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.

Dr. Heather Jensen Smith is a Research Assistant Professor, Director of the Multiphoton Intravital and Tissue Imaging Research Core (MITI), and member of the Rapid Autopsy Programs for Pancreas and Prostate at the University of Nebraska Medical Center (UNMC). She earned her PhD in Biomedical Sciences from Creighton University in 2006.

Over the last 15 years Dr. Jensen Smith has managed and/or Directed research imaging cores at both Creighton University and UNMC, supporting a broad spectrum of biomedical studies, as well as, her studies investigating the use of endogenous fluorophores as biomarkers of disease progression. As part of the Fred and Pamela Buffett Cancer Center and Eppley Institute for Research in Cancer and Allied Diseases, Dr. Jensen Smith is focused on building a Preclinical Imaging Center integrating clinical, translational, and basic research(ers). In collaboration with Dr. Paul Grandgenett (Director RAP), Dr. Jensen Smith has helped conduct, collect, maintain, and distribute research specimens from 139 autopsies (as of 2020) totaling over 22,000 samples and 60 liters of biofluids.

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.

We will discuss patient-specific effects, sample collection, transport and handling of samples, and tissue preparation when acquiring and interpreting mass spectrometry data. We will especially focus on how these steps effect imaging mass spectrometry data, but many of these topics translate universally across mass spectrometry approaches in general.

This will be an open forum with predefined topics and panelists to guide the conversation.

Join us for some informal networking and to hear from Lauren Pepi, Vineeta Rai, and Hossein Shokri on the research they have been working on in their laboratories! Employers, be sure to join us to find your next perfect hire!

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.

Patrick Mathias, M.D., Ph.D., is a board-certified clinical pathologist and Associate Director of Informatics for UW Laboratory Medicine.

Lab medicine has large impact on the general practice of medicine. It is key to correctly diagnosing diseases and selecting the right treatments for patients. Dr. Mathias's goal is to combine technical and medical knowledge to fulfill the triple aim--reduce the per capita cost of health care, improve the health of populations and most importantly improve the patient experience of care.

Dr. Mathias earned his M.D. and Ph.D. from the University of Illinois. His clinical and research interests include clinical informatics, clinical chemistry and molecular diagnostics.

My lab performs research and clinical testing using mass spectrometry methods, develops new assays, and applies data analytics to enable improved quality and efficiency. My computational pathology efforts are aimed at building the capacity for advanced data analytics in the department through innovations in infrastructure, education, and research to facilitate data-informed decision making for clinical care, operations, and quality assurance.

Looking for an opportunity to hone your interview skills? This is the place for those looking to transition in entry-level positions. Two interviewees will present their elevator pitch and respond to a series of interview questions from a panel of experts and/or hiring managers in a particular field. After their mock interview, the panelists will provide their feedback. This month’s career focus is on data science in proteomics.

this isn't it

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

Daniel Holmes did his undergraduate training in Chemistry and Physics at the University of Toronto before deciding to pursue medicine as a career. He attended medical school at the University of British Columbia where pathology became his area of major interest. The strong influence of his academic mentors led him to enter the Medical Biochemistry residency training program at UBC. This allowed him to use his background knowledge of chemistry in application to medicine. Areas of clinical interest are diagnostic lipidology/endocrinology and research interests are in the utilization of mathematics and computer diagnostics to laboratory medicine.

Patrick Mathias, M.D., Ph.D., is a board-certified clinical pathologist and Associate Director of Informatics for UW Laboratory Medicine.

Lab medicine has large impact on the general practice of medicine. It is key to correctly diagnosing diseases and selecting the right treatments for patients. Dr. Mathias's goal is to combine technical and medical knowledge to fulfill the triple aim--reduce the per capita cost of health care, improve the health of populations and most importantly improve the patient experience of care.

Dr. Mathias earned his M.D. and Ph.D. from the University of Illinois. His clinical and research interests include clinical informatics, clinical chemistry and molecular diagnostics.

The COVID-19 pandemic has introduced challenge upon challenge for health care systems throughout the US and the world, from implementing new workflows in support of delivering routine care to improving access to testing to navigating constrained supply chains. Clinical laboratories have been critical to the COVID-19 response, as identification of cases with testing is a critical step in containing and managing the SARS-CoV-2 virus. The University of Washington Virology Laboratory has played a key role expanding access to COVID-19 testing across the Pacific Northwest, scaling from performing 5,000 tests per month to 5,000 tests per day and growing. Open source software tools have supported this rapid growth along every step of our journey. In this talk, we will discuss the key capabilities R and Python have enabled that have helped us navigate the daily challenges of managing staffing and turnaround times, adjusting operations in response to supply chain limitations, and enabling testing at scale for the population outside of typical health care settings.

We will hear a short summary from Dr. Dan Holmes regarding the workflow he has implemented at St. Paul’s Hospital followed by an in depth analysis by Dr. Patrick Mathias of the workflow developed at University of Washington. Ample time for discussion post-presentation will be available.

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

Come and meet members of the Early Career Network community in our first monthly networking meeting. Open to anyone wanting to be an active member of the network. Trivia games and opportunities for networking included! This month's session is hosted by the Chairs of Europe and Americas.

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?

