{"id":3727,"date":"2020-11-16T11:43:11","date_gmt":"2020-11-16T16:43:11","guid":{"rendered":"https:\/\/its-cuthemedev1.carleton.ca\/chemistry\/?page_id=3727"},"modified":"2026-01-15T13:38:56","modified_gmt":"2026-01-15T18:38:56","slug":"machine-learning-and-big-data-as-tools-for-chemistry-research","status":"publish","type":"page","link":"https:\/\/carleton.ca\/chemistry\/research\/research-strengths\/machine-learning-and-big-data-as-tools-for-chemistry-research\/","title":{"rendered":"Machine Learning and Big Data as Tools for Chemistry Research"},"content":{"rendered":"\n<section class=\"w-screen px-6 cu-section cu-section--white ml-offset-center md:px-8 lg:px-14\">\n    <div class=\"space-y-6 cu-max-w-child-5xl  md:space-y-10 cu-prose-first-last\">\n\n            <div class=\"cu-textmedia flex flex-col lg:flex-row mx-auto gap-6 md:gap-10 my-6 md:my-12 first:mt-0 max-w-5xl\">\n        <div class=\"justify-start cu-textmedia-content cu-prose-first-last\" style=\"flex: 0 0 100%;\">\n            <header class=\"font-light prose-xl cu-pageheader md:prose-2xl cu-component-updated cu-prose-first-last\">\n                                    <h1 class=\"cu-prose-first-last font-semibold !mt-2 mb-4 md:mb-6 relative after:absolute after:h-px after:bottom-0 after:bg-cu-red after:left-px text-3xl md:text-4xl lg:text-5xl lg:leading-[3.5rem] pb-5 after:w-10 text-cu-black-700 not-prose\">\n                        Machine Learning and Big Data as Tools for Chemistry Research\n                    <\/h1>\n                \n                                \n                            <\/header>\n\n                    <\/div>\n\n            <\/div>\n\n    <\/div>\n<\/section>\n\n\n\n<section class=\"w-screen px-6 cu-section cu-section--white ml-offset-center md:px-8 lg:px-14\">\n    <div class=\"space-y-6 cu-max-w-child-5xl  md:space-y-10 cu-prose-first-last\">\n\n        \n        \n    <dl class=\"cu-description cu-component\">\n                                    <div class=\"grid py-3 border-b accordion border-cu-black-100 md:py-4 first:border-t\">\n    <dt class=\"font-semibold not-prose\">\n        <div class=\"flex items-center w-full accordion__button\" aria-expanded=\"false\" aria-controls=\"accordion-3609-1\" role=\"button\" tabindex=\"0\">\n            Barry, Sean\n            <svg xmlns=\"http:\/\/www.w3.org\/2000\/svg\" fill=\"none\" viewbox=\"0 0 24 24\" stroke-width=\"1.5\" stroke=\"currentColor\" aria-hidden=\"true\" data-slot=\"icon\" class=\"w-5 h-5 ml-auto transition-transform rotate-0 accordion__icon text-cu-black-500\">\n                <path stroke-linecap=\"round\" stroke-linejoin=\"round\" d=\"m8.25 4.5 7.5 7.5-7.5 7.5\"><\/path>\n            <\/svg>\n        <\/div>\n    <\/dt>\n    <dd class=\"accordion__content !p-0 md:p-0 mt-0 md:mt-0\" hidden=\"\" id=\"accordion-3609-1\">\n        <!-- wp:cu-block\/page-header {\"title\":\"Barry, Sean\",\"isFirstBlock\":true} \/--><!-- wp:paragraph -->\n<p>The Barry Lab is interested in the development of precursors and processes for atomic layer deposition (ALD) and was the first academic research group in Canada to work in this field.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>We have previously discovered processes for the deposition of the coinage metals (Cu, Au), used in microelectronic chip manufacturing and sensing applications. Our present research is centred on earlier transition metals (Co, Ni, Mo, W) for next-generation nano-electronic interconnects, as well as upgrading additive manufacturing processes through thin film coating and sequential infiltration.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>As synthetic chemists, we try to determine the mechanism of the surface chemistry and thermal decomposition routes to better design precursors and tune our processes. We look at many different processes and target films, but the theme of mechanistic inorganic chemistry can broadly be drawn through our work.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>For more information, visit the&nbsp;<a href=\"https:\/\/carleton.ca\/barrylab\/\">Barry Lab<\/a>.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>&nbsp;<\/p>\n<!-- \/wp:paragraph -->\n    <\/dd>\n<\/div>\n                                                <div class=\"grid py-3 border-b accordion border-cu-black-100 md:py-4 first:border-t\">\n    <dt class=\"font-semibold not-prose\">\n        <div class=\"flex items-center w-full accordion__button\" aria-expanded=\"false\" aria-controls=\"accordion-5808-2\" role=\"button\" tabindex=\"0\">\n            Gregoire, Daniel\n            <svg xmlns=\"http:\/\/www.w3.org\/2000\/svg\" fill=\"none\" viewbox=\"0 0 24 24\" stroke-width=\"1.5\" stroke=\"currentColor\" aria-hidden=\"true\" data-slot=\"icon\" class=\"w-5 h-5 ml-auto transition-transform rotate-0 accordion__icon text-cu-black-500\">\n                <path stroke-linecap=\"round\" stroke-linejoin=\"round\" d=\"m8.25 4.5 7.5 7.5-7.5 7.5\"><\/path>\n            <\/svg>\n        <\/div>\n    <\/dt>\n    <dd class=\"accordion__content !p-0 md:p-0 mt-0 md:mt-0\" hidden=\"\" id=\"accordion-5808-2\">\n        <!