Sankha (Bobby) Basu, MD, PhD received his BS in Biology and Chemical Engineering in 2003 at MIT and obtained his MD and PhD (Pharmacology) degrees in 2013 from the University of Pennsylvania School of Medicine. His thesis work involved the development and application of stable isotope LC-MS/MS methods to study mitochondrial disease, which was conducted in the laboratory of Dr. Ian Blair. He then went back to Boston to complete a residency in Clinical Pathology and a fellowship in Medical Microbiology at the Brigham and Women's Hospital (BWH). Following his clinical training, he joined the laboratory of Dr. Nathalie Agar at BWH as a post-doctoral research fellow working on a variety of applications including intraoperative MS and MALDI MSI. He recently joined the faculty at BWH as Assistant Director of Clinical Chemistry and Mass Spectrometry and Instructor of Pathology at Harvard Medical School. His clinical roles include the development and implementation of LC-MS methods in clinical chemistry and MALDI TOF based microbial identification in microbiology. Additionally, he continues his work with the Agar lab on clinical and translational applications of MS.

Kyana Garza graduated from the University of St. Thomas in Houston in 2016 with a B.S. in Chemistry. She is currently a fourth-year graduate student at the University of Texas at Austin and works under the supervision of Prof. Livia S. Eberlin. Kyana has worked on several projects that focus on developing and applying mass spectrometry techniques for enhanced and expedited breast cancer diagnosis, with the goal being to improve patient management and outcome.

My PhD and first postdoc focused on analysis of peptides, various nano-materials and antibiotic compounds using mass spectrometry-based techniques, and the localization and distribution study of various drugs in rat plasma and brain tissues via Mass Spectrometry Imaging (MSI). I recently joined Dr. Kumar Sharma’s Lab (Center for Renal Precision Medicine) at the University of Texas Health, San Antonio, to continue my postdoctoral studies, and am mainly focused on the kidney precision medicine project (KPMP) which extends to the study of diabetic complications [e.g., diabetic kidney diseases (DKD) and diabetic ketoacidosis (DKA)], spatial metabolomics and MSI in kidney tissues. I have also been involved in developing novel quantitative methods for targeted metabolomics for plasma and urine samples, and have extensive experience in method development for small molecules in biosamples.

Emily Sekera received her B.S. in chemistry from Rochester Institute of Technology in 2015. In the same year, she joined the chemistry PhD program at the University of Buffalo. Emily is now a 5th year graduate student working under the advisement of Dr. Troy Wood and acts as a departmental ambassador. In the lab, she investigates metabolomics, proteomics, and lipidomics using a wide variety of MS techniques particularly those with high resolution. She plans to move forward in her career by completing a post-doc in imaging mass spectrometry.

I started conducting research in my sophmore year at Coker College in Dr. Joseph Flaherty's lab, where I focused on the phenotypic characterization of knock-out mutants of Fusarium graminearum with a focus on the systems of conidiagenesis and stress response. I was fortunate enough to spend a semester in Dr. Stephen Rossiter's lab at Queen Mary University of London analyzing and interpreting RNA-seq data sets in order to examine if there was differential expression of genes associated with sensory organs in bats with different diets. I participated in the University of Chicago's Cell and Molecular Biology REU program and conducted a project on optimizing the conditions for a dinucleosome remodeling assay in Dr. Alexander Ruthenburg's lab. I am currently pursuing a Ph.D. in Biomedical Sciences at the Medical University of South Carolina in Dr. Richard Drake's lab in order to contribute to the understanding of cancer glycobiology using mass spectrometry imaging.

I graduated from Meredith College in 2017 with a B.S. in Chemistry (Magna Cum Laude). While at Meredith College, I double majored in Chemistry and Environmental Sustainability with a minor in mathematics. Currently, I am a third year PhD Candidate in the Department of Chemistry at North Carolina State University under the advisement of Professor David Muddiman. My research focuses on the development of mass spectrometry imaging methodologies by infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) for applications in exposomics.

I am a rising second-year chemistry graduate student working under the advisement of Dr. Erin Baker at North Carolina State University (NCSU). Thus far, my research has been focused on the development of multidimensional lipid spectral libraries for the rapid and confident identification of lipid species in complex samples. This work is essential for current and future applications in our lab and the broader lipidomics community. I primarily focus on clinical and environmental applications ranging from elucidating lipid markers associated with smoke inhalation injury to evaluating lipid dysregulation in plants following exposure to perfluoroalkyl substances. I am currently serving as the Communications Committee Chair of Females in Mass Spectrometry (FeMS). Prior to graduate school, I completed a B.S. in chemistry with a minor in biological sciences at NCSU. I did undergraduate research with Dr. David Muddiman, where I utilized capillary electrophoresis-mass spectrometry for the measurement of small molecules associated with amyotrophic lateral sclerosis.

Altered Metabolic Profiles of Small Molecule Map of Diabetic Mice Kidney Tissue Revealed by Mass Spectrometry Imaging
Annapurna Pamreddy
University of Texas Health Science Center

The Utilization of Graphene to Enhance Mass Spectrometry Imaging in Murine Brain Tissue
Emily Sekera
University at Buffalo
>> VIEW POSTER (PDF)

IR-MALDESI Mass Spectrometry Imaging of Rat Placenta Tissue After Exposure to Flame Retardants
Crystal Pace
North Carolina State University
>> VIEW POSTER (PDF)

Developing High-throughput MALDI Mass Spectrometry Imaging Methods for N-glycan Profiling of Clinical Biofluids
Calvin Blaschke
Medical University of South Carolina

The Development and Clinical Application of Multidimensional Lipid Spectral Libraries in Skyline
Kaylie Kirkwood
North Carolina State University

Join the FeMS network (Females in Mass Spectrometry) with guest MJ Paulines from Merck for tips, tricks and advice for successful industry and pharmaceutical job interviews.

There will be time for discussion and a breakout networking session. This is a fun, informal way to stay connected and meet people in the field.

All are encouraged to join!

Follow FeMS on Twitter: @FemalesMassSpec
Join the FeMS LinkedIn Group.

Paula M. Ladwig, M.S., MT (ASCP), is a Development Technologist Coordinator with the Clinical Mass Spectrometry Development Laboratory, Department of Laboratory Medicine and Pathology at Mayo Clinic in Rochester, MN. She has over 10 years of experience in the development and validation of new mass spectrometry tests. Her interests include the implementation of therapeutic drug monitoring of monoclonal antibody therapeutics by mass spectrometry.

Session Overview

The clinical laboratory will have many roles as monoclonal antibody therapeutics (t-mAbs) expand: identifying potential interferences in routine immunoassays; developing new assays to differentiate a t-mAb from an endogenous, disease-causing plasma cell clone and monitoring therapeutic drugs for better patient outcomes and assessing loss of response to therapy. This session will provide an overview of mass spec techniques available to the clinical laboratory for t-mAb detection and quantitation along with their advantages and disadvantages. Finally this session will offer a few examples of hurdles in the implementation into the clinical laboratory setting.

Target Audience

This session is intended for clinical laboratory directors and pathologists, clinical technologists, IVD manufacturers, pharmaceutical scientists, and anyone interested in the mass spectrometry applications for therapeutic monoclonal antibodies especially those involved in development of new methods for t-mAb monitoring.

Needs Assessment

There are over 60 different therapeutic monoclonal antibodies (t-mAbs) approved by the FDA; used to treat a variety of diseases. The market for monoclonal antibodies is rapidly growing, with over 500 new t-mAbs in several stages of development. Laboratorians are quite familiar with the detection, screening, and quantitative therapeutic drug monitoring for small molecules as the methodologies have been well established, therapeutic ranges for many drugs have been defined, and the metabolic pathways for many small molecules have been elucidated in detail. However, this is not the case for the t-mAbs. The detection, screening, and quantitative measurement of these monoclonal antibodies require different technologies.

Mass spectrometry is an important tool in the field of t-mAbs; mostly because it is relatively simple and so versatile once you understand how to apply the basic principles, challenges and limitations of each different approach and instrumentation. This session will provide examples of approaches for mass spectrometry assay development for chimeric, humanized and fully human t-mAbs quantitation; from peptide by quadrupole MS to intact or subunit detection by time-of-flight or orbitrap MS.

Following the completion of this session, the participant will be able to:

1. Describe mass spectrometry techniques available for the assessment of monoclonal antibody therapeutics along with their advantages and disadvantages.