Dr. Rob Haselberg is an assistant professor at the Vrije Universiteit Amsterdam in the department of Chemistry and Pharmaceutical Sciences. He specialized over the last 10+ years in capillary electrophoresis and liquid chromatography hyphenated with mass spectrometry to characterize intact proteins. He is interested in determining protein heterogeneity, getting insights in degradation processes, mapping intentional modifications and studying protein-protein interactions. All of this is done in the context of biopharmaceutical, clinical, and doping analysis.

Classical electrophoresis has a long history in clinical diagnostics. Being used to separate proteins and nucleic acids, it is still an indispensable tool. Over the years, technological advances have allowed for these slab-gel format to be performed in capillaries enabling higher throughput and more accurate quantitation. However, capillary electrophoresis (CE) also has other application areas for clinical diagnostics, especially when hyphenated with mass spectrometry (MS). To show this added values and to understand and appreciate the diversity of this technique, in this seminar the basics of CE and its hyphenation with mass spectrometry will be covered. Separation mechanisms and technical / practical aspects will be covered, using (amongst others) data obtained in our lab. Moreover, some key applications of CE-MS related to clinical diagnostics will be highlighted. They focus on small molecules, lipids, but also intact proteins. Throughout the seminar and at the end there will be ample opportunity to ask questions.

Jody M.W. van den Ouweland, PhD is a Clinical Chemist at the Department of Clinical Chemistry at Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands. He studied Chemistry at Leiden University and received his PhD degree in 1994 on the discovery of a type 2 diabetic subtype (MIDD). His main interest is in the field of diabetes and endocrinology. In the area of analytical chemistry his focus is on mass spectrometric and chromatographic methods for quantitative measurement of low molecular weight biomarkers, such as vitamin D.

Jona Walk is a resident physician specializing in Internal Medicine at the Canisius Wilhelmina Hospital in Nijmegen. She conducted her PhD research on cellular immune responses after vaccination with the human malaria parasite Plasmodium falciparum at the Radboud university medical center in Nijmegen. She is currently studying vitamin K metabolism as a possible factor in pulmonary damage and coagulopathy in COVID-19, and the potential role for vitamin K supplementation in the treatment of severe SARS-CoV-2 infections.

In this webinar we will present results from our recent study on vitamin K status in SARS-CoV-2 patients. We found severely impaired vitamin K-dependent activation of matrix-Gla-protein (MGP), strongly correlated with increased elastic fiber degradation (as measured by levels of plasma desmosine with LC-MS/MS). Our data suggest a mechanism of pneumonia-induced extrahepatic vitamin K depletion leading to accelerated elastic fiber damage in severe COVID-19 due to impaired activation of MGP. The talk includes a detailed description of the role of vitamin K in hepatic as well as extrahepatic metabolism and its inter-relationship with elastin calcification and elastin degradation as pathological processes that impair elastin’s functioning. Also, details of our LC-MS/MS assay for measurement of desmosine in body fluids will be presented.

PrePrint : Reduced Vitamin K Status as a Potentially Modifiable Prognostic Risk Factor in Covid-19

# Originally scheduled for MSACL2020 US in the Scientific Session : Fentanyl at the Forefront : Using Non-traditional Approaches to Identify Fentanyl Analogs

Introduction

Deaths due to opioid overdoses have been on the rise in the United States, with a particular spike in this trend caused by the emergence of synthetic opioids including fentanyl and analogues. There have been numerous reported cases of synthetic opioids as adulterants in heroin, methamphetamine, cocaine, and counterfeit pills. As a result, they are often times consumed unknowingly, causing mixed toxidromes and confounding diagnosis. Proper routine drug monitoring is essential in addressing the ever-expanding magnitude of the opioid epidemic.

Objectives

The primary objective of this study was to observe prevalence of fentanyl analogs and other false positives in positive fentanyl screens of emergency medicine populations in order to evaluate trends in the dynamic landscape of substance abuse.

Methods

Analysis of remnant clinical samples was approved by the UCSF Institutional Review Board. Urine samples from emergency department (ED) patients with drugs-of-abuse screens performed were monitored from October 2018 to March 2019 for presence of fentanyl (via immunoassay). Samples with a positive fentanyl screen were collected and further characterized by high resolution mass spectrometry (LC-HRMS). Urine samples were diluted 1:5. Chromatography was performed using a Kinetex C18 column with a 10-minute gradient from 2%-100% organic. Data was collected on a SCIEX TripleTOF®5600 using a positive-ion mode TOF-MS survey scan with IDA-triggered collection of high resolution product ion spectra (20 dependent scans). Data was screened for fentanyl, norfentanyl, 13 literature-reported synthetic opioids, and compounds reported/suspected to cause false positives with fentanyl immunoassays.

Results

158 emergency department patient samples screened positive via EMIT fentanyl immunoassay (7.44% of all ED samples screened for drugs of abuse). These samples were analyzed via LC-HRMS and analysis was targeted for 15 synthetic opioids and commonly prescribed or over-the-counter pharmaceuticals with chemical structures similar to that of fentanyl. 6.9% of samples were found to be positive for both fentanyl and acetyl fentanyl. Additionally, risperidone, its metabolite 9-hydroxyrisperidone (paliperidone), and loperamide with its metabolite desmethylloperamide were discovered as sources of false positive for fentanyl screens.

