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Critical Assessment of Small Molecule Identification 2016

Authors :
Schymanski, Emma L.
Ruttkies, Christoph
Krauss, Martin
Brouard, Céline
Kind, Tobias
Dührkop, Kai
Allen, Felicity
Vaniya, Arpana
Verdegem, Dries
Böcker, Sebastian
Rousu, Juho
Shen, Huibin
Tsugawa, Hiroshi
Sajed, Tanvir
Fiehn, Oliver
Ghesquière, Bart
Neumann, Steffen
Swiss Federal Institute of Aquatic Science and Technology
Leibniz Institute of Plant Biochemistry
Helmholtz Centre for Environmental Research
Department of Computer Science
University of California Davis
Friedrich Schiller University Jena
University of Alberta
KU Leuven
RIKEN
King Abdulaziz University
Aalto-yliopisto
Aalto University
Publication Year :
2017

Abstract

Background: The fourth round of the Critical Assessment of Small Molecule Identification (CASMI) Contest ( www.casmi-contest.org ) was held in 2016, with two new categories for automated methods. This article covers the 208 challenges in Categories 2 and 3, without and with metadata, from organization, participation, results and post-contest evaluation of CASMI 2016 through to perspectives for future contests and small molecule annotation/identification. Results: The Input Output Kernel Regression (CSI:IOKR) machine learning approach performed best in "Category 2: Best Automatic Structural Identification - In Silico Fragmentation Only", won by Team Brouard with 41% challenge wins. The winner of "Category 3: Best Automatic Structural Identification - Full Information" was Team Kind (MS-FINDER), with 76% challenge wins. The best methods were able to achieve over 30% Top 1 ranks in Category 2, with all methods ranking the correct candidate in the Top 10 in around 50% of challenges. This success rate rose to 70% Top 1 ranks in Category 3, with candidates in the Top 10 in over 80% of the challenges. The machine learning and chemistry-based approaches are shown to perform in complementary ways. Conclusions: The improvement in (semi-)automated fragmentation methods for small molecule identification has been substantial. The achieved high rates of correct candidates in the Top 1 and Top 10, despite large candidate numbers, open up great possibilities for high-throughput annotation of untargeted analysis for "known unknowns". As more high quality training data becomes available, the improvements in machine learning methods will likely continue, but the alternative approaches still provide valuable complementary information. Improved integration of experimental context will also improve identification success further for "real life" annotations. The true "unknown unknowns" remain to be evaluated in future CASMI contests. Graphical abstract .

Details

Language :
English
Database :
OpenAIRE
Accession number :
edsair.od.......661..072d33765cabcc85dcfc90a62a4627b1