2. Discuss screening and quantitation approaches.

3. Describe common hurdles and how to avoid them.

Richard B. van Breemen is the Linus Pauling Endowed Chair of Pharmaceutical Sciences and Director of the Linus Pauling Institute at Oregon State University. Prof. van Breemen received his B.A. in chemistry from Oberlin College and Ph.D. in Pharmacology and Experimental Therapeutics with Catherine Fenselau from the Johns Hopkins University. He carried out post-doctoral research in laser desorption mass spectrometry with Robert Cotter at Johns Hopkins. His research concerns biomedical mass spectrometry applied to natural products, chemoprevention, drug metabolism, natural product-drug interactions, and toxicology.

In her former role as an associate professor at the University of Toronto, Amy Caudy was a principal investigator in the Stand Up to Cancer Canada Brain Tumor Stem Cell Dream Team where she directed full scan metabolomics of clinical samples as part of a multi-omics study. She is now managing operations at Maple Flavored Solutions LLC, a provider of mass spectrometry analysis and consulting.

Evgeny Berdyshev is an Associate Professor at National Jewish Health in Denver, CO where he leads mass spectrometric laboratory and the Core. He is a lipid biochemist with a long-standing interest in analytics of lipid signaling molecules and in lipid mass spectrometry. Dr. Berdyshev special focus during last five years is in the area of skin sphingolipidomics/metabolomics and understanding the role of lipids in atopic skin diseases and how they can be used to discriminate subphenotypes of atopic dermatitis or evaluate the efficacy of therapeutic interventions.

Our laboratory is specialized on mass spectrometric approaches to study the involvement of lipid signaling molecules in the development of different pulmonary diseases. Our main current focus is at sphingolipid signaling molecules as the inducers and modulators of COPD and pulmonary fibrosis. In particular, we have established an important link between sphingolipid de novo biosynthesis and the development of emphysema. We also investigate how natural, synthetic, and endogenous ligands for cannabinoid receptors affect fibrotic processes in the lung. Another focus area for our group is the involvement of polyunsaturated molecular species of lysophosphatidic acids in the allergic responses in the lung. We try to understand metabolic pathways involved and sources of lysophosphatidic acid production in the lung and to link lysophosphatidic acid generation to the severity and subtypes of asthma.

I currently work as a Chemistry Informatics Specialist for the Department of Laboratory Medicine at the University of Washington under Patrick Mathias. I help build and support efficiency improvements and automation for our mass spectrometry assays performed in the chemistry division. I previously worked in mass spectrometry method development and clinical testing at the Johns Hopkins University.

Dr. Lima joined Cerilliant Corporation at MilliporeSigma as a Senior Scientist in 2012 after earning a Ph.D. in Chemistry at the University of Texas at Arlington. Her graduate research focused on the total synthesis of imidazole-containing natural products, and a manufacturing technology internship at Abbott Laboratories focused on API manufacturing process improvements and scale up. Dr. Lima earned her B.S. in Biochemistry in 2005 also at the University of Texas at Arlington.

As Principal Scientist at MilliporeSigma, Dr. Lima has extensive experience in reference material development and certification. Her expertise includes design and synthesis of drugs, their metabolites and stable isotope labeled internal standards, particularly steroids, cannabinoids, opiates and opioids. She leads the synthesis of new products in a team of fourteen full time synthetic chemists supporting the manufacture of Certified Reference Materials (CRM’s) at the Round Rock site. The synthesis group is responsible for the design and development of the raw materials used in the formulation of solution CRM’s that make up the Cerilliant portfolio.

Dr. Suhandynata is a Clinical Chemistry Fellow at the UC San Diego Center for Advanced Laboratory Medicine, under the direction of Dr. Robert Fitzgerald. He attended the State University of New York at Stony Brook where he received his Ph.D. in Biochemistry and Structural Biology. His graduate work was performed under the mentorship of Dr. Nancy Hollingsworth, where he applied quantitative phospho-proteomics to identify kinase targets by LC-MS/MS. His post-doctoral work was performed at the Ludwig Institute for Cancer Research at the University of California San Diego, and focused on applying quantitative LC-MS/MS to identify sumoylated proteins and the roles they play in chromosome segregation. As a Clinical Chemistry fellow, he is expanding his skills in the areas of small molecule analysis and clinical method validation with future hopes to apply these skills towards a career in clinical toxicology.

Cannabidiol (CBD), a non-psychoactive constituent of hemp, has been increasingly promoted and studied for pharmacological uses as regulations regarding cannabis and hemp evolve rapidly at a state and federal level. In response to these recent regulations, novel Cannabinoid Certified Reference Materials (CRMs) and testing methods have been developed for the main human metabolites of CBD, 7-hydroxy cannabidiol (7-OH CBD) and 7-carboxy cannabidiol (7-COOH CBD). We will touch on recent legal changes for cannabinoid testing in a Clinical setting, as well as discuss the synthesis, certification, and evaluation of these cannabinoid CRMs in patient whole blood samples at the Center for Advanced Laboratory Medicine at UCSD.

Dr. Benjamin Owusu is a Senior Clinical Chemistry Fellow at the University of Washington School of Medicine. Benjamin received his PhD degree in Biochemistry and Molecular Genetics and went on to do a one-year postdoctoral research fellowship at the University of Alabama at Birmingham (UAB). He obtained his Bachelor of Science degree in Biochemistry at the University of Ghana, where he also served as a Teaching Assistant at the Department of Biochemistry upon completion of his undergraduate training. He later moved to Emory University School of Medicine in Atlanta, GA on a visiting research scholarship prior to starting his doctoral training at UAB. His research over the years span across cancer, cardiovascular, hematological and endocrinological diseases. In addition to clinical service and research, Benjamin is passionate about teaching and mentoring, particularly in STEM education.

Meng Wang is a postdoctoral research fellow at the University of British Columbia. Her work focuses specifically on the development, optimization, and validation of targeted mass spectrometry protein assays.

Andrea Geistanger is Head of Systems Data Analytics, at Roche Diagnostics in Germany. Her department of biostatisticians supports system and assay development through the whole life cycle of Roche’s cobas products. Her team is involved in the early development phases, including biomarker search projects with machine learning and multivariate statistics analysis. During product development phases, Andrea’s data analysts support scientists in experimental planning with Design of experiments, as well as in the experiment of validation studies according to regulatory requirements. Furthermore, they develop standardization schemes and calibration concepts for cobas analyzers. Throughout the development phase, software tools are designed and developed as needed. These programs are also made available to a broader community through open software projects.

Andrea Geistanger recently gave a talk at MSACL Connect on the mcr and VCA R packages for method comparison and precision analysis. That talk was dedicated to statistical tools, the actual one will address the soft topics of these experiments, as study design, analysis and interpretation.

Within this 2 hours workshop important points of method comparison and precision experiments in terms of study design, data analysis and interpretation of results will be covered.

Method comparison experiments address the trueness of an analytical method or the comparison of two analytical measurement methods for the same measurand. The study design addresses not only the question of how many samples to incorporate, but also how to distribute these samples among the measuring interval and which samples to use. From a statistical point of view, method comparison data results in error-in-variables regression models, which need special regression techniques as Deming or Passing-Bablok regression. The main ideas behind these regression techniques will be explained. In addition it will be discussed how to interprete the results of regression estimation and its relationship to the calculated bias.

The second half of the workshop covers precision experiments and the set-up of nested precision designs. Variance-components estimation is explained and the approach to deduce from the lowest precision level to the highest the individual components. Finally, the interpretation of the different variability measures is shown.

Curious about Career options in Industry? Join this Fireside Chat with Agilent Director of Marketing, Tiffany Payne.

Learn what career paths are available at Agilent, tips regarding hiring practices and application strategies, paths to management positions, and making the pivot from academia to industry.

This session will be interactive and offers networking opportunities.

Stephen Roper is an Assistant Professor of Pathology and Immunology at Washington University of School of Medicine and the Assistant Director of Pediatric Laboratory Services at St. Louis Children's Hospital. He received his PhD in Biomedical Science from the Medical University of South Carolina in 2015, where his research focused on the identification of alternatively-sialylated glycoproteins in non-small cell lung cancer progression and imaging mass spectrometry with Richard Drake, PhD. Following the completion of graduate school, Stephen began his postdoctoral training in clinical chemistry at Baylor College of Medicine and Texas Children's Hospital. His research interests include pediatric clinical chemistry, toxicology, and broadening the applications of LC-MS/MS in clinical laboratories.

Ethan Yang is a PhD candidate in Prof. Pierre Chaurand’s lab at the University of Montreal. His research primarily focuses on elaborating new techniques to enhance the sensitivity and selectivity of MALDI-TOF imaging mass spectrometry for use in fundamental and clinical research to better elucidate lipid biomarkers on thin tissue sections. He obtained his B.Sc. at McGill University, majoring in Biochemistry. Since 2012, he has been an active member of the Let’s Talk Science site in Montreal, a national non-profit organization focused on promoting interest in STEM (science, technology, engineering and mathematics) in youth. He is also a founding member and one of the main organizers of the MSACL Early Career Network (MSACL ECN).