Conclusion

This data reveals the non-trivial prevalence of fentanyl in the ED patient population being screened for drugs of abuse. In many of the cases, fentanyl was not suspected or discovered as exposure agent prior to more comprehensive testing or patient discharge. The identification of acetyl fentanyl along with fentanyl via HRMS analysis can hint to a changing trend in provenance of illicitly manufactured fentanyl. Finally, HRMS is a valuable tool to identify compounds responsible for reoccurring false positives that can inform better patient care and offer a more accurate picture of the continually evolving opioid epidemic.

Daniel Holmes did his undergraduate training in Chemistry and Physics at the University of Toronto before deciding to pursue medicine as a career. He attended medical school at the University of British Columbia where pathology became his area of major interest. The strong influence of his academic mentors led him to enter the Medical Biochemistry residency training program at UBC. This allowed him to use his background knowledge of chemistry in application to medicine. Areas of clinical interest are diagnostic lipidology/endocrinology and research interests are in the utilization of mathematics and computer diagnostics to laboratory medicine.

I did my undergraduate training in Medical Laboratory Science, and post-graduate training in Pathology and Laboratory Medicine, as well as Clinical Chemistry. Currently, I work with the clinical mass spectrometry laboratory at Lurie Children’s, and use data analytics and data science principles and tools on a day-to-day basis. I’ve used R for assay development, test utilization, quality assurance, clinical reporting, and process improvement projects. I also use Excel but don’t tell Dan that.

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.

William Slade, PhD did his undergraduate degree in Biology from Concord University with a focus on Recombinant Gene Technology. He completed a PhD in Biological Sciences at Virginia Tech with a focus on Biological Mass Spectrometry before postdoctoral work at the University of North Carolina at Chapel Hill in the Analytical Chemistry department. He is currently a Researcher in the Mass Spectrometry Research and Development group at Laboratory Corporation of America Holdings in Burlington, North Carolina. His interests include clinical mass spectrometry and informatics.

My lab performs research and clinical testing using mass spectrometry methods, develops new assays, and applies data analytics to enable improved quality and efficiency. My computational pathology efforts are aimed at building the capacity for advanced data analytics in the department through innovations in infrastructure, education, and research to facilitate data-informed decision making for clinical care, operations, and quality assurance.

This is a VIRTUAL 4-Day Course with 16 total contact hours. CE to be provided.

Overview

Have you ever tried to do Deming regression in Excel only to discover that it is not available? Have you had your figure rejected by a journal because the resolution was not good enough? Have you wished that you could figure out a way to stop manually transcribing your LC-MS/MS results into the LIS?

Well, your wait is over because this 4-day ONLINE ONLY course (via Zoom) for complete programming newbies will help you get going analyzing real data related to LC-MS/MS assay development, validation, implementation and publication. The only background expected is the ability to use a spreadsheet program. The skills that you will acquire will allow you to take advantage of the many tools already available in the R language and thereafter, when you see that your spreadsheet program does not have the capabilities to do what you need, you will no longer have to burst into tears. You will be empowe-R-ed.

The course will be run over four days (4 contact hours per day) and time will be evenly split between didactic sessions and hands on problem solving with real data sets. The instructors will adopt a “no student left behind policy”. Students will be given ample time to solve mini problems taken from real life laboratory work and focused on common laboratory tasks. All attendees will need a laptop or desktop computer with both the R language installed and R Studio interface installed. Students may use Windows, Mac OSX or Linux environments. Both R and R studio are free and open-source. No cash required.

Students should be prepared for learning what computer programming is really like. This may involve some personal frustration but it will be worth it.

Obtaining the Software

Instructions for installing the R language are here:
http://cran.r-project.org/

Instructions for installing R Studio are here:
http://www.rstudio.com/

Course Description

The course will cover:

1. The major types of R variables: vectors (numerical, character, logical), matrices, data frames and lists.
2. The important classes: numeric, character, list and changing between them
3. Importing data from Excel
4. Dealing with non-numeric instrument data: the “<10”s and “>1000”s.
5. Manipulating your data: sub-setting, which, match, sort, unique, cut
6. Simple statistical tests: mean, median, quantiles (normal ranges), t-tests, ANOVA, Wilcoxon.
7. Data merges: matching rows between sets
8. Exporting data to Excel-like format.
9. Regressions: Ordinary Least Squares,Passing Bablok, Deming, weighted regressions.
10. Non-linear regressions
11. Looping: Doing things repeatedly
12. Writing your own functions
13. Making highly customized graphs: scatter plots, regression lines, histograms, box plots, qq-plots
14. Putting it all together projects:
--> Preparing method comparison regression and Bland Altman plots
--> Preparing mass spectrometry data for upload to LIS.

Laura Owen is a Consultant Clinical Scientist at Salford Royal NHS Foundation Trust and honorary senior lecturer at the University of Manchester where she teaches chromatography and mass spectrometry at Master’s level. Laura is also proud to be the chair of the practical training committee of MSACL EU and a past member of the endocrinology committee. While working at Wythenshawe hospital and in collaboration with the Christie hospital she became interested in the limitations of immunoassay measurement especially when using it in the breast cancer population. Laura developed and implemented the UK’s first LC-MS/MS assay for oestradiol in an NHS UKAS accredited laboratory which was made available for patient care and clinical trials.

