I am giving a number of presentations at the ACS meeting in Orlando in April 2019. If you are interested in coming to listen and maybe chat after please see the list below.
1) PAPER ID: 3080890
PAPER TITLE: Consensus ranking and fragmentation prediction for identification of unknowns in high resolution mass spectrometry (final paper number: AGFD 10)
DIVISION: Division of Agricultural and Food Chemistry
SESSION: Recent Advances in Food Fraud & Authenticity Analysis
SESSION TIME: 8:30 AM – 10:55 AM
PRESENTATION FORMAT: Oral
DAY & TIME OF PRESENTATION: Sunday, March, 31, 2019 from 9:25 AM – 9:50 AM
ROOM & LOCATION: Florida Ballroom B – Hyatt Regency Orlando
Title:
Consensus ranking and fragmentation prediction for identification of unknowns
in high resolution mass spectrometry
Antony J. Williams1, Andrew McEachran2, Tommy
Cathey3, Tom Transue3, Jon Sobus4
High
resolution mass spectrometry (HRMS) and non-targeted analysis (NTA) are
advancing the identification of emerging contaminants in environmental and
agricultural matrices. However,
confidence in structure identification of unknowns in NTA presents challenges
to analytical chemists. Structure
identification requires integration of complementary data types such as
reference databases, fragmentation prediction tools, and retention time
prediction models. The goal of this
research is to optimize and implement structure identification functionality
within the US EPA’s CompTox Chemicals Dashboard, an open chemistry resource and
web application containing data for ~760,000 substances. Rank-ordering the number of sources
associated with chemical records within the Dashboard (Data Source Ranking)
improves the identification of unknowns by bringing the most likely candidate
structures to the top of a search results list.
Incorporating additional data streams contained within the database
underlying the Dashboard further enhances identifications. Integrating tandem mass spectrometry data
into NTA workflows enables spectral match scores and increases confidence in
structural assignments. We have
generated and stored predicted MS/MS fragmentation spectra for the entirety of
the Chemistry Dashboard using the in
silico prediction tool CFM-ID.
Predicted fragments incorporated into the identification workflow were
used as both a scoring term and as a candidate threshold cutoff. Combining these steps within an open chemistry
resource provides a freely available software tool for structure identification
and NTA. This abstract does not
necessarily represent the views or policies of the U.S. Environmental
Protection Agency.
2) PAPER ID: 3081133
PAPER TITLE: Applications of the US EPA’s
CompTox chemicals dashboard to support structure identification and chemical
forensics using mass spectrometry (final paper number: ANYL 320)
DIVISION: Division of Analytical Chemistry
SESSION: Frontiers in Forensic Mass Spectrometry
SESSION TIME: 8:00 AM – 12:10 PM
PRESENTATION FORMAT: Oral
DAY & TIME OF PRESENTATION: Tuesday, April,
02, 2019 from 11:40 AM – 12:10 PM
ROOM & LOCATION: Plaza International
Ballroom K – Hyatt Regency Orlando
Title: Applications of the US EPA’s CompTox Chemicals
Dashboard to support structure identification and chemical forensics using mass
spectrometry
Antony J. Williams, Andrew
D. McEachran, Jon R. Sobus and Emma Schymanski
High resolution mass spectrometry (HRMS) and non-targeted analysis (NTA)
are of increasing interest in chemical forensics for the identification of
emerging contaminants and chemical signatures of interest. At the US
Environmental Protection Agency, our research using HRMS for non-targeted and
suspect screening analyses utilizes databases and cheminformatics approaches
that are applicable to chemical forensics. The CompTox Chemicals Dashboard is
an open chemistry resource and web-based application containing data for
~760,000 substances. Basic functionality for searching through the data is
provided through identifier searches, such as systematic name, trade names and
CAS Registry Numbers. Advanced Search capabilities supporting mass spectrometry
include mass and formula-based searches, combined substructure-mass searches
and searching experimental mass spectral data against predicted fragmentation
spectra. A specific type of data mapping in the underpinning database, using
“MS-Ready” structures, has proven to be a valuable approach for structure
identification that links structures that can be identified via HRMS with
related substances in the form of salts, and other multi-component mixtures
that are available in commerce. This presentation will provide an overview of
the CompTox Chemicals Dashboard and demonstrate its utility for supporting
structure identification and NTA in chemical forensics. This abstract does not necessarily represent the views or policies of
the U.S. Environmental Protection Agency.