Zoe is a lecturer in the Division of Systems Medicine, Imperial College London. Prior to this, she carried out her PhD at the University of Oxford and held post-doctoral appointments at the London School of Hygiene and Tropical Medicine and the University of Cambridge. Zoe’s research interests lie at the intersection of mass spectrometry imaging, lipid metabolism and spatial systems biology, with a focus on non-alcoholic fatty liver disease and cancer.

Andrew DelaCourt is a second-year Ph.D student in Dr. Anand Mehta's lab at the Medical University of South Carolina. His research project in Dr. Mehta's lab focuses on the study of glycan biomarkers for hepatocellular carcinoma. He received his undergraduate degree with honors in chemistry from Wake Forest University in 2018.

I am a research fellow at Department of Medicine, National University of Singapore. I work on the lipidomics of non-alcoholic fatty liver disease.

Peggi Angel is Assistant Professor in the Department of Pharmacology at the Medical University of South Carolina. Her research focuses on development and application of imaging mass spectrometry studies on human disease. She has developed novel IMS approaches to investigate phosphoinositol lipids and fatty acids, collagen type regulation in tissue sections, and N-glycosylation of single cell layers. Dr. Angel applies these approaches to understand fibrosis in heart, liver and cancer progression of breast, prostate and lung. Dr. Angel is a co-founder of Glycopath LLC, a company that focuses on glycosylation analysis as a prognostic or diagnostic tool. She serves on the board of N-Zyme Scientifics, a company that produces enzymes for mass spectrometry. Dr. Angel is committed to serving the imaging mass spectrometry community and serves on the Imaging Mass Spectrometry Society Executive Committee and the MSACL Scientific Committee.

Research Specialty: Proteomics analysis in development and disease; mass spectrometry technology development.

The Schey lab is interested in both method/instrument development in proteomics analysis as well as in applications of state-of-the-art proteomics technologies in the study of development and disease. Method development/technology projects include methods for integral membrane protein analysis, tandem mass spectrometry of intact proteins (top-down proteomics), spatially-resolved proteomics analysis, and quantitative proteomics. The major area of application is human lens protein modifications and protein-protein interactions. Other areas of interest are: proteomics analysis of heart valve development, and invertebrate (shrimp and oyster) innate immunity. Integral membrane proteins play key roles in signaling, transport, and adhesion, yet they remain difficult to analyze using conventional proteomics methods.

Our lab has developed methods to analyze integral membrane proteins and membrane associated proteins including their modifications. In addition, we have developed methods for membrane proteome analysis. Currently we are developing methods for spatially-resolved studies (see below), for tissue imaging of membrane proteins, and for examining the membrane protein phosphoproteome. Standard proteomics analyses typically require tryptic digestion of the protein sample followed by LC/MS/MS analysis of the peptides in order to identify and quantitate the proteins present in the sample. This bottom-up approach relies on inferring protein level information from peptide level measurements. Top-down analysis involves analysis of the intact proteins for identification but requires sophisticated technologies and software.

We have developed a method for top-down proteomics analysis in a MALDI TOF-TOF platform and generated a new software application for the interpretation of resulting data. Spatially-resolved proteomics represents a critically important area of development that takes advantage of recent advances in instrumental sensitivity. The ability to examine region-specific changes in a proteome has wide applicability in both development and disease processes. Two approaches are being developed in our lab to address this issue: 1) laser capture microsdissection (LCM) coupled with shotgun proteomics analysis and 2) MALDI tissue imaging. We have combined our membrane protein analysis protocols with LCM capture to examine region-specific changes in the ocular lens membrane proteome. Also, we have developed new sample preparation methods to allow MALDI imaging of membrane proteins. The MALDI imaging method is being applied to lens aging, chick and mouse heart development, shrimp viral infection, brain changes in addiction, and lung infection. Our long-standing project on ocular lens membrane proteins is focused on how these proteins change as lens cells differentiate and as they age. Since the proteins in the lens core are as old as the individual, the lens serves as a model tissue to study protein aging. Age- and cataract-specific modifications have been identified and regional changes in the membrane proteome are being examined. Functional consequences of lens protein modification are also being examined with confocal microscopic, molecular biology, and spectroscopic methods.

Holly Cox received her Ph.D. in Biochemistry from The Ohio State University. In 2010, she joined the Sports Medicine Research and Testing Laboratory (SMRTL). She has published methods for the measurement of IGF-1 and several banned peptides in athlete urine, serum, and dried blood spot samples. As the Senior Research Scientist, her research is focused on developing new methods to detect blood doping practices and abuse of erythropoiesis stimulating agents, human growth hormone, and insulin analogues.

Born in Ukraine. Obtained an MS degree there and came to the US for the graduate school. Graduated from Oregon State University with a Ph.D. in Chemistry. There I met my (then future) wife, with whom I moved around the country looking for a place to settle: Pittsburgh, Ithaca and finally Southern California. Favorite hobby: hiking and camping.

Dr. Surendra Dasari is an Associate Professor of Biomedical Informatics at the Mayo Clinic. He specializes in the development of analytical and informatics methods for new diagnostics. Dr. Dasari's efforts underlie the development and implementation of mass spec-based methods for amyloid typing and monoclonal gammopathy detection and isotyping. Dr. Dasari also has an active research base in cancer biology of t-cell lymphomas, insulin resistance, aging and renal diseases where he utilizes multi-omics to understand the pathobiology of diseases.

Dr. Hoofnagle's laboratory focuses on the precise quantification of recognized protein biomarkers in human plasma using LC-MRM/MS. In addition, they have worked to develop novel assays for the quantification of small molecules in clinical and research settings. His laboratory also studies the role that the systemic inflammation plays in the pathophysiology of obesity, diabetes, and cardiovascular disease.

Robert L. Fitzgerald, PhD, DABCC Dr. Fitzgerald received his BS degree in Chemistry at Loyola College of Maryland, and his PhD in Pharmacology/Toxicology at the Medical College of Virginia/Virginia Commonwealth University. After two and a half years as a forensic toxicologist for the State of Virginia, he took a position as the Director of the Mass Spectrometry Laboratory at the San Diego VA Hospital. Currently, Dr. Fitzgerald is a Professor in the Department of Pathology at the University of California, San Diego where he is the director of the toxicology laboratory and associate director of the clinical chemistry laboratory. He is board certified in toxicology and clinical chemistry by the American Board of Clinical Chemistry. He is the director of the clinical chemistry fellowship at UCSD.

Dr. Joe El-Khoury is Assistant Professor of Laboratory Medicine at Yale School of Medicine, Director of the Clinical Chemistry Lab and Co-Director of the Clinical Chemistry Fellowship program at Yale-New Haven Health. He is board certified by the American Board of Clinical Chemistry (ABCC) and a fellow of the AACC Academy. He currently serves on the Board of Directors of CLMA, as well as the SYCL Core Committee, IFCC Task Force for Young Scientists and as Chair of the AACC NY Metro Section. His research interests are pre-analytical errors, biomarkers of kidney disease, and liquid chromatography-mass spectrometry in the clinical laboratory.

Not sure what to do with your PhD in mass spectrometry after graduation? Interested in having a direct impact on patient outcomes? Consider a career in clinical chemistry! Come and learn about what this field is all about and what it takes to become a clinical chemist, including the fellowship application process, the fellowship itself, and much more. Live interview of Clinical Chemistry Program Heads followed by open discussion and networking sessions in breakout rooms.

Natalicia de Jesus Antunes is a Brazilian Pharmacist. Currently, she is a Visiting Researcher at Queen Mary University of London, London under supervision of Professor Atholl Johnston. In Brazil, she is a Post-Doctoral researcher at the Department of Pharmacology, Faculty of Medical Sciences, State University of Campinas - UNICAMP, Campinas. She studied Pharmacy at the Federal University of Alfenas, Brazil. Her master and doctoral studies were conducted at the Faculty of Pharmaceutical Sciences of Ribeirão Preto of the University of São Paulo, in Ribeirão Preto. Since her Master's, she has been working with bioanalyses using LC-MS/MS in Clinical Pharmacokinetic studies.

Gang Xu is currently a first-year clinical chemistry postdoctoral fellow in the Department of Pathology and Laboratory Medicine at Medical University of South Carolina. He received his B.E. in Pharmaceutical Engineering in 2007 at Xi`an University of Technology, M.S. in Chemistry in 2012 and Ph.D. in Clinical-Bioanalytical Chemistry in 2019 at Cleveland State University. During his PhD studies he has successfully completed several LC-MS/MS-related projects. His experience with development of LC-MS/MS-based assay spans five years and encompasses both targeted (small molecule quantitation) and untargeted analysis (biomarker studies using metabolomics or lipidomics) with oral or poster presentations in local and national conferences and several publications in peer-reviewed journals and prepared manuscripts pending submission.