Oestradiol (also spelled Estradiol) measurement by LC-MS/MS has demonstrated superior sensitivity and specificity over immunoassay but despite this, use of immunoassay remains commonplace. Measuring oestradiol by LC-MS/MS is not without its challenges for which there are several approaches. One particular challenge is the very low levels that there is a clinical need to measure accurately, especially in patients with breast cancer. This presentation will look at the issues around accurate measurement and review how different authors have approached them. It will also examine how oestradiol measurement is used in a breast cancer population as a guide for treatment decisions and how different analytical approaches might impact upon these decisions.

When you register for this webinar, your contact details will be passed to the sponsor who will provide you with information relevant to this topic

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.

Obtain ultimate sensitivity. Join us live and learn techniques to leverage selectivity that drives increased analytical performance.

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.

# Originally scheduled to be presented at MSACL 2020 US. Moved from August 10 make-up session due to timing conflict.

Introduction

Type 2 diabetes mellitus (T2D) represents a major public health challenge. The total plasma N-glycome (TPNG) reflects the levels and glycosylation of major plasma glycoproteins, among which are immunoglobulins, acute-phase proteins and apolipoproteins. Although associations of TPNG with T2D have been recently reported by us and others, data on the association between TPNG and T2D complications are scarce. Here, we applied our new ultrahigh-resolution MS method to assess associations of TPNG with T2D complications.

Methods

We determined the TPNG in a subsample of the Hoorn Diabetes Care System cohort (n = 1519 T2D cases and 192 nondiabetic controls from the New Hoorn study cohort) using our Fourier-transform ion cyclotron resonance MS method. Blood plasma samples were randomized over 21 96-well plates, together with technical replicates. Prior to MS analysis, N-glycans were released using PNGase F. For stabilization and linkage differentiation, sialic acids were derivatized. Released glycans were purified and spotted using an automated liquid handling platform. In total, 68 individual glycan compositions were quantified after total-area normalization and summarized into derived traits representing structural features. By applying logistic regression models, we tested for associations of TPNG with case-control status and micro- or macrovascular complications, such as nephropathy, retinopathy, or cardiovascular disease (cross-sectional). T2D complications were also assessed prospectively by Cox regression. Models were adjusted for age, sex, and T2D risk factors. The outputs were meta-analyzed together with our MALDI-TOF-MS data from the independent cohort DiaGene (1815 T2D cases and 836 controls) which we obtained and described previously.

Results

The recently developed method using MALDI-FTICR-MS improved resolution, mass accuracy, dynamic range and the signal-to-noise ratio, especially for larger glycans, in comparison to our previous MALDI-TOF workflow. The relative standard deviation over the 68 detected glycan species was on average 6.6%, based on the relative intensities from 93 technical replicates of pooled plasma, representing total method repeatability.

We found significant associations of all major glycosylation traits, i.e. sialylation, fucosylation, galactosylation, bisection, and glycan complexity with T2D in the meta-analyses of both cross-sectional and prospective data. For example, the bisection and galactosylation of immunoglobulin-related glycans were associated with macrovascular complications and nephropathy. We aim to confirm these results in the near future on protein-specific level, by isolating IgG prior to released-glycan analysis.

Conclusions

Our new method improved the detection of several glycan species, thus providing possible new insights into the association between TPNG and T2D. Our results will be taken forward to improve personalized approaches in T2D and related complications in the future.

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.

Dr. Robert Everly is an experienced group leader with a keen focus on the use of proteomics to advance the discovery of novel medicines. Aspects of proteomics of interest include: protein-ligand interactions e.g. Chemical Biology, protein-protein interactions, protein degradation, and changes in protein localization, cleavage, and post-translational modification.

Chris received his PhD in Analytical Chemistry from the University of Wisconsin Madison where he developed novel quantitative proteomics approaches in the lab of Joshua Coon. Chris continued his post-doctoral studies in the lab of Steve Gygi at Harvard Medical School where he co-developed TOMAHAQ - a targeted mass spectrometry method that combines sample and peptide multiplexing - and developed the proof-of-principle implementation of real-time search for isobaric label based quantitation. Following his post-doc, Chris joined the Microchemistry, Proteomics & Lipidomics department at Genentech where his group develops and applies leading edge quantitative proteomics methods to explore biological pathways related to potential therapeutic targets. Chris' group also focuses on analysis of low-level proteomes with a special focus on understanding technical challenges of current approaches to single cell proteomics and proposing new methods to analyze such samples.

The pharmaceutical industry is an important sector where analytical chemists, particularly mass spectrometrists, are in growing demand. What positions are available for new graduates? Join our Fireside Chat with Dr. Robert Everley and Dr. Christopher Rose to learn about a career in pharma. This session will be interactive and offers opportunities to network.

Dr. Robert D. Voyksner received his B.S. in Chemistry at Canisius College in 1978 and his Ph.D. at the University of North Carolina at Chapel Hill in 1982.

