Revisiting Five Years of CASMI Contests with EPA Identification Tools
Software applications for high resolution mass spectrometry (HRMS)-based non-targeted analysis (NTA) continue to enhance chemical identification capabilities. Given the variety of available applications, determining the most fit-for-purpose tools and workflows can be difficult. The Critical Assessme...
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doaj-7fcdc1b80bdc4cfd96f39135c849ac352020-11-25T03:04:08ZengMDPI AGMetabolites2218-19892020-06-011026026010.3390/metabo10060260Revisiting Five Years of CASMI Contests with EPA Identification ToolsAndrew D. McEachran0Alex Chao1Hussein Al-Ghoul2Charles Lowe3Christopher Grulke4Jon R. Sobus5Antony J. Williams6Oak Ridge Institute for Science and Education (ORISE) Participant, 109 T.W. Alexander Drive, Research Triangle Park, NC 27709, USAOak Ridge Institute for Science and Education (ORISE) Participant, 109 T.W. Alexander Drive, Research Triangle Park, NC 27709, USAOak Ridge Institute for Science and Education (ORISE) Participant, 109 T.W. Alexander Drive, Research Triangle Park, NC 27709, USACenter for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, 109 T.W. Alexander Drive, Research Triangle Park, NC 27709, USACenter for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, 109 T.W. Alexander Drive, Research Triangle Park, NC 27709, USACenter for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, 109 T.W. Alexander Drive, Research Triangle Park, NC 27709, USACenter for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, 109 T.W. Alexander Drive, Research Triangle Park, NC 27709, USASoftware applications for high resolution mass spectrometry (HRMS)-based non-targeted analysis (NTA) continue to enhance chemical identification capabilities. Given the variety of available applications, determining the most fit-for-purpose tools and workflows can be difficult. The Critical Assessment of Small Molecule Identification (CASMI) contests were initiated in 2012 to provide a means to evaluate compound identification tools on a standardized set of blinded tandem mass spectrometry (MS/MS) data. Five CASMI contests have resulted in recommendations, publications, and invaluable datasets for practitioners of HRMS-based screening studies. The US Environmental Protection Agency’s (EPA) CompTox Chemicals Dashboard is now recognized as a valuable resource for compound identification in NTA studies. However, this application was too new and immature in functionality to participate in the five previous CASMI contests. In this work, we performed compound identification on all five CASMI contest datasets using Dashboard tools and data in order to critically evaluate Dashboard performance relative to that of other applications. CASMI data was accessed via the CASMI webpage and processed for use in our spectral matching and identification workflow. Relative to applications used by former contest participants, our tools, data, and workflow performed well, placing more challenge compounds in the top five of ranked candidates than did the winners of three contest years and tying in a fourth. In addition, we conducted an in-depth review of the CASMI structure sets and made these reviewed sets available via the Dashboard. Our results suggest that Dashboard data and tools would enhance chemical identification capabilities for practitioners of HRMS-based NTA.https://www.mdpi.com/2218-1989/10/6/260non-targeted analysishigh-resolution mass spectrometrymass spectral fragmentation predictioncompound databasespectral library |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Andrew D. McEachran Alex Chao Hussein Al-Ghoul Charles Lowe Christopher Grulke Jon R. Sobus Antony J. Williams |
spellingShingle |
Andrew D. McEachran Alex Chao Hussein Al-Ghoul Charles Lowe Christopher Grulke Jon R. Sobus Antony J. Williams Revisiting Five Years of CASMI Contests with EPA Identification Tools Metabolites non-targeted analysis high-resolution mass spectrometry mass spectral fragmentation prediction compound database spectral library |
author_facet |
Andrew D. McEachran Alex Chao Hussein Al-Ghoul Charles Lowe Christopher Grulke Jon R. Sobus Antony J. Williams |
author_sort |
Andrew D. McEachran |
title |
Revisiting Five Years of CASMI Contests with EPA Identification Tools |
title_short |
Revisiting Five Years of CASMI Contests with EPA Identification Tools |
title_full |
Revisiting Five Years of CASMI Contests with EPA Identification Tools |
title_fullStr |
Revisiting Five Years of CASMI Contests with EPA Identification Tools |
title_full_unstemmed |
Revisiting Five Years of CASMI Contests with EPA Identification Tools |
title_sort |
revisiting five years of casmi contests with epa identification tools |
publisher |
MDPI AG |
series |
Metabolites |
issn |
2218-1989 |
publishDate |
2020-06-01 |
description |
Software applications for high resolution mass spectrometry (HRMS)-based non-targeted analysis (NTA) continue to enhance chemical identification capabilities. Given the variety of available applications, determining the most fit-for-purpose tools and workflows can be difficult. The Critical Assessment of Small Molecule Identification (CASMI) contests were initiated in 2012 to provide a means to evaluate compound identification tools on a standardized set of blinded tandem mass spectrometry (MS/MS) data. Five CASMI contests have resulted in recommendations, publications, and invaluable datasets for practitioners of HRMS-based screening studies. The US Environmental Protection Agency’s (EPA) CompTox Chemicals Dashboard is now recognized as a valuable resource for compound identification in NTA studies. However, this application was too new and immature in functionality to participate in the five previous CASMI contests. In this work, we performed compound identification on all five CASMI contest datasets using Dashboard tools and data in order to critically evaluate Dashboard performance relative to that of other applications. CASMI data was accessed via the CASMI webpage and processed for use in our spectral matching and identification workflow. Relative to applications used by former contest participants, our tools, data, and workflow performed well, placing more challenge compounds in the top five of ranked candidates than did the winners of three contest years and tying in a fourth. In addition, we conducted an in-depth review of the CASMI structure sets and made these reviewed sets available via the Dashboard. Our results suggest that Dashboard data and tools would enhance chemical identification capabilities for practitioners of HRMS-based NTA. |
topic |
non-targeted analysis high-resolution mass spectrometry mass spectral fragmentation prediction compound database spectral library |
url |
https://www.mdpi.com/2218-1989/10/6/260 |
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