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27 January 2023
Article (Scientific journals)
Joint structural annotation of small molecules using liquid chromatography retention order and tandem mass spectrometry data
Bach, Eric; Schymanski, Emma; Rousu, Juho
2022In Nature Machine Intelligence, 4 (12), p. 1224--1237
Peer reviewed


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Abstract :
[en] Abstract Structural annotation of small molecules in biological samples remains a key bottleneck in untargeted metabolomics, despite rapid progress in predictive methods and tools during the past decade. Liquid chromatography–tandem mass spectrometry, one of the most widely used analysis platforms, can detect thousands of molecules in a sample, the vast majority of which remain unidentified even with best-of-class methods. Here we present LC-MS2Struct, a machine learning framework for structural annotation of small-molecule data arising from liquid chromatography–tandem mass spectrometry (LC-MS2) measurements. LC-MS2Struct jointly predicts the annotations for a set of mass spectrometry features in a sample, using a novel structured prediction model trained to optimally combine the output of state-of-the-art MS2 scorers and observed retention orders. We evaluate our method on a dataset covering all publicly available reversed-phase LC-MS2 data in the MassBank reference database, including 4,327 molecules measured using 18 different LC conditions from 16 contributors, greatly expanding the chemical analytical space covered in previous multi-MSscorer evaluations. LC-MS2Struct obtains significantly higher annotation accuracy than earlier methods and improves the annotation accuracy of state-of-the-art MS2 scorers by up to 106\%. The use of stereochemistry-aware molecular fingerprints improves prediction performance, which highlights limitations in existing approaches and has strong implications for future computational LC-MS2 developments.
Disciplines :
Life sciences: Multidisciplinary, general & others
Author, co-author :
Bach, Eric
Schymanski, Emma  ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Rousu, Juho
External co-authors :
Language :
Title :
Joint structural annotation of small molecules using liquid chromatography retention order and tandem mass spectrometry data
Publication date :
Journal title :
Nature Machine Intelligence
Volume :
Issue :
Pages :
Peer reviewed :
Peer reviewed
Focus Area :
Computational Sciences
FnR Project :
FNR12341006 > Emma Schymanski > ECHIDNA > Environmental Cheminformatics To Identify Unknown Chemicals And Their Effects > 01/10/2018 > 30/09/2023 > 2018


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