As a member of the Research Triangle Institute staff since 1983, Robert has been responsible for developing extraction, separation and mass spectrometric methods for biologically and environmentally significant compounds. He has primarily employed HPLC/MS on quadrupoles, sectors and ion trap mass spectrometers for positive and negative ion detection for specific compounds. His pioneering work in HPLC/MS and HPLC/ion trap MS has demonstrated the capability to perform analysis of compounds not amenable to analysis by GC/MS. Specifically, he has worked on the development and evaluation of electrospray HPLC/MS methods for the analysis of high molecular weight opioid peptides, antimalarials, anticancer drugs, nucleotides, antibiotics, proteins and cyclodextrins. He has been working with FDA for the past nine years to develop new methodology using electrospray HPLC/MS and capillary electrophoresis-MS to detect and measure antibiotics (-lactams and aminoglycosides) in food and milk to insure human food safety.
In addition, he is has developed methods and evaluated the use of electrospray HPLC/MS and ion trap MS/MS for environmental monitoring, particularly for the detection of azo dyes and pesticides (including carbamate, methyl urea, triazine, organophosphorous and phenolic acid ). He has developed CE/MS and CE/Ion trap MS methods for the identification of DNA adducts from exposure to nitrocompounds and pesticides.

Dr. Voyksner's research in mass spectrometry has resulted in over 230 publications and presentations, primarily in the area of HPLC/MS. He has served on the Board of The American Society For Mass Spectrometry (ASMS), is on the organization committee for The Montreux LC/MS Symposium, and was the organizer for the 1995, 1999 and 2003 Montreux LC/MS Symposium. He is the organizer for the 2007 Montreux LC/MS Symposium (location yet to be determined). Dr. Voyksner has taught LC/MS short courses for the past 15 years for ASMS, every major pharmaceutical company, ISSX, PBA, HPCE and other HPLC focused meetings.

Now, as president of LCMS Limited, Robert has brought his expertise in mass spectrometry along with years of experience in training and problem solving together into focus and guides LCMS Limited to strive for excellence in its mission of "...chasing tomorrow through research, innovation and education today....."

This is a VIRTUAL 4-Day Course with 16 total contact hours. CE to be provided.

This course is designed for the chromatographer / mass spectrometrist who wants to be successful in developing methods, method optimization and solving problems using LC-MS/MS. The course covers the atmospheric pressure ionization (API) techniques of electrospray, pneumatically assisted electrospray and atmospheric pressure chemical ionization (APCI) and atmospheric pressure photo ionization (APPI) using single quadrupole, triple quadrupole, time-of-flight and ion trap mass analyzers.

Discussions of sample preparation and chromatography will target method development and optimization for the analysis of "real-world" samples by LC-MS/MS.

The course highlights the following topics with respect to optimization a method to achieve the best sensitivity, specificity and sample throughput:

1. Optimization ionization in API techniques,
2. Understanding and minimizing matrix suppression,
3. Relative merits of various LC column lengths, particle sizes and column diameters for LC-MS/MS analysis,
4. Introduction into the interpretation of MS/MS spectra,
5. Important issues in LC/MS/MS quantitation, and
6. Optimization of an quantitative analysis.

Applications of LC-MS/MS to analyze compounds of clinical interest in biological matrices will be discussed throughout the course to emphasize the topics covered.

Course material will be provided electronically.

John A. McLean is Stevenson Professor of Chemistry, Chair of the Department of Chemistry, Past Chair of the Faculty Senate, Director of the Center for Innovative Technologies, Deputy Director of the Institute for Integrative Biosystems Research and Education at Vanderbilt University. He received his Ph.D. from George Washington University, was a postdoctoral fellow at Forschungszentrum Jülich in Germany with Prof. Dr. Sabine Becker, and a postdoctoral at Texas A&M University with Prof. David H. Russell before joining the Vanderbilt Faculty as an assistant professor in 2006. McLean and colleagues focus on the conceptualization, design, and construction of structural mass spectrometers, specifically targeting complex samples in systems, synthetic, and chemical biology. His group applies these strategies to forefront translational research areas in drug discovery, precision medicine, and ‘human-on-chip’ synthetic biology platforms. He served on the board of directors for the American Society for Mass Spectrometry and serves in an editorial role on the boards of several leading scientific journals. He has been honored to work closely with the NAS and NSF in several roles, including recently co-authoring an NSF report on big data science in chemistry. He has received many professional and teaching awards including his laboratory being designated as a Waters Center of Innovation and an Agilent Thought Leader Laboratory for their work in ion mobility-mass spectrometry and translational biosciences. He has published over 150 manuscripts and 30 patents in the areas of innovative bioanalytical chemistry and quantitative sciences.

One of the predominant challenges in systems-wide analyses and molecular phenomics is the broad-scale characterization of the molecular inventory in cells, tissues, and biological fluids. Advances in computational systems biology rely heavily on the experimental capacity to make omics measurements, i.e. integrated metabolomics, proteomics, lipidomics, glycomics, etc., accompanied with fast minimal sample preparation, fast measurements, high concentration dynamic range, low limits of detection, and high selectivity. This confluence of figures-of-merit place demanding challenges on analytical platforms for such analyses. Ion mobility-mass spectrometry (IM-MS) provides rapid (ms) gas-phase electrophoretic separations on the basis of molecular structure and is well suited for integration with rapid (us) mass spectrometry detection techniques. This report will describe recent advances in IM-MS integrated omics measurement strategies in the analyses of complex biological samples of interest in systems, synthetic, and chemical biology in clinical chemistry applications. New advances in bioinformatics and biostatistics will also be described to approach biological queries from an unbiased and untargeted perspective and to quickly mine the massive datasets gathered to provide targeted and actionable information.

