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PRESENTATION ACS SPRING 2018: Structure identification by Mass Spectrometry Non-Targeted Analysis using the US EPA’s CompTox Chemistry Dashboard

Structure identification by Mass Spectrometry Non-Targeted Analysis using the US EPA’s CompTox Chemistry Dashboard

Identification of unknowns in mass spectrometry based non-targeted analyses (NTA) requires the integration of complementary pieces of data to arrive at a confident, consensus structure. Researchers use chemical reference databases, spectral matching, fragment prediction tools,…

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PRESENTATION ACS SPRING 2018: US EPA CompTox Chemistry Dashboard as a source of data to fill data gaps for chemical sources of risk

US EPA CompTox Chemistry Dashboard as a source of data to fill data gaps for chemical sources of risk

Chemical risk assessment is both time-consuming and difficult because it requires the assembly of data for chemicals generally distributed across multiple sources. The US EPA CompTox Chemistry Dashboard is a publicly accessible web-based application providing access to various data streams on…

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PRESENTATION ACS SPRING 2018: Accessing information for chemicals in hydraulic fracturing fluids using the US EPA CompTox Chemistry Dashboard

Accessing information for chemicals in hydraulic fracturing fluids using the US EPA CompTox Chemistry Dashboard

EPA’s National Center for Computational Toxicology is developing automated workflows for curating large databases and providing accurate linkages of data to chemical structures, exposure and hazard information. The data are being made available via the EPA’s CompTox Chemistry Dashboard…

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PRESENTATION ACS SPRING 2018: Development of a Tool for Systematic Integration of Traditional and New Approach Methods for Prioritizing Chemical Lists

Development of a Tool for Systematic Integration of Traditional and New Approach Methods for Prioritizing Chemical Lists

Multiple regulatory bodies (EPA, ECHA, Health Canada) are currently tasked with prioritizing chemicals for data collection and risk assessments. These prioritization efforts are in response to regulatory mandates to identify chemicals for further assessment. We have developed a…

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PRESENTATION ACS SPRING 2018: New developments in delivering public access to data from the National Center for Computational Toxicology at the EPA

New developments in delivering public access to data from the National Center for Computational Toxicology at the EPA

Researchers at EPA’s National Center for Computational Toxicology integrate advances in biology, chemistry, and computer science to examine the toxicity of chemicals and help prioritize chemicals for further research based on potential human health risks. The goal of this…

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PRESENTATION ACS SPRING 2018: Overview of open resources to support automated structure verification and elucidation

Overview of open resources to support automated structure verification and elucidation

Cheminformatics methods form an essential basis for providing analytical scientists with access to data, algorithms and workflows. There are an increasing number of free online databases (compound databases, spectral libraries, data repositories) and a rich collection of software approaches that can be used to…

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PRESENTATION ACS SPRING 2018: Sharing chemical structures with peer-reviewed publications. Are we there yet?

Sharing chemical structures with peer-reviewed publications. Are we there yet?

In the domain of chemistry one of the greatest benefits to publishing research is that data can be shared. Unfortunately, the vast majority of chemical structure data associated with scientific publications remain locked up in document form, primarily in PDF files or trapped on webpages. Despite the explosive growth…

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PRESENTATION ACS SPRING 2018: Using the US EPA’s CompTox Chemistry Dashboard for structure identification and non-targeted analyses

Using the US EPA’s CompTox Chemistry Dashboard for structure identification and non-targeted analyses

Antony J. Williams, Andrew D. McEachran, Seth Newton, Kristin Isaacs, Katherine Phillips, Nancy Baker, Christopher Grulke and Jon R. Sobus

High resolution mass spectrometry (HRMS) and non-targeted analysis (NTA) are advancing the identification of emerging contaminants in environmental matrices,…

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PRESENTATION ACS SPRING 2018: Adding Complex Expert Knowledge into Chemical Database and Transforming Surfactants in Wastewater

Adding Complex Expert Knowledge into Chemical Databases: Transforming Surfactants in Wastewater