Dr. Dubland completed his BSc in chemistry at Simon Fraser University, followed by an MSc in organic chemistry at the University of Toronto. He was then employed as a research associate in the pharmaceutical industry for 4 years, working at both BRI Biopharmaceutical Research Inc. and QLT Inc. Work in the pharmaceutical industry focused on bioanalytical mass spectrometry development, validation, and data acquisition to support clinical and preclinical drug trials. Following this, Dr. Dubland completed his PhD in Experimental Medicine at UBC where his research focused on cellular mechanisms of lipid accumulation and removal in atherosclerosis. Dr. Dubland is currently a Laboratory Scientist in the Newborn Screening and Biochemical Genetics Laboratories at BC Children’s Hospital.

Austin Pickens received his doctorate in Human Nutrition from Michigan State University, investigating biomarker discovery using targeted and untargeted high resolution mass spectrometry. He then joined a cancer informatics startup within the ORACLE Corporation as a data scientist. Austin joined the Biochemical Mass Spectrometry Laboratory (BMSL) at the Centers for Disease Control and Prevention in November 2017, where he develops methods, evaluates new technologies, and investigates metabolomics in newborn screening.

I have a PhD in Bioanalytical chemistry in proteomics and metabolomics from Memorial University of Newfoundland (NL, Canada). I worked in the Newborn Screening and Biochemical Genetics laboratory in the Department of Genetics at King Faisal University Hospital and Research Center (KFSHRC). I work on Clinical Metabolomics and leading a research-based activity to establish comprehensive metabolomics platforms for biochemical genetic diseases. The metabolomics platforms that we have established in our lab are readily used for Biomarker discovery.

Anna Krieger received her B.A. in Chemistry from Gustavus Adolphus College in Saint Peter, Minnesota in 2017. She is currently a graduate student in Prof. Livia S. Eberlin’s lab at the University of Texas at Austin. Her research is focused on developing the MasSpec Pen and other ambient ionization techniques for molecular characterization of brain cancers.

Emma is a graduate student at Vanderbilt University studying under Drs. Richard Caprioli and Jeffrey Spraggins. She finished her undergraduate studies at the University of Notre Dame in 2018 with degrees in Chemistry and Philosophy while working in the Warren Center for Drug Discovery. Her current work involves applying spatially-targeted mass spectrometry methods to better understand host-pathogen interactions in infectious diseases, especially those in the gastrointestinal tract.

Anand Mehta, D.Phil., is the SmartState Endowed Chair in Proteomic Biomarkers and Professor, Department of Cell and Molecular Pharmacology at the Medical University of South Carolina. Dr. Mehta’s laboratory is focused on understanding and developing diagnostic methods and treatments for hepatocellular carcinoma (HCC). HCC is a primary cancer of the liver and kills close to 1 million people every year. The Mehta lab was one of the first to perform total serum glycan analysis for biomarker detection and one of the first to perform serum glycoproteomics. His laboratory remains on the forefront in the development of tools for the analysis of complex carbohydrates and the discovery and validation of biomarkers of HCC.

Professor Michel salzet (Distinguish Professor) Is a member of the Institut Universitaire de France in the speciality of immunoproteomic. He is director of the unit, UMR 1192 Inserm. He discovered with Professor Xavier Roucou, the ghost proteins through proteomic approaches combined with Bioinformatic analyses. For this achievement, they received the Quebec science Award for the discovery of the year 2014. Professor Michel Salzet has (co-)authored more than 335 papers (H-index 58, google scholar) and he has published in Top notch journals like Cancer Cells, Nature protocols, Nature Immunology, Circulation, Blood, Trends in immunology.

Dr. Thomas is a clinical chemist and a faculty member of the Advanced Research and Diagnostics Laboratory (ARDL) and a member of the Masonic Cancer Center. She is also the Associate Medical Director of the West Bank Laboratory. Motivated by the growing prevalence of mass spectrometry in the clinical laboratory, Thomas applies discovery and targeted proteomics methods to elucidate the biology of ovarian cancer and analyze proteins derived from alterations in cancer genomes and related biological processes.

Expertise: Mass spectrometry, clinical proteomics, analytical chemistry

Jacqueline Hubbard graduated from the University of Vermont in 2010 with a B.S. in Biochemistry and a minor in Pharmacology. She then enrolled in the Biochemistry and Molecular Biology program at the University of California, Riverside (UCR) where she earned M.S. and Ph.D. After completing a one year postdoc at UCR, she took a position as a Clinical Chemistry Postdoctoral Fellow at the University of California, San Diego. She is now in her second year working in the Toxicology lab under the supervision of Robert Fitzgerald, Ph.D., D.A.B.C.C. Her main research focus is detecting levels of cannabinoids in various biological matrices.

Personal Statement:
I became a Clinical Chemist because I wanted to do research in a lab that has a direct effect on patient care. As the Assistant Director of Chemistry, I help providers give their patients the best care possible by making sure that they receive quality and timely laboratory results.

Sometimes the scariest part about being a patient is the unknown. I offer providers clear interpretations of laboratory test results so they and their patients have all the information they need.

Every day in the lab we are faced with new intellectual challenges. We solve problems, find more efficient ways to report out quality data, and run additional experiments to help us interpret any confusing results. Tackling these challenges to better serve our patients is very rewarding!

Expertise:
Clinical Chemistry
Toxicology

What positions in academia are available to clinical chemists in academia? Can a clinical chemistry fellowship help with tenure track professorship? Join in our live interview of two clinical chemists who will share their career journey towards earning their clinical chemistry certification and their current position as professors at universities. Bring your questions and be ready for the networking opportunity after the interview!

Innovative mass spectrometry-based analytical methods and sample preparation designs that are transferable to other analytical laboratories. Modulations in hormone biosynthesis and metabolism from consumption of botanical dietary supplements. Metabolism and pharmacokinetics of small molecules. Design of data-mining strategies for efficient metabolite identification.

Andrew Reckers is a Staff Research Associate at the University of California San Francisco. He has industry and academic LCMS experience working with anti-TB drug detection in hair, environmental biomonitoring in human and food samples, and identifying novel psychoactive substances in overdose patients.

EU Marie Curie Actions Global Fellow based at the University of Birmingham and ANZAC Research Institute, University of Sydney.

Dr. Chia-Ni Lin joined Chang Gung Memorial Hospital in 2012. She received her Ph.D. degree in Clinical Laboratory Sciences and Medical Biotechnology from National Taiwan University in Taiwan followed by a fellowship in Clinical Chemistry at ARUP/University of Utah. She is board certificated by the American Board of Clinical Chemistry (ABCC) and a fellow of AACC academy. Her research interests are development, method improvement and validation of clinical laboratory assays, and mass spectrometry applications in clinical laboratory including metabolites in biological fluids, illicit drugs, trace elements and hormones.

He is a Research Associate at the Clinical Mass Spectrometry Facility in the Division of Pathology and Laboratory Medicine at Cincinnati Children’s Hospital Medical Center. He is currently focusing on the biomarker discovery with metabolomics and lipidomics approaches to study pathogenesis of pediatric diseases. He has also been developing mass spectrometry assays for pharmacokinetic studies and clinical assays. He obtained his PhD degree from University of Georgia and MS from Stanford University.

I am the Waters Senior Lecturer in Molecular Spectroscopy in the Department of Surgery and Cancer. I joined Imperial College in 2006 after working as a postdoctoral researcher at the Scripps Research Institute in La Jolla, CA. At Imperial College, I was initially a postdoctoral researcher for the Consortium for Metabonomic Toxicology (COMET) group.

My research focuses primarily on the development and application of novel mass spectrometry (MS) based techniques for metabolic phenotyping and on the fusion of mass spectrometric methods with chemometric analysis, which is currently a significant bottleneck in the analysis pipeline. Broadly, my research at Imperial College has involved the development, optimisation and application of UPLC-MS methodologies for the analysis of biological samples, largely in the context of metabolic phenotyping: serum, urine, tissue, amniotic fluid, and microdialysates. These developmental advances have resulted in shorter analysis times – and therefore higher sample throughput – key for large scale metabolic phenotyping studies. Peak detection and analytical reproducibility have been enhanced, improving metabolome coverage and the potential for biomarker identification and quantification.

I am applying these methods to biomedical research areas including toxicology, cardiovascular disease, neonatal disease and development, maternal exposures and effects on early childhood, and neurological diseases.