-- wp:cu-block\/page-header {\"title\":\"Gregoire, Daniel\",\"isFirstBlock\":true} \/-->\n\n<!-- wp:paragraph {\"placeholder\":\"Type \/ to choose a block\"} -->\n<p>The Environmental Biogeochemistry and Biotechnology (EBB) Lab explores how <strong>microbes<\/strong> and the <strong>chemical reactions<\/strong> they drive influence the fate of critical materials and environmental contaminants. Our research integrates <strong>microbial cultivation, advanced analytical chemistry, and high-resolution imaging<\/strong> to better understand biochemical transformations for metals and organic pollutants. Many research projects also leverage in-demand <strong>computational skills<\/strong> to analyze large-scale environmental chemistry, DNA, and RNA data to characterize biogeochemical cycles in diverse habitats.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>We foster a collaborative, interdisciplinary environment spanning chemistry, biochemistry, earth science, and engineering. We work closely with partners in government including Environment and Climate Change Canada and Natural Resources Canada to translate our research into effective environmental policies that protect Canadians. We also work closely with partners in the solid waste and biotechnology sectors to develop environmental remediation strategies tailored to their needs. We are committed to inclusive mentorship and work with students to design projects that help them build skills in line with their career goals. Our team\u2019s overarching vision is to develop sustainable, microbe-driven strategies for waste management tailored to real-world applications.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph {\"placeholder\":\"Type \/ to choose a block\"} -->\n<p>If you want to learn more about projects where you would be a good fit in the EBB lab, check out our website to learn more: <a href=\"https:\/\/carleton.ca\/envbiotech\/\">https:\/\/carleton.ca\/envbiotech\/<\/a><\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p><\/p>\n<!-- \/wp:paragraph -->\n    <\/dd>\n<\/div>\n                                                <div class=\"grid py-3 border-b accordion border-cu-black-100 md:py-4 first:border-t\">\n    <dt class=\"font-semibold not-prose\">\n        <div class=\"flex items-center w-full accordion__button\" aria-expanded=\"false\" aria-controls=\"accordion-4831-3\" role=\"button\" tabindex=\"0\">\n            Hu, Yaxi\n            <svg xmlns=\"http:\/\/www.w3.org\/2000\/svg\" fill=\"none\" viewbox=\"0 0 24 24\" stroke-width=\"1.5\" stroke=\"currentColor\" aria-hidden=\"true\" data-slot=\"icon\" class=\"w-5 h-5 ml-auto transition-transform rotate-0 accordion__icon text-cu-black-500\">\n                <path stroke-linecap=\"round\" stroke-linejoin=\"round\" d=\"m8.25 4.5 7.5 7.5-7.5 7.5\"><\/path>\n            <\/svg>\n        <\/div>\n    <\/dt>\n    <dd class=\"accordion__content !p-0 md:p-0 mt-0 md:mt-0\" hidden=\"\" id=\"accordion-4831-3\">\n        <!-- wp:cu-block\/page-header {\"title\":\"Hu, Yaxi\",\"isFirstBlock\":true} \/--><!-- wp:paragraph -->\n<p>Safeguarding <strong>food integrity<\/strong>&nbsp;is about ensuring the <strong>safety<\/strong>, <strong>quality<\/strong>, and <strong>authenticity<\/strong>&nbsp;of food products. We, the FACT Lab, focus on the advancement and application of analytical chemistry and technologies to solve the persisting and emerging food integrity issues faced by the food industry. We take an <strong>interdisciplinary<\/strong>&nbsp;approach by organically integrating <strong>Analytical Chemistry<\/strong>, <strong>Nanomaterials<\/strong>, <strong>Microfluidic \u201cLab-on-a-Chip\u201d Platform<\/strong>, <strong>Metabolomics<\/strong>, <strong>Bioinformatics<\/strong>, and <strong>Data Science<\/strong>&nbsp;to develop simple, rapid, cu_event_cost-effective, reliable and smart <strong>point-of-need sensors<\/strong>&nbsp;and <strong>instrumental methods<\/strong>&nbsp;to monitor and trace food products.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>Using these novel technologies, we aim to provide the last barrier of protection to food integrity from farm to fork and thus to protect consumers, genuine food industries and government, as well as to reduce food waste and loss during the supply chain.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>For more information, visit <a href=\"https:\/\/carleton.ca\/fact-lab\/\">The FACT Lab<\/a><\/p>\n<!