3) PAPER ID: 3084559
PAPER TITLE: Antony Williams, the ChemConnector:
A career path through a diverse series of roles and responsibilities (final
paper number: CINF 25)
DIVISION: Division of Chemical Information
SESSION: Careers in Chemical Information
SESSION TIME: 1:30 PM – 4:25 PM
PRESENTATION FORMAT: Oral
DAY & TIME OF PRESENTATION: Sunday, March,
31, 2019 from 3:05 PM – 3:25 PM
ROOM & LOCATION: West Hall B4 – Theater
11 – Orange County Convention Center
Antony Williams, the ChemConnector – a career path through a diverse
series of roles and responsibilities
Authors: Antony Williams
Antony Williams is a Computational Chemist at the US Environmental Protection Agency in the National Center for Computational Toxicology. He has been involved in cheminformatics and the dissemination of chemical information for over twenty-five years. He has worked for a Fortune 500 company (Eastman Kodak), in two successful start-ups (ACD/Labs and ChemSpider), for the Royal Society of Chemistry (in publishing) and, now, at the EPA. Throughout his career path he has experienced multiple diverse work cultures and focused his efforts on understanding the needs of his employers and the often unrecognized needs of a larger community. Antony will provide a short overview of his career path and discuss the various decisions that helped motivate his change in career from professional spectroscopist to website host and innovator, to working for one of the world’s foremost scientific societies and now for one of the most impactful government organizations in the world. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.
4) PAPER ID: 3084590
PAPER TITLE: US-EPA CompTox chemicals dashboard:
A web-based data integration hub for environmental chemistry data (final paper
number: CINF 43)
DIVISION: Division of Chemical Information
SESSION: Web-Based Chemoinformatics Platforms
SESSION TIME: 8:00 AM – 11:50 AM
PRESENTATION FORMAT: Oral
DAY & TIME OF PRESENTATION: Monday, April,
01, 2019 from 11:20 AM – 11:50 AM
ROOM & LOCATION: West Hall B4 – Theater
10 – Orange County Convention Center
The
EPA Comptox Chemicals Dashboard as a Data Integration Hub for Environmental
Chemistry Data
Authors: Antony Williams, Andrew McEachran, Imran Shah, Richard Judson, John
Wambaugh, Nancy Baker, George Helman, Chris Grulke, Kamel Mansouri, Grace
Patlewicz, Ann Richard and Jeff Edwards.
The U.S. Environmental Protection Agency (EPA) Computational Toxicology
Program integrates advances in biology, chemistry, and computer science to help
prioritize chemicals for further research based on potential human health
risks. This involves computational and data-driven approaches that integrate
chemistry, exposure and biological data. The National Center for Computational
Toxicology (NCCT) has measured, assembled and delivered an enormous quantity
and diversity of data for the environmental sciences, including high-throughput
in vitro screening data, in vivo and functional use data,
exposure models and chemical databases with associated properties. The CompTox
Chemicals Dashboard is a web-based application providing access to data
associated with ~760,000 chemical substances. New data are continuously added
to the database on an ongoing basis, along with registration of new and
emerging chemicals. This includes data extracted from the literature,
identified by our analytical labs, and otherwise of interest to support
specific research projects to the agency. By adding these data, with their
associated chemical identifiers (names and CAS Registry Numbers), the dashboard
uses linking approaches to allow for automated searching of PubMed, Google
Scholar and an array of public databases. This presentation will provide an
overview of the CompTox Chemicals Dashboard, how it has developed into an
integrated data hub for environmental data, and how it can be used for the
analysis of emerging chemicals in terms of sourcing related chemicals of
interest, and deriving read-across as well as QSAR predictions in real time. This abstract does not necessarily represent
the views or policies of the U.S. Environmental Protection Agency.