As an undergraduate, I studied Biomedical Engineering and Mathematics. I also developed microfluidic devices to study signaling dynamics in single immune cells. I then went out to the Bay Area, where I applied a combination of live-cell imaging and mathematical modeling to understand the dynamics of innate immune signaling. They eventually gave me a PhD in Bioengineering. I then did a postdoc, where I learned the wonder of applying computational methods to publicly available data to address basic biological questions and clinical needs. My research group uses data and computation to learn about biological systems relevant to human health and disease.

Sydney C. Povilaitis received her B.A. in Chemistry from St. Olaf College in Northfield, Minnesota in 2018. Currently, she is a graduate student in Prof. Livia S. Eberlin’s lab at the University of Texas at Austin. Her research focuses on developing the MasSpec Pen for molecular differentiation of microbes and skin lesions.

Dr. Candice Ulmer, a native of South Carolina, graduated from the College of Charleston in 2012 with a B. S. in Chemistry and Biochemistry. While at the College of Charleston, Candice investigated the pharmaceutical photodegradation of NSAIDs using ESI-LC-MS/MS under the direction of Dr. Wendy Cory. Dr. Ulmer graduated (May 2016) with a PhD in Chemistry as a McKnight Doctoral Fellow from the University of Florida in Dr. Richard Yost’s research group. For her doctoral work, she applied UHPLC-HRMS techniques to profile the metabolome/lipidome of human cells and tissues to better understand the disease etiology of Type 1 Diabetes and melanoma skin cancer. Dr. Ulmer’s research comprised experience with various modes of ionization (e.g., MALDI, ESI, APCI, DESI, FlowProbe, and DART). She also incorporated novel stable isotope labeling methodologies such as Isotopic Ratio Outlier Analysis (IROA) to aid in the identification of metabolites as compound identification is still considered a bottleneck in metabolomics studies. In addition to her duties as a graduate student, she was an active researcher with the NIH-funded Southeast Center for Integrated Metabolomics (SECIM). Dr. Ulmer was a member of the Florida mass spec discussion group and the ASMS diversity committee in an effort to increase diversity at conferences and ASMS supported events. Dr. Candice Ulmer was a NIST NRC Post-Doctoral Research Associate (June 2016 – August 2017) and was involved with multi-omic UHPLC-HRMS method development, the first lipidomics interlaboratory study, and experiments that monitored the effects of environmental exposures on human/marine life. Dr. Ulmer is currently a Clinical Chemist Battelle contractor at the Centers for Disease Control and Prevention in Atlanta, GA (National Center for Environmental Health, Division of Laboratory Sciences, Clinical Chemistry Branch). Her responsibilities include the accurate measurement of chronic disease biomarkers and the assessment of clinical analytical methods in patient care.

David Herold is CEO of MSACL & Professor in Residence at UCSD

What roles do clinical chemists play in the government? Which agencies do they work for? Join in our live interview of two clinical chemists who will share their career journey towards earning their clinical chemistry certification and their positions in government. Bring your questions and be ready for the networking opportunity after the interview!

Alyson is a 4th year PhD student working under the mentorship of Drs. Anand Mehta and Richard Drake. She has developed a new tool for analysis of glycoproteins from biofluids and is using this to discover new cancer biomarkers. She is passionate about interdisciplinary science communication and teaching.

Jianhui Zhu, PhD, is a Lead Research Scientist in the Laboratory of Cancer Proteomics within the Department of Surgery at the University of Michigan. Dr. Zhu received her PhD degree from the Nanjing University, China. She joined the Lubman Group at the University of Michigan as a postdoc in 2010. She was appointed senior research scientist at the University of Michigan in 2015 and lead research scientist in 2018. Her research focuses on the development of mass spectrometry-based methods to identify cancer-related proteomic/glycomic/glycoproteomic markers in patient’s serum and tissue biopsies for early cancer detection and monitoring. She received the NCI Research Specialist Award in 2018 for novel glyco-marker research aimed at early detection of hepatocellular carcinoma.

I graduated in analytical chemistry from the faculty of chemistry at Shahid Beheshti University (Tehran,Iran).For my Master's thesis I was working on the Optimization of solid phase microextraction and electromembrane extraction techniques to measure certain pollutants and drugs. During my studies,I was also awarded medals and honorary diplomas from international and national competitions and expositions because of my inventions. In June 2017, I started my Glysign PhD project, conducting research at Genos Ltd., Zagreb, Croatia, and the Leiden University Medical Centre in Leiden, the Netherlands. My research is geared towards the quantification of serum protein glycosylation for patient stratification in early-onset and other diabetes types.

I hold a bachelor degree in Pharmacy from the Hebrew University of Jerusalem, Israel. I did my PhD at the same university specializing in nanocscience and drug delivery with Prof. Shlomo Magdassi (Chemistry Department). During my postdoctoral training with Prof. Richard Zare at Stanford University, USA I worked on ambient mass spectrometry imaging of clinical specimens, mostly employing Desorption Electrospray Ionization Mass Spectrometry Imaging (DESI-MSI).
I started a tenure track position as a Senior Lecturer (Assistant Professor) at the School of Pharmacy, the Faculty of Medicine, the Hebrew University of Jerusalem, Israel, in September 2019.

Dr. E. Ellen Jones is a Staff Fellow at the National Center for Toxicological Research, which is part of the Food and Drug Administration, in Jefferson, AR. At NCTR Dr. Jones leads the MALDI Imaging team located within the Biomarkers and Alternative Models Branch (BAMB) in the Division of Systems Biology with the overall goal of utilizing this approach to better understand drug toxicities. The implementation of cutting-edge technologies such as high resolution MALDI IMS within the Food and Drug Administration (FDA) is critical as it corresponds to efforts ongoing in pharmaceutical companies whom are using it both in preclinical and clinical studies to identify biomarkers of drug efficacy and toxicity; data which is beginning to be included within FDA drug filings. Thus, the MALDI IMS team at NCTR recently acquired a state-of-the-art high resolution FTICR mass spectrometer (scimaX MRMS 7T FTICR MS) capable of the mass accuracy and resolution required for small molecule and metabolomic imaging.

I studied biology at the University of Zurich, Switzerland, and made my PhD in Molecular Plant Physiology in the lab of Prof. Enrico Martinoia, focusing on ABC transporters and comparative molecular phylogenetics. Subsequently, I became as researcher at the University Hospital of Zurich, where I was involved in establishing an LC/MS-based assay for the peptide hormone hepcidin and in projects studying Fabry Disease mechanisms. Biological processes, bioanalysis, clinical applications and the use of informatics to improve workflows have been my constant research interests. With this background I am now working as a senior researcher at the Singapore Lipidomics Incubator (SLING), heading our new data team that is focusing on developing workflows and software pipelines for the analytical data processing, QA/AC and exploration of the diverse lipidomics datasets generated by our lab.

Irene van den Broek has a PhD in analytical chemistry from the Utrecht University, the Netherlands and over 10 year experience in quantitative mass spectrometry for clinical and proteomics applications.

Distinguished Professor I. Fournier (IF, PRISM, U1192, Lille) is senior member of the University Institute (IUF) with a chair in Clinical Mass Spectrometry. She is currently co-director of PRISM lab INSERM U1192. Prof. Fournier is a specialist of Mass Spectrometry applied to clinics and proteomics. She was pioneer a novel technology in Europe of molecular imaging namely MALDI Mass Spectrometry Imaging in 2002 (Fournier et al., Neuroend. Letters 2003) and in 2007 demonstrated that MALDI MS Imaging could be perform from archived Formalin fixed and Paraffin Embedded hospital tissue samples (Lemaire et al., J. Proteome Res 2007). In 2005, she developed the multiplex targeted imaging, Tag-mass technology (Lemaire J. Proteome Res. 2007; Gagnon et al., Prog Histochem Cytochem 2012). In 2013, she introduced the concept of the spatially-resolved tissue proteomic and applied this technology on different cancers (Longuespee et al., Cancer Metastasis Rev 2012; Quanico et al Chem Com, 2015, Simeone et al., Semin Cancer Biol., 2018). Since 2011, Pr. I. Fournier with Pr. X. Roucou have evidenced the Ghost proteome (Samandi et al., Elife 2017, Delcourt et al., EBioMedicine et al., 2017, Brunet et al., Nucleic. Acid. Res., 2019). In 2014, she performed the development of a novel technology based on mass spectrometry and allowing to realize in vivo real time tissue molecular imaging and for guiding surgery, with an instrument named SpiderMass (Saudemont et al., Cancer cells, 2018; Ogrinc et al., Nature Protocols, 2019).