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.

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. At Prof. Cooks lab, she created 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 is also the project manager for a large effort (Purdue Make-It System) for high-throughput screening and analysis of chemical reactions using DESI-MS.

Michelle Reyzer received her BS in Chemistry from the College of William and Mary in Virginia in 1991, and after that worked at the NIH at the National Institute for Alcohol Abuse and Alcoholism (NIAAA) in the Laboratory of Membrane Biochemistry and Biophysics for 5 years. She then went to the University of Texas at Austin where she received a PhD in Analytical Chemistry in 2000 in the laboratory of Jennifer Brodbelt. The was followed by a post-doctoral fellowship at Vanderbilt in the laboratory of Richard Caprioli where she was introduced to MALDI Imaging Mass Spectrometry. She has been focused on the use of MALDI for imaging biological tissues for the past 14 years. Michelle is currently a Research Assistant Professor at Vanderbilt University Medical Center, and also serves as the Associate Director of the Tissue Imaging Core laboratory, where she routinely develops methods for the analysis of small molecules in tissue sections for investigators within Vanderbilt as well as external collaborators. In addition, Michelle oversees the collaboration and service projects for the National Research Resource for Imaging Mass Spectrometry.

This is a VIRTUAL 2-Day Course with 8 total contact hours. CE to be provided.

Overview: OVer the past two decades we have seen considerable scientific and technological advancements in imaging mass spectrometry (IMS), as these approaches continue to be implemented in research and industry. There has, however, been limited adoption of these techniques into the clinical arena, in part due to gaps between the mass spectrometrists developing these tools, and the clinical stakeholders, such as surgeons and pathologists, who may one day use them in their practices.

The goal of this course is to bridge these gaps by (1) providing an overview of the principles, strengths, limitations and applications of IMS techniques, such as MALDI-IMS and ambient mass spectrometry (AMS), and (2) offering insight into clinical workflows and potential opportunities for applications. The target audiences include both clinicians, surgeons, and pathologists interested in learning more about IMS applications as well as mass spectrometrists interested in clinical applications of IMS. The first day will focus on MALDI IMS, while the second day will cover ambient MS.

Prof. Hewison is currently Professor of Molecular Endocrinology within the Institute of Metabolism and Systems Research (IMSR) at the University of Birmingham, UK, having worked from 2005 – 2014 at the University of California Los Angeles. Prof. Hewison’s main research interest is vitamin D and its importance to human health. He has published over 230 research papers on classical (skeletal) and non-classical (extra-skeletal) actions of vitamin D. Prof. Hewison’s group is at the forefront of research linking vitamin D and the immune system, with implications for a wide range of clinical disorders including infectious, inflammatory and autoimmune disease. Current studies are focused on the analysis of vitamin D-insensitivity in T lymphocytes from the inflamed joints of patients with rheumatoid arthritis. This may provide an explanation for the limited success of vitamin D supplementation in some clinical trials. Other projects have explored the role of cell metabolism pathways in mediating the immunomodulatory effects of vitamin D, and the opportunities this may provide for improved therapeutic use of vitamin D. The Hewison group has also pioneered a range of studies to explore alternative markers of vitamin D ‘status’. This includes development of novel high throughput liquid chromatography-tandem mass spectrometry technology to measure multiple metabolites of vitamin D – the vitamin D metabolome – and analysis of the role of the serum vitamin D binding protein as a determinant of vitamin D bioavailability within the immune system. Prof. Hewison is a recipient of a Royal Society Wolfson Fellowship. His research is supported by grants from the Medical Research Council and Biotechnology and Biological Sciences Research Council (UK), and the National Institutes of Health (USA).

Prof. Hewison’s group is at the forefront of research linking vitamin D and the immune system, with implications for a wide range of clinical disorders including infectious, inflammatory and autoimmune disease. Current studies are focused on the analysis of vitamin D-insensitivity in T lymphocytes from the inflamed joints of patients with rheumatoid arthritis. This may provide an explanation for the limited success of vitamin D supplementation in some clinical trials. Other projects have explored the role of cell metabolism pathways in mediating the immunomodulatory effects of vitamin D, and the opportunities this may provide for improved therapeutic use of vitamin D. The Hewison group has also pioneered a range of studies to explore alternative markers of vitamin D ‘status’. This includes development of novel high throughput liquid chromatography-tandem mass spectrometry technology to measure multiple metabolites of vitamin D – the vitamin D metabolome – and analysis of the role of the serum vitamin D binding protein as a determinant of vitamin D bioavailability within the immune system.

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.

Ilaria is currently a postdoc scientist at Imperial College London. Her main research interest is the discovery and validation of volatile biomarkers in human breath using mass spectrometry, for the development of non-invasive diagnostic techniques for early cancer detection. She obtained her PhD in analytical chemistry, working between Italy and France as part of a European PhD program.