5) PAPER ID: 3084575
PAPER TITLE: EPA CompTox chemicals dashboard: An
online resource for environmental chemists (final paper number: CINF 94)
DIVISION: Division of Chemical Information
SESSION: Applications of Cheminformatics to Environmental Science
SESSION TIME: 8:00 AM – 12:00 PM
PRESENTATION FORMAT: Oral
DAY & TIME OF PRESENTATION: Wednesday,
April, 03, 2019 from 8:25 AM – 8:45 AM
ROOM & LOCATION: West
Hall B4 – Theater 10 – Orange County Convention Center
EPA CompTox Chemicals Dashboard – an online resource for environmental
chemists
Authors: Antony Williams, Chris Grulke, Jennifer Smith, Kamel Mansouri,
Andrew McEachran, Kathie Dionisio, Katherine Phillips, Grace Patlewicz, Jeremy
Fitzpatrick, Nancy Baker, Todd Martin, Ann Richard and Jeff Edwards
The U.S. Environmental Protection Agency (EPA) Computational Toxicology
Program integrates advances in biology, chemistry, and computer science to help
prioritize chemicals for further research based on potential human health
risks. This work involves computational and data driven approaches that
integrate chemistry, exposure and biological data. As an outcome of these
efforts the National Center for Computational Toxicology (NCCT) has measured,
assembled and delivered an enormous quantity and diversity of data for the
environmental sciences including high-throughput in vitro screening data, in
vivo and functional use data, exposure models and chemical databases with
associated properties. A series of software applications and databases have
been produced over the past decade to deliver these data. Recent work has
focused on the development of a new architecture that assembles the resources
into a single platform. With a focus on delivering access to Open Data streams,
web service integration accessibility and a user-friendly web application the
CompTox Chemicals Dashboard provides access to data associated with ~720,000
chemical substances. These data include research data in the form of bioassay
screening data associated with the ToxCast program, experimental and predicted
physicochemical properties, product and functional use information and related
data of value to environmental scientists. This presentation will provide an
overview of the CompTox Chemicals Dashboard and its value to the community as
an informational hub. This abstract does
not necessarily represent the views or policies of the U.S. Environmental
Protection Agency.
6) PAPER ID: 3095464
PAPER TITLE: Cheminformatics approaches to
support chemical identification delivered via the EPA CompTox Chemicals
Dashboard (final paper number: ENVR 173)
DIVISION: Division of Environmental Chemistry
SESSION: Accurate Mass/High Resolution Mass
Spectrometry for Environmental Monitoring & Remediation
SESSION TIME: 1:00 PM – 4:10 PM
PRESENTATION FORMAT: Oral
DAY & TIME OF PRESENTATION: Monday, April,
01, 2019 from 1:25 PM – 1:45 PM
ROOM & LOCATION: Valencia Ballroom B-D –
Theater 8 – Orange County Convention Center
Cheminformatics approaches to support
chemical identification delivered via the EPA CompTox Chemicals Dashboard
Antony J. Williams, Andrew McEachran, Chris
M. Grulke, Elin M. Ulrich and Jon R. Sobus
The identification of chemicals in environment
media depends on the application of analytical methods, the primary approach
being one of the multiple mass spectrometry techniques. Cheminformatics
solutions are critical to supporting the chemical identification process. This
includes the assembly of large chemical substance databases, prioritization
ranking of potential candidate search hits, and search approaches that support
both targeted and non-targeted screening approaches. The US Environmental
Protection Agency CompTox Chemicals Dashboard is a web-based application
providing access to data for over 760,000 chemical substances. This includes
access to physicochemical property, environmental fate and transport data, both
human and ecological toxicity data, information regarding chemicals contained in
products in commerce, and in vitro
bioactivity data. Searches are allowed based on chemical identifiers, product
and use, genes and assays associated with the EPA ToxCast assays and, specific
to supporting mass spectrometry, searches based on masses and formulae. These
searches make use of a novel “MS-Ready structures” approach collapsing
chemicals related as mixtures, salts, stereoforms and isotopomers. The
dashboard supports both singleton or batch searching by accurate mass/chemical
formula, supported by MS-ready structures, and utilizes rich meta data to
facilitate candidate ranking and the prioritization of chemicals of concern
based on toxicity and exposure data. The dashboard also hosts tens of chemical
lists that have been assembled from public databases, many supporting
non-targeted analysis and mass spectrometry databases.
This presentation will provide an overview of the dashboard and will
review our latest research into structure identification by searching
experimental mass spectrometry data against predicted fragmentation spectra for
LC-MS (positive and negative ion mode) and GC-MS (EI), a total of 3 million
predicted spectra. We will also provide an overview of our progress supporting
structure and substructure searching, using mass and formula-based filtering,
and report on the latest applications of the dashboard to support structure
identification projects of interest to the EPA. This abstract does not necessarily represent the views or policies of
the U.S. Environmental Protection Agency.