David C. Muddiman is the Jacob and Betty Belin Distinguished Professor of Chemistry and Director, Molecular Education, Technology, and Research Innovation Center (METRIC) at North Carolina State University in Raleigh, NC. Prior to moving his research group to North Carolina State University in 2006, David was a Professor of Biochemistry and Molecular Biology and Founder and Director of the Proteomics Research Center at the Mayo Clinic College of Medicine in Rochester, MN. Prior to this appointment, David was an Associate Professor of Chemistry at Virginia Commonwealth University. It was there that he began his professional career as an assistant professor with an adjunct appointment in the Department of Biochemistry and Molecular Biophysics and as a member of the Massey Cancer Center in 1997. These academic appointments followed a postdoctoral fellowship at Pacific Northwest National Lab

In 2018, Prof. David Muddiman was named the Director of the Molecular Education, Technology, and Research Innovation Center. METRIC provides NC State researchers and University partners with world-class state-of-the-art measurement science facilities across four buildings throughout campus, encompassing three key molecular characterization technologies including mass spectrometry, magnetic resonance (NMR and EPR), and X-Ray Crystallography (small molecule and macromolecular).

The Muddiman Group focuses on the development of innovative mass spectrometry measurements to solve important biological problems. Research projects include developing an ambient ionization method called IR-MALDESI and its application to a diverse range of materials, including soft tissue, plants, textiles and bone. Moreover, the group is working on advanced separations to enable detailed characterization of complex biological samples.

Wojciech Michno has a highly international background. He is a United World College (Norway) scholar and a Macalester College (USA) alumnus. At the university he completed two degrees in parallel, one in Chemistry and one in Neuroscience, with a focus on molecular neurobiology. Wojciech did his master’s thesis in pharmacology, and recently defended his PhD in analytical neurochemistry at Sahlgrenska Academy, University of Gothenburg, Sweden. The focus of his work is Alzheimer’s disease.

What does clinical chemistry have to do with industry? What opportunities are available for me as a clinical chemistry? Join in our live interview of two clinical chemists who will share their career journey towards earning their clinical chemistry certification and their current position in various industries. Bring your questions and be ready for the networking opportunity after the interview!

Christina R. Ferreira works as Lipidomics Scientist in the Metabolite Profiling Facility at Purdue University. Her main research interest is the application of the MRM-profiling method for the exploratory analysis of lipids and metabolites in developmental biology models. She created of the MRM-profiling method and contributes to diverse projects from the Cooks lab related to further developing this method. Dr. Ferreira also supports the application MRM-profiling in research projects served by the multi-user Purdue Metabolite Profiling Facility at Bindley Bioscience Center. She iss the project manager for a large effort (Purdue Make-It System) for high-throughput screening and analysis of chemical reactions using DESI-MS.

R. Graham Cooks is the Henry Bohn Hass Distinguished Professor in the Department of Chemistry at Purdue University. He has served as major professor to 140 PhD students. Dr. Cooks’ was a pioneer in the conception and implementation of tandem mass spectrometry (MS/MS) and of desorption ionization, especially molecular secondary ionization mass spectrometry (SIMS). In 2015 his lab performed exploratory analysis of small molecules in cerebrospinal fluid from which the MRM-profiling method emerged. His work also includes the development of miniature portable mass spectrometers using ambient ionization and application of this combination to problems of trace chemical analysis at point-of-care. His interests in the fundamentals of ion chemistry focus on chiral analysis based on the kinetics of cluster ion fragmentation. His group also studies collisions of ions at surfaces for new methods of molecular surface tailoring and analysis, and nanomaterials preparation by soft-landing of ions and charged droplets. Dr. Cooks also launched new method of preparative mass spectrometry based on accelerated reactions in microdroplets. Dr. Cooks has been recognized with the Mass Spectrometry and the Analytical Chemistry awards of the American Chemical Society, the Robert Boyle Medal and the Centennial Prize of the Royal Society of Chemistry, and the Camille & Henry Dreyfus Prize in the Chemical Sciences. He is an elected fellow of the American Academy of Arts and Sciences, the Academy of Inventors and the U.S. National Academy of Sciences.

In this talk, we invite the audience to critically investigate the predominant mass spectrometry workflows used for the exploratory analysis of small molecules and discuss its analytical aspects. We will then present an approach for exploratory lipidomics and metabolomics, multiple reaction monitoring (MRM)-profiling, which initially explores small molecules present in biological samples based on their chemical functionalities using precursor ion (Prec) and neutral loss (NL) scans without the use of chromatographic separation. In a second step the Prec and NL information is translated into MRM scans and these are used to obtain mass profiles to be compared among samples by univariate and multivariate statistical methods. The MRM profiling methodology is characterized by high speed and excellent classification of samples. Identification and quantitation of individual molecules is also achieved.

*This talk was originally scheduled to be presented at MSACL 2020 US by John Yates. It is expected to be about 20 minutes, not including Q&A.

INTRODUCTION: Proteins have exquisite three-dimensional structure. Their structures dictate the functions and interactions within the cell. Most of what we know about the structures of proteins comes from methods like x-ray crystallography, NMR and more recently cyro-EM. These methods are all in vitro methods that often look at proteins as single entities or as a protein complex. What is often missing is the in vivo context to the protein structure, e.g. what is the structure that exists in the cell. Several mass spectrometry-based methods are emerging to examine the 3D proteome or the conformations of proteins in their in vivo context.

OBJECTIVES: The primary objective of this work is to develop methods to measure the "structures" or confirmations of protein in the in vivo environment and to apply them to common diseases.

METHODS: We’ve developed a strategy to measure the surface accessibility of proteins in vivo that provides information about protein conformations and does so in a quantitative manner.

RESULTS: This method has been used to study protein misfolding diseases. This method has been applied to WT and mutant DF508 CFTR to examine structural changes induced by the mutation. A significant change has been observed at a critical interface between the NBD1 and NBD2 domains. This method is also being applied in Alzheimer's disease (AD)and Lewy body disease (LBD) to measure extent of conformational changes to proteins. This method is applied to AD and LBD patient brain tissue lysates and extensive protein comformational changes are observed.

CONCLUSIONS: Substantial changes beyond misfolded aBeta and Tau are observed and based on the molecular changes observed it is difficult to distinguish at the molecular level between advanced AD and LBD suggesting in neurodegenerative misfolding diseases the collapse of proteostasis has a similar endpoint. The studies of CFTR show a critical interface is disrupted between WT and DF508.

I am an analytical chemist focused on infection metallomics and clinical mass spectrometry (MS). From 1991 I have had the main contract with the Institute of Microbiology in Prague, where I run an analytical lab with 25 employees now benefitting from mass spectrometry, nuclear magnetic resonance spectroscopy, and electron microscopy (https://ms.biomed.cas.cz/). As a professor of analytical chemistry, I am also active at Palacky University in Olomouc, CZ, providing me with access to elemental imaging mass spectrometry and infection models. I have a scientific profile with 3582 citations (access date May 21, 2020), 1517 citations since 2015. My current h-index is 30 (Google Scholar). In 2020 I contributed to 11 peer-reviewed papers, nine of them I corresponded.

*This talk was originally scheduled to be presented at MSACL 2020 US. It is expected to be about 35-45 minutes, not including Q&A.

Background: The detection and quantitation of siderophores in urine represents an innovative early indication of pathogenic microorganisms in a host [1]. In this presentation, we document why the general application of siderophores in invasive infectious diagnostics will soon represent the same clinical breakthrough as ribosomal protein typing ten years ago. In addition to handling co-infections or polymicrobial frenemies, with mass spectrometry, we can monitor the antimicrobial drug metabolism [2].

Methods: A database of 700 microbial siderophores was used for screening a patient’s status with invasive infections caused by Aspergillus fumigatus, Pseudomonas aeruginosa, and zygomycetes. Human urine samples were examined by liquid chromatography and Fourier-transform ion cyclotron resonance (FTICR) mass spectrometer [3]. The biomarkers were quantified against matrix-matched standards, and our in-house tool called CycloBranch (https://ms.biomed.cas.cz/cyclobranch) was used for compound dereplication [4].

Results: For the diagnosis of aspergillosis, we used an array of ferri-triacetylfusarinine C (TAFC)/ferri-ferricrocine (FC)/gliotoxin (GTX) in a cohort of 28 patients (14 positive and 14 negative controls). LOD for TAFC in human urine was 0.1 ng/mL. The maximum experienced concentration was 1.7 ug/mL. In the working dataset of critically ill, mostly non-neutropenic humans, the TAFC/FC/GTX sensitivity in urine was 93% compared to standard GM in serum (36%). The kinetic profiles upon antimycotic treatment showed a quick drop in siderophore production in vivo. In the same cohort, ferri-pyoverdines and pyochelin were detected as urinal biomarkers in the patients with Pseudomonas aeruginosa. The LOD for Fe-PVD in urine was 10 ng/mL. In serum samples, the LOD and LOQs were 1 and 5 ng/mL, respectively. In the seminar I will also show the co-infecting frenemies studied in animal models of bacterial [5] or fungal infections [6].