-- \/wp:paragraph -->\n    <\/dd>\n<\/div>\n                                                <div class=\"grid py-3 border-b accordion border-cu-black-100 md:py-4 first:border-t\">\n    <dt class=\"font-semibold not-prose\">\n        <div class=\"flex items-center w-full accordion__button\" aria-expanded=\"false\" aria-controls=\"accordion-3690-4\" role=\"button\" tabindex=\"0\">\n            Rowley, Christopher\n            <svg xmlns=\"http:\/\/www.w3.org\/2000\/svg\" fill=\"none\" viewbox=\"0 0 24 24\" stroke-width=\"1.5\" stroke=\"currentColor\" aria-hidden=\"true\" data-slot=\"icon\" class=\"w-5 h-5 ml-auto transition-transform rotate-0 accordion__icon text-cu-black-500\">\n                <path stroke-linecap=\"round\" stroke-linejoin=\"round\" d=\"m8.25 4.5 7.5 7.5-7.5 7.5\"><\/path>\n            <\/svg>\n        <\/div>\n    <\/dt>\n    <dd class=\"accordion__content !p-0 md:p-0 mt-0 md:mt-0\" hidden=\"\" id=\"accordion-3690-4\">\n        <!-- wp:cu-block\/page-header {\"title\":\"Rowley, Christopher\",\"isFirstBlock\":true} \/--><!-- wp:paragraph -->\n<p>The Rowley Group uses computer simulations to study biological and materials chemistry. We use a combination of molecular simulation, quantum chemistry, and machine learning to understand complex chemical systems and then to use these ideas to predict and design new chemical systems. Our core areas of interest are protein\u2013drug binding, covalent modifier drugs, membrane permeation, and cryo-EM structure refinement. To make our models more accurate and to explore new types of chemistry, we develop new methods for computational chemistry, such as our hybrid neural network potential \/ molecular mechanical model.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>For more information, visit <a href=\"http:\/\/www.rowleygroup.net\/\">the&nbsp;Rowley Group<\/a>.<\/p>\n<!-- \/wp:paragraph -->\n    <\/dd>\n<\/div>\n                                                <div class=\"grid py-3 border-b accordion border-cu-black-100 md:py-4 first:border-t\">\n    <dt class=\"font-semibold not-prose\">\n        <div class=\"flex items-center w-full accordion__button\" aria-expanded=\"false\" aria-controls=\"accordion-3618-5\" role=\"button\" tabindex=\"0\">\n            Smith, Jeffrey C.\n            <svg xmlns=\"http:\/\/www.w3.org\/2000\/svg\" fill=\"none\" viewbox=\"0 0 24 24\" stroke-width=\"1.5\" stroke=\"currentColor\" aria-hidden=\"true\" data-slot=\"icon\" class=\"w-5 h-5 ml-auto transition-transform rotate-0 accordion__icon text-cu-black-500\">\n                <path stroke-linecap=\"round\" stroke-linejoin=\"round\" d=\"m8.25 4.5 7.5 7.5-7.5 7.5\"><\/path>\n            <\/svg>\n        <\/div>\n    <\/dt>\n    <dd class=\"accordion__content !p-0 md:p-0 mt-0 md:mt-0\" hidden=\"\" id=\"accordion-3618-5\">\n        <!-- wp:cu-block\/page-header {\"title\":\"Smith, Jeffrey C.\",\"isFirstBlock\":true} \/--><!-- wp:paragraph -->\n<p><strong>Overview<\/strong><\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>Mass spectrometry (MS) has proven to be a powerful analytical tool in many scientific fields for nearly a century. Advances made in soft ionization techniques such as electrospray ionization (ESI) and matrix-assisted laser desorption ionization (MALDI) have expanded the use of MS to the biological sciences, allowing biomolecules to be ionized and sampled in the gas phase without fragmentation. These advances have been echoed in an explosion of publications over the past 20 years that have used MS as a tool to illuminate information pertaining to a biological question. The majority of MS-based bioanalytical studies to date have focused on cataloguing the species present in a sample at a static moment in time. Although this is important, measuring the dynamics of a system in response to a stimulus not only aids identification efforts, but offers mechanistic insight into the cellular processes involved. Gaining a better understanding of these dynamics, often expressed through a change in concentration or in the degree of modification, enhances the accuracy of cellular models, assigns functional roles to the identified species, as well as highlights new diagnostic and therapeutic strategies. The research program of the Smith group focuses on developing novel methods to efficiently measure biomolecular dynamics in living systems with the downstream goals of elucidating disease biomarkers and further characterizing biosynthetic and biochemical pathways.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p><strong>Instrumentation<\/strong><\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>The Smith Lab uses mass spectrometry as a tool to probe the dynamics of various biomolecules. At present, we mainly conduct research in the area of protein analysis (\u201cproteomics\u201d) and lipid analysis (\u201clipidomics\u201d). The laboratory is equipped with high-resolution hybrid quadrupole time of flight, triple quadrupole and linear ion trap mass spectrometers. All of these instruments achieve ionization via electrospray ionization and are coupled to high performance liquid chromatographs. The lab additionally houses two gas chromatography-MS systems, one equipped with a headspace sampler.