7) PAPER
ID: 3084594
PAPER TITLE: US-EPA comptox chemicals dashboard:
an information hub for over five thousand per- & polyfluoroalkyl chemical
substances (final paper number: ENVR 217)
DIVISION: Division of Environmental Chemistry
SESSION: Per- & Polyfluoroalkyl Substances in the Environment: From Legacy
To Emerging Contaminants
SESSION TIME: 8:30 AM – 12:00 PM
PRESENTATION FORMAT: Oral
DAY & TIME OF PRESENTATION: Tuesday, April,
02, 2019 from 10:10 AM – 10:30 AM
ROOM & LOCATION: Valencia Ballroom B-D –
Theater 10 – Orange County Convention Center
Title: The US-EPA CompTox Chemicals Dashboard
– an information hub for over five thousand per- & polyfluoroalkyl chemical
substances
Authors: Antony Williams, Chris Grulke, Grace
Patlewicz and Ann Richard
The EPA’s CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) is a
publicly accessible website providing access to data for ~770,000 chemical
substances, the majority of these represented as chemical structures. The web
application delivers a wide array of computed and measured physicochemical
properties, in vitro high-throughput
screening data and in vivo toxicity
data, product use information extracted from safety data sheets, and integrated
chemical linkages to a growing list of literature, toxicology, and analytical
chemistry websites. The application provides access to segregated lists of
chemicals that are of specific interest to relevant stakeholders, including
Per- & Polyfluoroalkyl Substances (PFAS) containing thousands of chemicals.
A procured testing library of hundreds of PFAS chemicals annotated into
chemical categories has been integrated into the dashboard with a number of
resulting benefits: a searchable database of chemical properties, with hazard
and exposure predictions, and links to the open literature. Several specific
search types have been developed to directly support the mass spectrometry
non-targeted screening community, enabling cohesive workflows to support data
generation for the detection and assessment of environmental exposures to
chemicals contained within DSSTox. This presentation will provide an overview
of the dashboard, the ongoing expansion of the PFAS chemical library, with
associated categorization, and new physicochemical property and environmental
fate and transport QSAR prediction models developed for these chemicals. The
application of the dashboard to support mass spectrometry non-targeted analysis
studies for the identification of PFAS chemicals will also be reviewed. This abstract does not necessarily represent
the views or policies of the U.S. Environmental Protection Agency.
8) PAPER
ID: 3084611
PAPER TITLE: CompTox chemicals dashboard: Data
and tools to support chemical and environmental risk assessment and the ENTACT
project (final paper number: ENVR 648)
DIVISION: Division of Environmental Chemistry
SESSION: True Positives in EPA’S Non-Targeted Analysis Collaborative Trial
(ENTACT)
SESSION TIME: 1:30 PM – 5:00 PM
PRESENTATION FORMAT: Oral
DAY & TIME OF PRESENTATION: Wednesday,
April, 03, 2019 from 2:15 PM – 2:35 PM
ROOM & LOCATION: Valencia Ballroom B-D –
Theater 13 – Orange County Convention Center
Title: The CompTox Chemicals Dashboard: Data and Tools
to Support Chemical and Environmental Risk Assessment and the ENTACT project
Authors and affiliations: Antony J.
Williams1, Christopher M. Grulke1, Andrew D. McEachran2,
Emma L. Schymanski3,4, Jon Sobus5, Elin Ulrich5,
Ann M. Richard1, Jeremy Dunne1 and Jeff Edwards1
1
EPA, National Center for Computational Toxicology, RTP, NC, USA
2 ORISE
Fellow, Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
3
Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg,
Campus Belval, 6, avenue du Swing, L-4367 Belvaux, Luxembourg
4 EPA, National
Exposure Research Laboratory, RTP, NC, USA
Information and data on
chemicals is used by scientists to evaluate potential health and ecological
risks due to environmental exposures. EPA’s CompTox Chemicals Dashboard (https://comptox.epa.gov)
helps evaluate the safety of chemicals by providing public access to a variety
of information on over 760,000 chemicals. Within the Dashboard, users can
access chemical structures, chemistry information, toxicity data, hazard data,
exposure information, and additional links to relevant websites and
applications. These data are compiled from sources including EPA’s
computational toxicology research databases, from public domain databases and
with collaborators across the world. Chemical lists have been added that
provide access to various classes of chemicals and project-based datasets are
under constant development. Specific functionality has been delivered within
the Dashboard to support mass spectrometry including “MS-ready forms” of
chemical substances that would be detectable by mass spectrometry. Workflows
have been developed to assist in candidate identification and have now been
proven with multiple published studies. An integration path between the
dashboard and MetFrag has also been established to provide users the
significant benefits resulting from the marriage between the two applications.
The datasets underpinning the dashboard are freely available (https://comptox.epa.gov/dashboard/downloads)
for integration into third party databases. This presentation will provide an
overview of the available data types and functionality of the dashboard prior
to examining how it is developing to support mass spectrometry based analyses
within the agency and for the community in general. This will include a review
of our research efforts to enhance the dashboard using in silico MS/MS fragmentation prediction for spectral matching. This abstract does not necessarily represent
the views or policies of the U.S. Environmental Protection Agency.