Conclusion: Urinal samples are analytically attractive due to less chemical background compared to serum and clinically interesting due to non-invasive applications. Optimized sample preparation could soon move siderophore analysis from FTICR equipment to standard MALDI-Biotyper-type labs.

References:

1. Luptáková, D.; Pluhá?ek, T.; Pet?ík, M.; Novák, J.; Palyzová, A.; Sokolová, L.; Škríba, A.; Šedivá, B.; Lemr, K. and Havlí?ek, V. Non-invasive and invasive diagnoses of aspergillosis in a rat model by mass spectrometry. Sci Rep 2017, 7, 16523.

2. Houst, J.; Spizek, J. and Havlicek, V. Antifungal Drugs. Metabolites 2020, 10, article No. 106.

3. Pluhacek, T.; Skriba, A.; Novak, J.; Luptakova, D. and Havlicek, V. Analysis of Microbial Siderophores by Mass Spectrometry. In: SK Bhattacharya (ed) Metabolomics: Methods and Protocols 2019: 131-153.

4. Novák, J.; Škríba, A. and Havlí?ek, V. CycloBranch 2: Molecular Formula Annotations Applied to imzML Data Sets in Bimodal Fusion and LC-MS Data Files. Anal Chem 2020, 92, 6844-6849.

5. Petrik, M.; Umlaufova, E.; Raclavsky, V.; Palyzova, A.; Havlicek, V.; Haas, H.; Novy, Z.; Dolezal, D.; Hajduch, M. and Decristoforo, C. Imaging of Pseudomonas aeruginosa infection with Ga-68 labelled pyoverdine for positron emission tomography. Sci Rep 2018, 8, 15698.

6. Skriba, A.; Pluhacek, T.; Palyzova, A.; Novy, Z.; Lemr, K.; Hajduch, M.; Petrik, M. and Havlicek, V. Early and Non-invasive Diagnosis of Aspergillosis Revealed by Infection Kinetics Monitored in a Rat Model. Front Microbiol 2018, 9, 2356.

Michael H. Gelb is Professor of Chemistry and Barbara L. Weinstein Endowed Chair in Chemistry, Adjunct Professor of Biochemistry at the University of Washington. Major developments in the Gelb lab include discovery of protein prenylation, development of ICAT proteomic reagents, identification of phospholipases involved in lipid mediator generation, development of anti-parasite drugs, and development of mass spectrometry for newborn screening. Awards include: Repligen Award in Chemistry of Biological Processes (Amer. Chem. Soc.), Univ.of Washington Faculty Lecture Award, Gustavus John Esselen Award (Harvard Univ.), AAAS Fellow, NIH Merit Award, Medicines for Malaria Project of the Year Award, Pfizer Award in Enzyme Chemistry, ICI Pharmaceuticals Award for Excellence in Chemistry. The Gelb lab has published more than 500 papers and 100 patents in biological chemistry. The Gelb laboratory has developed mass spectrometry for worldwide newborn screening of lysosomal storage diseases (the latest expansion of newborn screening panels).

Mass spectrometry has a strong presence in newborn screening laboratories because of the ability to quantify numerous metabolites in dried blood spots on newborn screening cards. Over the past decade mass spectrometry has been developed to measure enzymatic activities in dried blood spots. We will present an 18-plex mass spectrometry assay that provides enzymatic activities and biomarkers for lysosomal diseases and allows consolidation with existing mass spectrometry newborn screening panels. In the second part of the presentation we will show the feasibility of using mass spectrometry for proteomics-based newborn screening. This allows screening for a panel of treatable diseaes for which no other methods exists.
As more and more inborn errors become treatable, in part due to gene therapy, it will be important to develop a universal screening platform that allows high throughput, consolidated newborn screening. Despite great progress in DNA sequencing technology, this will not replace biochemical newborn screening in the foreseable future.

INTRODUCTION: Cystic Fibrosis is a disease caused by mutations in the cystic fibrosis ion transport regulator gene (CFTR). The most common mutation, deletion of Phe at position 508 (DF508), results in a loss of function phenotype that causes a large number of clinical symptoms including chronic respiratory infections. At the protein level, the DF508 mutation causes the protein to misfold which results in rapid degradation of the protein in the ER.

OBJECTIVES: The objective of this study is to understand the mechanisms involved in regulating protein misfolding to learn how to rescue the misfolded protein. A detailed understanding of the mechanism should lead to the identification of drug targets for treatment of the disease.

METHODS: Mass spectrometry-based proteomics was used to identify the proteins interacting with wild type CFTR and DF508 CFTR to identify those proteins interacting with the mutant protein, but not the wild type. Proteins interacting uniquely with the mutant were knocked down to identify those proteins whose “inhibition” could potentially rescue the misfolded protein. In addition, regulation of the trafficking process by post translational modifications was also determined using mass spectrometry.

RESULTS: A much better understanding of the mechanisms behind rescue of the mutant protein has been derived from these studies. A disease specific interactome was identified. Proteins interacting with DF508 whose knockdown rescue the mutant protein have been identified. A PTM code has been identified that must be present for the protein to exit the ER. In addition, structural details of the misfolded protein have been determined using a surface accessibility method.

CONCLUSION: By understanding the mechanism behind the loss of function phenotype of DF508 CFTR we now have better routes to rescue the protein and treat CF disease. This knowledge can be used to understand other mutations in the gene that also result non-trafficking of the protein.

Dr. Yonghao Yu received his Ph.D. in Chemistry from the University of California, Berkeley in 2006 under the direction of Julie Leary, where he developed mass spectrometric approaches for the study of tyrosine sulfation, a protein post-translational modification that is implicated in regulating protein-protein interactions in the extracellular space. In 2007, Dr. Yu joined the laboratories of Steven Gygi and John Blenis in the Department of Cell Biology at Harvard Medical School for his post-doctoral training. There he developed quantitative mass spectrometric strategies for the study of protein phosphorylation.

In 2012, Dr. Yu began his independent research career as an Assistant Professor in the Department of Biochemistry at UT Southwestern Medical Center. He was promoted to Associate Professor with tenure in 2017. Throughout his career, Dr. Yu has been the recipient of numerous awards for his research, including the Tuberous Sclerosis Alliance Postdoctoral Fellowship, a CPRIT Scholar in Cancer Research award, a Virginia Murchison Linthicum Scholar in Medical Research award, a Research Scholar award from the American Cancer Society, a UT System Rising STARs Award and most recently, an R35 MIRA award from NIGMS. He has served on many NIH and DoD advisory panels, including as a current member of the NIH Enabling Bioanalytical and Imaging Technologies (EBIT) Study Section.

The long-term goals of the Yu lab are to develop cutting-edge, mass spectrometry-based proteomic technologies, and applying them to systematically identify and characterize novel protein modification events implicated in various pathophysiological conditions. These data-driven strategies are then combined with classical biochemistry approaches to identify aberrant protein modification patterns, decipher the mechanisms of their deregulation, establish the functional consequences of these molecular events, facilitate the development of relevant therapeutic strategies, and finally, identify proteomic signatures that may serve as diagnostic, prognostic or predictive biomarkers for the relevant diseases (e.g., cancer, diabetes and neurodegenerative disease).

Our understanding of how the biology of various diseases relates to the central dogma that DNA encodes RNA, which encodes protein has been buoyed by rapid technological advances in DNA and RNA sequencing and has led to some of the first advances in personalized medicine. However, characterization of the final and arguably most actionable element of the central dogma, protein, has lagged behind. We are interested in developing mass spectrometry-based quantitative proteomic technologies for the comprehensive characterization of the proteome, with a particular focus on post-translational modifications (PTMs)

Poly-ADP-ribosylation (PARylation) is a protein posttranslational modification (PTM) that was first documented in 1963. PARylation is catalyzed by a family of enzymes called Poly-ADP-ribose polymerases (PARPs). In particular, PARP1 is a nuclear protein that is activated as a result of sensing DNA strand breaks. The critical roles of PARP1 in mediating DNA repair and also cell death provide the rationale for developing PARP1 inhibitors to treat a number of human diseases, including cancer and ischemia reperfusion injury. Indeed, late-stage clinical studies revealed that PARP1 inhibitor treatment significantly prolonged progression-free survival of BRCA-deficient ovarian and breast cancer patients. This led to the recent FDA approval of four PARP1 inhibitors in these two indications. However, the signaling mechanism of PARP enzymes is poorly understood, because PARylation is a labile and heterogenous modification.