An overview of the fundamentals that are driving research and development in the field of Breath Analysis.
This is part of a series of Primers on topics relevant to Clinical Mass Spectrometry.

Learning objectives include:
1. Be able to define what Breath Analysis is, why it matters, and why you personally should care. What is the clinical relevance?
2. Understand what role mass spectrometry plays in this field. Where does mass spec fit in to the big picture of the field?
3. Define any terminology that is specific to this field.
4. Describe how it works, what are the methods and workflows used when studying this field and/or how is it implemented in clinical labs.
5. Identify any challenges to implementation/adoption, where do the opportunities lie?

Grace is an LC-MS/MS Applications Development Specialist at St Paul’s Hospital in Vancouver BC. She is passionate about developing the most user friendly and streamlined LC-MS/MS assays as possible for routine use in the Special Chemistry Mass Spec Lab. She loves troubleshooting, especially when the cause of problem has been discovered and the issue solved!

Deborah French Ph.D., DABCC (CC, TC) is currently Assistant Director of Chemistry and Director of Mass Spectrometry at the University of California San Francisco Clinical Laboratories. Her work currently focuses on the development and validation of LC-MS/MS assays for small molecules, specifically therapeutic drug monitoring, steroid hormones and toxicology. Deborah received her Ph.D. in biochemistry from the University of Strathclyde in Glasgow, Scotland and then completed a postdoctoral fellowship at St. Jude Children’s Research Hospital in Memphis, TN. She subsequently completed a ComACC Clinical Chemistry postdoctoral fellowship under the direction of Dr Alan Wu at the University of California San Francisco and is now board certified in Clinical Chemistry and Toxicological Chemistry by the American Board of Clinical Chemistry.

Lorin Bachmann joined the VCU Department of Pathology in 2007. She currently serves as Co-Director of Clinical Chemistry, Co-Director of Point-of-Care Testing, Director of the New Kent Emergency Department Laboratory, Technical Advisor for the Operating Room Laboratory, Pathology Outreach and Clinical Trials, and Laboratory Director for multiple VCUHS outreach laboratories. Dr. Bachmann received her PhD in Molecular Medicine from the University of Virginia, followed by a fellowship in clinical chemistry and proteomics research at the University of Virginia. Dr. Bachmann is certified by the American Board of Clinical Chemistry.

Dr. Bachmann is active within the American Association for Clinical Chemistry (AACC), where she serves on the Board of Directors. She also serves as the Chair of the Chemistry and Toxicology Expert Panel for the Clinical Laboratory and Standards Institute (CLSI).

Dr. Bachmann’s research interests include evaluation and validation of new clinical laboratory assays, clinical laboratory analyzer design, development of mass spectrometry-based assays for the clinical laboratory and standardization of laboratory testing. She serves as the Chair of the National Kidney Disease Education Program (NKDEP)/International Federation of Clinical Chemistry Laboratory (IFCC) Joint Lab Working Group, whose goal is to accomplish standardization of urine albumin methods to enable utility of clinical decision thresholds.

Dr. Bachmann has received numerous awards for her contributions to professional societies, education and research. She serves as principal investigator for multiple industry-sponsored studies.

This is a VIRTUAL 4-Day Course with 16 total contact hours. CE to be provided.

Online Format

This is a virtual version of the short course that has been presented at MSACL. This online course includes 4 hours of live lecture each day for four days. Using Zoom (live online lectures, breakout rooms for interactive sessions) and Google Classroom (forms and job aids for download, on demand short lecture videos) provides additional opportunities for interactive and self-paced learning, both during the four-day course and beyond.

The resources posted in Google Classroom will be available to registrants for at least 3 months. We can’t give you hands-on experience with cutting PEEK tubing or changing check valves in an online course. But the potential with a virtual platform for networking and updates with actionable information to help you with your daily LC-MS/MS clinical practice seems almost limitless.

Course Content Description

Is your laboratory under pressure to purchase an LC-tandem MS or is the ROI you wrote last year haunting you now? This short course is designed for attendees implementing quantitative LC-tandem MS for patient testing who have laboratory medicine experience but no mass spectrometry training - CLS bench analysts, supervisors, R&D scientists, and laboratory directors. Theoretical concepts necessary for a robust implementation of clinical mass spectrometry will be presented – but the emphasis is on practical recommendations for:

1. LC-MS/MS system purchasing
2. site preparation and installation
3. defining preliminary MSMS and LC parameters for your first method
4. selecting and optimizing sample preparation for your first method
5. choosing internal standards, solvents, and water, making reagents and calibrators
6. adjusting sample preparation, LC and MSMS parameters to achieve the desired assay performance
7. establishing data analysis & batch review criteria
8. pre-validation stress testing and method validation
9. preventative maintenance and troubleshooting
10. maintaining quality in production.

Our goal is to present just enough theory so you can report high quality results, while opening a window to the depth and complexity of clinical mass spectrometry such that your appetite is whetted to learn more. The IFCC Committee for Distance Learning published a curriculum guideline for post-graduate trainees in laboratory medicine in 2017. This course includes all of the IFCC mass spectrometry curriculum listed in the “Principles of Analysis X-MS” section, except that we focus only on triple quadrupole mass spectrometry; metabolomics, proteomics and inborn errors of metabolism are not discussed. See also this reference by one of the team of short course instructors “Liquid chromatography-mass spectrometry education for clinical laboratory scientists”.

