nature Methods·Hiroshi TsugawaMasanori Arita
May 15, 2015·Metabolomics : Official Journal of the Metabolomic Society·Mingshu CaoChris Jones
Jul 7, 2015·Analytical Chemistry·Fabian AichelerOliver Kohlbacher
Aug 21, 2015·Analytical Chemistry·Jan StanstrupUrška Vrhovšek
Nov 16, 2017·Nucleic Acids Research·David S WishartAugustin Scalbert
Jan 31, 2018·Analytical Chemistry·Carlos GuijasGary Siuzdak
Feb 8, 2018·Journal of Cheminformatics·Hirotomo MoriwakiTatsuya Takagi
Oct 30, 2018·Nucleic Acids Research·Sunghwan KimEvan E Bolton

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Citations

Mar 12, 2021·Emerging Topics in Life Sciences·Sophie Alvarez, Michael J Naldrett
May 13, 2021·Metabolomics : Official Journal of the Metabolomic Society·Biswapriya B Misra
Sep 5, 2021·Magnetic Resonance in Chemistry : MRC·Stefan KuhnRicardo Moreira Borges

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Methods Mentioned

BETA
SPLASH

Software Mentioned

MH Qual
QSRR Automator
scikit
MH Quant
QSRR
Agilent Mass Hunter ( MH ) Workstation
learn
SLogP
Mordred
kit learn

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