To address these pressing questions, we developed a large-scale mass spectrometric approach towards comprehensive characterization of the Asp- and Glu-PARylated proteome. Remarkably, the modified proteins are involved in not only DNA damage repair, but also a surprisingly wide array of other nuclear functions. Using a quantitative mass spectrometry experiment, we also identified many previously unknown PARP1 downstream targets, whose PARylation is sensitive to clinically relevant PARP1 inhibitors. More recently, we generated a cell-specific atlas for protein PARylation map in breast cancer. In doing so, we identified PARylation signatures that correlated with the selective cytotoxicity of PARP1 inhibitors in certain breast cancer cells. These results provide potential predictive biomarkers for PARP1 inhibitors. Finally, using the PROTAC technology, we recently developed a small molecule compound that selectively induces the degradation of PARP1. This compound is able to inhibit PARP1, without eliciting the deleterious effects of PARP1 trapping. We showed that this “non-trapping” PARP1 degrader protects primary cardiomyocytes from genotoxicity-induced cell death. These compounds therefore provide an ideal approach for the amelioration of the various pathological conditions caused by PARP1 hyperactivation.

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My research activities focus on improving existing analytic diagnostic tools and expanding the repertoire of informative biomolecules available for disease detection in children. We have developed novel analytic tools for the detection of inborn errors of metabolism and drug exposure in children and continue to explore the value of broad metabolic profiling in conditions such as pre-eclampsia, intrauterine growth retardation, liver failure, and neonatal hypoglycemia.

Mass spectrometry continues to play a prominent role in the field of laboratory medicine. In this session, each speaker will highlight a clinical case where Mass Spec Analysis has made all the difference in a patient's care and outcome.

After completing this activity, the learner will be able to:
1. site examples where mass spectrometry made a difference in patient care
2. describe how mass spectrometry could play an important in their institutions
3. summarize the role of mass spectrometry played in each of these case studies

Robin oversees all Research &Product Development programs within Metabolomic Diagnostics, a company focused on developing early pregnancy risk stratification tests for obstetrical syndromes like preeclampsia and preterm birth. He trained as an analytical chemist, specialized in mass spectrometry, and received a PhD from the University of Antwerp in 2006. After 7 years with a Belgian proteomics biomarker discovery company, where he led the preeclampsia biomarker discovery program, Robin joined Metabolomic Diagnostics in 2013. Since then, he and his team established a translational research workflow which aims to overcome the challenges of translating promising biomarkers into novel products.

Operating at the interface of translational research and commercialisation, he has always keenly engaged in conversations with members of the clinical research community on how to deliver on a shared mission of improving pregnancy outcomes.

Robin has co-authored 20+ original research articles and is a named inventor on 10 patent applications.

Grégoire is a biostatistician specialised in clinical diagnostics and medical devices. Based on complexity estimations, he implements data analysis strategies and statistical frameworks which mitigate risks and therefore increase the chance of successful outcomes. This is achieved by working at the crossroads of statistics, machine learning, medical sciences, and epidemiology whilst adopting IT solutions which are compliant with regulatory and legal frameworks. As a consultant, Grégoire has an established track record of fruitful collaborations with both academic and industry partners.

The area under the receiver operating characteristic (AUROC) curve is a widely used statistic to evaluate performance of prognostic and diagnostic tests. Because AUROC does not depend on disease prevalence, the statistic has also gained prominence in biomarker discovery and development, as it enables biomarker evaluation using cost-effective case-control study designs.
However, end-users in clinical settings typically assess the merits of prognostic / diagnostic tests in function of patient harm and benefit. Disease prevalence and clinical context are critical determinants in clinical utility evaluations and therefore different statistics, like positive and negative predictive values (PPV and NPV), which account for these determinants are typically used to gauge clinical utility. Albeit most biomarker work is performed with the goal of improving clinical care, clinical utility is rarely considered during test development.

To address this lacuna, we devised a method for plotting PPV or NPV criteria, which account for prevalence, in the receiver operating characteristic (ROC) space. Herewith, test developers and clinical end-users are provided with a common framework to discuss and evaluate prognostic / diagnostic test performances.

In this talk we will briefly review key concepts like Sensitivity (Sn), Specificity (Sp) and Prevalence (Pr), and how they are used to create ROC curves (Sn, Sp) and calculate predictive values (Sn, Sp, Pr). We will highlight the limitations of solely depending on AUROC in test evaluations and the importance of considering the shape of ROC curves. Then we will demonstrate how PPV and NPV criteria can be plotted on the ROC space and how this information can be used to discuss test performance in function of clinical utility with different stakeholders. We will conclude with the demonstration of a freely accessible web-tool developed to allow people to explore the dynamic interplay between the test characteristics Sn, Sp, Pr, AUROC, ROC curve shape, PPV and NPV.

Paper: A novel method for interrogating receiver operating characteristic curves for assessing prognostic tests

Software Tools : Positive and negative predictive values

Hubert W. Vesper, Ph.D., is the director of the Clinical Standardization Programs at the
Centers for Disease Control and Prevention’s (CDC) National Center for Environmental
Health. He leads CDC’s clinical laboratory standardization programs to improve the
diagnosis, treatment, and prevention of selected chronic diseases and oversees and
represents specific biomonitoring programs to assess human exposure to environmental
chemicals and its potential impact on human health. He also is co-chair of the steering
committee of the Partnership for Accuracy in Tests for Hormones (PATH), a member of
the steering committee of the National Glycohemoglobin Standardization Program, and
an adjunct faculty member in the Nutrition and Health Sciences Program at Emory
University. Previously he was a consultant at the Kuwait Institute for Scientific
Research, co-chair of the Cardiovascular Biomarker Standardization Steering
Committee, and a member of the World Health Organization (WHO)/Pan American
Health Organization/CDC Emergency Response Team. He received his B.S. in food
science and M.Sc. in food chemistry from the University of Karlsruhe, Germany, and his
Ph.D. from the Technical University of Munich, Germany

Overview of ongoing and new CDC’s Standardization Programs

EDUCATION:
Graduate School: University of Virginia (Chemistry), Charlottesville, VA
Clinical Chemistry and Laboratory Medicine Fellowship: University of Virginia, Charlottesville, VA

CLINICAL:
Laboratory testing in Clinical Chemistry, Toxicology, Hemostasis, and Endocrinology.

RESEARCH:
Liquid chromatography mass spectrometry assay methods.

Dustin R. Bunch, PhD, DABCC, is the assistant director of Clinical Chemistry and Laboratory Informatics at Nationwide Children's Hospital. He is board certified by The Commission on Accreditation in Clinical Chemistry (ComACC) in clinical chemistry and completed his clinical chemistry fellowship at Yale-New Haven Hospital/Yale University in Jun 2019. He received his PhD in Clinical/Bioanalytical Chemistry from Cleveland State University in 2016 and BA in Biochemistry from Case Western Reserve University in 2004. Over the years his research has focused mainly on development and validation of liquid chromatography tandem mass spectrometry (LC-MS/MS) methods; however, recently he has been performing research on hospital and clinical informatics. He is active in professional organizations (AACC, ASCP, and MSACL) for both the local and national level serving on boards and committees.

Working with R for Validation Summaries in the Clinical Laboratory
Lindsay Bazydlo

Putting R Skills to Use in Clinical Laboratories
Dustin Bunch

Dr. Mark Marzinke is Associate Professor of Pathology and Medicine at the Johns Hopkins University School of Medicine. Dr. Marzinke serves as the Director of General Chemistry in the Johns Hopkins Hospital Core Laboratories, and is the Director of the Clinical Pharmacology Analytical Laboratory within the Division of Clinical Pharmacology. He is also Co-Director of the HIV Prevention Trials Network Laboratory Center.

He received his A.B. from the College of the Holy Cross and earned his Ph.D. at the University of Wisconsin-Madison. He completed a fellowship in clinical chemistry at the Johns Hopkins School of Medicine

An overview of the fundamentals that are driving research and development with respect to Sample Preparation.
This is part of a series of Primers on topics relevant to Clinical Mass Spectrometry.

Learning objectives include:
1. Be able to define what Sample Preparation is, why it matters, and why you personally should care. What is the clinical relevance?
2. Understand how sample prep relates to mass spectrometry.
3. Define any terminology that is specific to Sample Preparation.
4. Describe how it works, what are the methods and workflows used and/or how is it implemented in clinical labs.
5. Identify any challenges to implementation/adoption, where do the opportunities lie?