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p><strong>TrEnDi<\/strong><\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>Trimethylation Enhancement using Diazomethane (TrEnDi) is a published technique developed by Professors Jeffrey Smith and Jeffrey Manthorpe at Carleton University. The method increases the sensitivity of mass spectrometric detection by assigning a fixed, permanent positive charge to amino groups. It allows for increased and predictable sequence coverage for peptides in proteomic analyses, and increased limits of detection for several important lipid classes in lipidomic analyses.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>Wasslen, K.V., Canez, C.R., Lee, H., Manthorpe, J.M., Smith, J.C. (2014) Trimethylation Enhancement using Diazomethane (TrEnDi) II: Rapid In-Solution Concomitant Quaternization of Glycerophospholipid Amino Groups and Methylation of Phosphate Groups via Reaction with Diazomethane Significantly Enhances Sensitivity in Mass Spectrometry Analyses via a Fixed, Permanent Positive Charge. Analytical Chemistry. Oct 7;86(19): 9523-9532. DOI: 10.1021\/ac501588y. PMID: 25208053.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p><strong>Quantitative Proteomics<\/strong><\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>The Smith Lab uses microfluidic devices to manipulate biological samples in a highly efficient manner to elucidate protein dynamics and post-translational modification patterns using MS in conjunction with TrEnDi. Through studying the dynamics of protein abundances or the modes in which they are modified in cells that are stimulated in some manner (or that are either diseased or healthy), our research will help define how cells communicate with each other, their environment and themselves.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p><strong>Quantitative Lipidomics<\/strong><\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>Although lipids have been studied for decades and have been largely regarded as energy storage or structural molecules, recent progress in lipid research has revealed many novel and important roles for lipids in cellular signaling. Many classes of lipids are easily analyzed by mass spectrometry; however, some are more difficult to observe. The Smith Laboratory will focus on developing novel methods to identify lipid species in the context of complicated biological samples. To date, the development of TrEnDi has achieved this goal by increasing the sensitivity of some lipid classes over an order of magnitude. Ultimately, we will apply the novel methods that are developed to investigate lipid dynamics in biological systems to aid our understanding of the roles they play in cellular life.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>For more information, visit <a href=\"https:\/\/carleton.ca\/smithlab\/\">The Smith Lab<\/a>.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>&nbsp;<\/p>\n<!-- \/wp:paragraph -->\n    <\/dd>\n<\/div>\n                        <\/dl>\n\n    \n    <\/div>\n<\/section>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":2,"featured_media":0,"parent":3584,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"_cu_dining_location_slug":"","footnotes":"","_links_to":"","_links_to_target":""},"cu_page_type":[],"class_list":["post-3727","page","type-page","status-publish","hentry"],"acf":{"cu_post_thumbnail":""},"_links":{"self":[{"href":"https:\/\/carleton.ca\/chemistry\/wp-json\/wp\/v2\/pages\/3727","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/carleton.ca\/chemistry\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/carleton.ca\/chemistry\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/carleton.ca\/chemistry\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/carleton.ca\/chemistry\/wp-json\/wp\/v2\/comments?post=3727"}],"version-history":[{"count":2,"href":"https:\/\/carleton.ca\/chemistry\/wp-json\/wp\/v2\/pages\/3727\/revisions"}],"predecessor-version":[{"id":5780,"href":"https:\/\/carleton.ca\/chemistry\/wp-json\/wp\/v2\/pages\/3727\/revisions\/5780"}],"up":[{"embeddable":true,"href":"https:\/\/carleton.ca\/chemistry\/wp-json\/wp\/v2\/pages\/3584"}],"wp:attachment":[{"href":"https:\/\/carleton.ca\/chemistry\/wp-json\/wp\/v2\/media?parent=3727"}],"wp:term":[{"taxonomy":"cu_page_type","embeddable":true,"href":"https:\/\/carleton.ca\/chemistry\/wp-json\/wp\/v2\/cu_page_type?post=3727"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}