PRESENTED by Emma Schymanski

The increasing popularity of high mass accuracy non-target mass spectrometry methods has yielded extensive identification efforts based on chemical compound databases. Candidate structures are often retrieved with either exact mass or molecular formula from large resources…

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PRESENTATION ACS Spring 2018: Curating “Suspect Lists” for International Non-target Screening Efforts

Curating “Suspect Lists” for International Non-target Screening Efforts

Emma L. Schymanski, Reza Aalizadeh, Nikolaos S. Thomaidis, Juliane Hollender, Jaroslav Slobodnik, Antony J. Williams5

1Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Campus Belval, Luxembourg. 2National and Kapodistrian University of Athens, Department of Chemistry, Panepistimiopolis Zografou, 157…

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PRESENTATION ACS Spring 2018: Curating and Sharing Structures and Spectra for the Environmental Community

Curating and sharing structures and spectra for the environmental community

Presented by Emma Schymanski

The increasing popularity of high mass accuracy non-target mass spectrometry methods has yielded extensive identification efforts based on spectral and chemical compound databases in the environmental community and beyond. Increasingly, new methods are relying on open data resources. Candidate…

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PRESENTATION ACS Spring 2018: Automated Structure Annotation and Curation for MassBank: Potential and Pitfalls

Automated Structure Annotation and Curation for MassBank: Potential and Pitfalls

Presented by Emma Schymanski

The European MassBank server (www.massbank.eu) was founded in 2012 by the NORMAN Network (www.norman-network.net) to provide open access to mass spectra of substances of environmental interest contributed by NORMAN members. The automated workflow RMassBank was developed as a part of this…

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Bias and Data-Driven and Probability-Based Decision Making in Trivia Crack

I’ve been playing Trivia Crack for a few years now and, as of today, I am a level 326. I am an iPhone/iPad user so grabbed it from the AppStore. In playing I have filled my brain with some useless information, learned a lot of history, geography and sports, and taken advantage of my Science background to win more than a few challenges. In terms of Entertainment its clear I stopped learning about…

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#Trivia Cracck

GUEST POST by Emma Schymanski: Suspect Screening with MetFrag and the CompTox Chemistry Dashboard

Identifying “known unknowns” via suspect and non-target screening of environmental samples with the in silico fragmenter MetFrag (http://msbi.ipb-halle.de/MetFragBeta/) typically relies on the large compound databases ChemSpider and PubChem (see e.g. Ruttkies et al 2016). The size of these databases (over 50 and 90 million structures, respectively), yield many false positive hits of structures…

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#MassBank #MetFrag

The National Chemical Database Service Allowing Depositions

The UK National Chemical Database Service (available here) has been online a few years now, since 2012. When I worked at RSC I was intimately involved in writing the technical response to the EPSRC call for the service and, in this blog, I outlined a lot of intentions for the project. A key part of the project from my point of view was to deliver a repository to store structures, spectra,…

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Call for Abstracts for ACS Spring 2018 Symposium " Applications of Cheminformatics to Environmental Chemistry"

Call for Abstracts for ACS Spring 2018 Symposium ” Applications of Cheminformatics to Environmental Chemistry”

Grace Patlewicz and I have the pleasure of hosting a symposium at the Spring 2018 ACS National Meeting in New Orleans as outlined below. We believe that a presentation from you would enhance the line-up for the gathering and encourage you to consider our invitation. Our expectations are that we will have a full day of stimulating presentations and discussions regarding the application of…

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Call for Abstracts for ACS Spring 2018 Symposium: "Open Resources for automated structure verification and elucidation"

Call for Abstracts for ACS Spring 2018 Symposium: “Open Resources for automated structure verification and elucidation”

I have the pleasure of hosting a symposium with Emma Schymanski at the Spring 2018 ACS National Meeting in New Orleans as outlined below. Our expectations are that we will have a full day of stimulating presentations and discussions regarding how Open Resources, specifically data and software, can support automated structure verification and elucidation. If this is an area of research for you…

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