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Revisiting Five Years of CASMI Contests with EPA Identification Tools.

ABSTRACT: 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.

SUBMITTER: McEachran AD

PROVIDER: S-EPMC7345619 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

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Revisiting Five Years of CASMI Contests with EPA Identification Tools.

McEachran Andrew D AD Chao Alex A Al-Ghoul Hussein H Lowe Charles C Grulke Christopher C Sobus Jon R JR Williams Antony J AJ

Metabolites 20200623 6

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/M ...[more]

PMID: 32585902

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Project description:BACKGROUND:The wars that ravaged the former Socialist Federal Republic of Yugoslavia in the 1990's resulted in the near destruction of the healthcare system, including education of medical students and the training of specialist physicians. In the latter stages of the war, inspired by Family Medicine programs in countries such as Canada, plans to rebuild a new system founded on a strong primary care model emerged. Over the next fifteen years, the Queen's University Family Medicine Development Program in Bosnia and Herzegovina played an instrumental role in rebuilding the primary care system through educational initiatives at the undergraduate, residency, Masters, PhD, and continuing professional development levels. Changes were supported by new laws and regulations to insure sustainability. This study revisited Bosnia and Herzegovina (B-H) 8-years after the end of the program to explore the impact of initiatives through understanding the perspectives and experiences of individuals at all levels of the primary care system from students, deans of medical schools, Family Medicine residents, practicing physicians, Health Center Directors and Association Leaders. METHODS:Qualitative exploratory design using purposeful sampling. Semi-structured interviews and focus groups with key informants were conducted in English or with an interpreter as needed and audiotaped. Transcripts and field notes were analyzed using an interpretative phenomenological approach to identify major themes and subthemes. RESULTS:Overall, 118 participants were interviewed. Three major themes and 9 subthemes were identified including (1) The Development of Family Medicine Education, (subthemes: establishment of departments of family medicine, undergraduate medical curriculum change), (2) Family Medicine as a Discipline (Family Medicine specialization, academic development, and Family Medicine Associations), and (3) Health Care System Issues (continuity of care, comprehensiveness of care, practice organization and health human resources). CONCLUSIONS:Despite the impact of years of war and the challenges of a complex and unstable postwar environment, initiatives introduced by the Queen's Program succeeded in establishing sustainable changes, allowing Family Medicine in B-H to continue to adapt without abandoning its strong foundations. Despite the success of the program, the undervaluing of Primary Care from a human resource and health finance perspective presents ongoing threats to the system.

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Revisiting Five Years of CASMI Contests with EPA Identification Tools.

Publications

Revisiting Five Years of CASMI Contests with EPA Identification Tools.

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