Previous exposure to the principles of clinical method validation, either didactic or practical, is assumed. A post-course online exam will be available, with a certificate of completion for those who take and pass the exam within the examination window of two weeks after the four day short course.

Dr. Xin Yan received her Ph.D. in Chemistry from Purdue University in 2015 under the supervision of Professor R. Graham Cooks. After graduation, she did her postdoctoral research with Professor Richard N. Zare at Stanford University.
Dr. Xin Yan joined the chemistry department, Texas A&M University as an assistant professor in the summer of 2018. Her research centers around the development and application of droplet chemistry in lipid/metabolite analysis, reaction acceleration, and new synthetic methods.

Lipids play a vital role in maintaining cellular functions. Altered lipid metabolism is currently considered a hallmark of many diseases, which highlights the importance of the characterization of lipid composition in understanding, diagnosing, and treating pathologies. Discrimination of isomeric species is challenging in lipidomics. In this talk, I will introduce the microdroplet electrochemical methods capable of resolving different types of isomers commonly encountered in lipid samples using electrospray ionization mass spectrometry. The methods take advantage of the voltage-controlled and dramatically accelerated electrochemical derivatization of lipid isomers in microdroplets to achieve structural elucidation. Applications of the electrochemical mass spectrometry methods in real sample analysis will also be included.

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.

Nicolás is a third year PhD student under the supervision of Prof. Graham Cooks at Purdue University. He earned two bachelor’s degrees, one in Chemistry (cum laude, 2017) and one in Industrial Engineering (summa cum laude, 2018), from the Universidad de los Andes (Bogotá, Colombia). Since joining the Cooks’ group his research has focused on several applications of ambient ionization mass spectrometry for the rapid and simple analysis of complex mixtures, particularly oriented towards forensics and high throughput bioanalysis. Recently he was awarded the 2020-2021 Charles H. Viol Memorial fellowship for his work during his first years as doctoral student.

We describe an automated high throughput screening system which is used to acquire mass spectra at a rate of 6,000 samples/hour using desorption electrospray ionization (DESI). The system has been used to screen organic reactions and select optimum conditions for scaled-up drug synthesis, to analyze biological fluids without sample workup, to examine tissue library arrays and to perform label-free quantitative measurements of enzyme kinetics. Extensions of the instrumentation to collection of small amounts of synthesis products for in situ bioassays are also described.

Patrick Mathias, M.D., Ph.D., is a board-certified clinical pathologist and Associate Director of Informatics for UW Laboratory Medicine.

Lab medicine has large impact on the general practice of medicine. It is key to correctly diagnosing diseases and selecting the right treatments for patients. Dr. Mathias's goal is to combine technical and medical knowledge to fulfill the triple aim--reduce the per capita cost of health care, improve the health of populations and most importantly improve the patient experience of care.

Dr. Mathias earned his M.D. and Ph.D. from the University of Illinois. His clinical and research interests include clinical informatics, clinical chemistry and molecular diagnostics.

My lab performs research and clinical testing using mass spectrometry methods, develops new assays, and applies data analytics to enable improved quality and efficiency. My computational pathology efforts are aimed at building the capacity for advanced data analytics in the department through innovations in infrastructure, education, and research to facilitate data-informed decision making for clinical care, operations, and quality assurance.

This is a VIRTUAL 4-Day Course with 16 total contact hours. CE to be provided.


Overview:

Having completed your first steps into the wonderful world of data analysis with R, would you like to go further? You’ve learned the basics of R, so now it’s time to put that knowledge to work and tackle some interesting clinical applications. Along the way you will also be introduced to even more of capabilities of R and the tools developed by the amazing R community.

The 4-DAY ONLINE ONLY virtual (via Zoom) short course will be split between lecture sessions, individual problem solving, and a highly interactive group-level data mining of real data sets. Like the introductory course, this class will maintain the “no student left behind policy”. Students will be given time to solve problems taken from real-life laboratory work and to do some more advanced analysis on large scale data sets. All attendees will need access to a laptop with both R language and R Studio interface installed. Students may use Windows, Mac OSX or Linux environments. Both R and R studio are free and open-source.

Students should be prepared to continue to expand their skill in programming – which, as you learned in the introductory course (Data Science 101) can be a little frustrating, but not as frustrating as not being able to get the computer to do what you want at all!

Obtaining the Software

Instructions for installing the R language are here:
http://cran.r-project.org/

Instructions for installing R Studio are here:
http://www.rstudio.com/

Course Description

The course will cover:

1. Core concepts in reproducible research
2. Introduction to R-Markdown for report generation
3. Conceptual basis for keeping data “tidy”
4. Using the Import -> Tidy -> Transform -> Visualize -> Model -> Communicate pipeline
5. Data wrangling and manipulation operations such as filtering, grouping, summarizing
6. Data exploration and visualization with the ggplot2 library
7. Prediction with linear regression and classification with logistic regression
8. Database basics & connecting to databases
9. Putting it all together project: analysis of large mass spectrometry data set using exploratory data analysis

Course material will be provided electronically.