I have extensive (26 years) experience in advanced mass spectrometry and advanced biological/lipidomic/metabolomics/proteomic applications. As Director of the UF Mass Spectrometry Research and Education Center (MSREC), I administer the day-to-day activities, analyze more complex data sets, supervise the complex mass spectrometry experiments, generate proposals for additional new instruments and upgrades, and interact with faculty to ensure that analytical needs are met in the most efficient way possible. I have a very broad experience in mass spectrometry (Orbitrap, QTOFs, Ion Traps, Triple quadrupoles, GC-MS, FT-ICR, ESI, MALDI, and various bioinformatics platforms). I also have a very broad expertise in applications including biological, environmental, polymer, lipidomic, glycomic and proteomic applications with over 90 publications to date. I completed my graduate work at Louisiana State University under the direction of Dr. Patrick A. Limbach (currently at the University of Cincinnati). I served as The Ohio State University Mass Spectrometry and Proteomics Facility Director (OSU MS&P) for 15 years where I had considerable experience in identifying proteins and protein modifications, lipids, metabolites, and carbohydrates for quantitative analysis and identification of biomolecules. I have previously published under K.B. Green-Church and K.B. Green before transitioning to K.B.Basso.

I received my BS in Chemistry in 2013 working in gas phase kinetics with Dr. David Dolson at Wright State University in Dayton, Ohio. Working with Dr. Nicolas Polfer at the University of Florida in Gainesville, Florida, I earned my PhD in Analytical Chemistry in 2019. I was part of the team developing the first mass selective cryogenic linear ion trap for performing ion spectroscopy. Additionally, my dissertation research focused on characterizing phosphopeptides using several mass spectrometric methodologies, including low energy collisional activation and laser induced activation schemes as well as ion spectroscopy. Upon completion of my graduate studies, I working collaboratively with Dr. Guo and Dr. Basso in the Mass Spectrometry Research and Education Center as a post doctoral associate to develop their lipidomic analytical methods. I have developed and optimized LC-MS(MS) methodologies for untargeted lipidomic analysis, including developing a quantitative assay for improved unlabeled lipid quantitation and creating a methodology to characterize glycolipids using in vitro MSMS pattern matching. In 2021, I was hired as a Chemist to continue in the Mass Spectrometry Research and Education Center under the direction of Dr. Kari Basso to continue working on lipidomic systems and to manage the Polymer Chemical Characterization Laboratory in collaboration with Dr. Brent Sumerlin.

I earned my PhD in Chemistry in 2015 at University of Florida under Dr. Richard Yost and Dr. Kevin Wang. My research focused on identifying protein biomarkers for traumatic brain injury (TBI). While working on my research, I had a great opportunity to be a teaching assistant in MSREC lab. This gave me an exposure to work on different types of mass spectrometers. After my defense, I was hired as a post doc in this facility under Dr. Kari Basso. During this time, I have worked on number of projects that includes label free proteomics, LC-MS/MS method development, lipidomics, small molecules, etc. In 2018, I was offered a Chemist position in MSREC lab. I currently look over majority of the projects that includes proteomics, targeted analysis, metabolites, lipids, etc. Being in the service lab, I also assist in training clients in sample prep, data analysis and also on using the instruments. I am also responsible for maintenance and troubleshooting of all the mass spectrometers in the lab.

I am a fifth year PhD student at the Department of Chemistry, University of Florida. I have received my Master’s Degree in Pharmaceutical Chemistry from Birla Institute of Technology, India. My current research is focused on discovering novel natural products produced by roundworm Caenorhabditis elegans using mass spectrometry and comparative metabolomics techniques.

Lab Showcase meetings are opportunities for lab PIs and Directors to share their scientific goals and ambitions, and introduce the labs' current projects and scientists to our community. This provides opportunities for
(1) identifying potential points of collaboration, and
(2) engaging with early career and underrepresented scientists.

MSREC – Mass Spectrometry Research and Education Center is the Core Mass Spec lab at University of Florida. We have capabilities for proteomics, lipidomics, metabolomics, polymer analysis, accurate mass analysis, LC-MS etc. On top of being a traditional service facility, we integrate MS training to undergraduates, graduate students, and post-docs. Students have the opportunity to not just drop off their sample but learn how to do sample preparation, learn how to run samples on the mass specs and how to analyze data. Our talk will describe the diverse range of research projects currently conducted in MSREC.

Questions regarding the science will be prioritized during Q&A, however, we hope to cover a few of these as well:

(1) What is your lab's super power? What does it excel at? Why?
(2) If you think about your lab, the work you do, the people you impact, what would "taking it to the next level" look like, and what would you need to make that happen?
(3) Can you tell us about any persistent challenges or pain points that you manage in your role, or from a more positive viewpoint, what are the greatest opportunities that you have identified in your lab?
(4) Can you describe a time when you stopped and thought to yourself, "I am successful."? In other words, can you identify a point when you decided that all the education, the PhD, the effort that you have put into science, was all totally and absolutely worth it?
(5) If you were to be invited to sit on a discussion panel, what topic would you be most passionate about or most interested in contributing to?
(6) Are there any lessons that you have learned from a mentor, colleague, or perhaps your own experience that you make a particular effort to pass on to those who enter your lab?

Join us for our next Mass Spec Mixer - We will be hosting three Transition Talks from PhD students Kate Fell, Ksenia Kuznetsova, and Crystal Pace on June 17th at 11am EDT/4pm GMT. A lucky attendee will receive a free Simple Science Tees t-shirt! All are welcome, employers looking to hire postdocs and industry scientists are particularly encouraged to attend.

Paul J. Jannetto, Ph.D., DABCC, FAACC, M.T.(ASCP), is an Associate Professor in the Department of Laboratory Medicine and Pathology and a Consultant at the Mayo Clinic (Rochester, MN), where he serves as the Co-Director for the Clinical Mass Spectrometry Laboratory, Clinical and Forensic Toxicology Laboratory and the Metals Laboratory. Previously, he was an Associate Professor of Pathology at the Medical College of Wisconsin (Milwaukee, WI) where he functioned as the Director of Clinical Chemistry/Toxicology at Dynacare Laboratories (Milwaukee, WI). He earned his BS in Clinical Laboratory Science from the University of Wisconsin-Milwaukee and worked five years as a Medical Technologist for Medical Science Laboratories before entering graduate school. He then earned a Ph.D. in Pharmacology and Toxicology at the Medical College of Wisconsin. He is board-certified by the American Board of Clinical Chemistry and American Society for Clinical Pathology. His clinical and scientific interests are centered on Clinical & Forensic Toxicology, Therapeutic Drug Monitoring, and Elemental Analysis.

Dr. Jannetto has been actively involved in the American Association for Clinical Chemistry (AACC) where he has participated in the TDM/Toxicology, Mass Spectrometry and Separation Sciences, Molecular Pathology, Management Sciences and Patient Safety, Personalized Medicine, and Critical and POCT divisions. In the past, he has served on numerous positions at the local level in both the Chicago and Midwest sections (e.g. Chair of the Chicago Section, Secretary of the Chicago Section, and Treasurer of the Midwest Section of AACC), and at the national level as a member of the Governance Review Advisory Taskforce, NACB Board of Directors, AACC Board of Directors, and Chair of the House of Delegates. Dr. Jannetto is also a member of the American Academy of Pain Medicine, International Association of Therapeutic Drug Monitoring and Clinical Toxicology, and was the President of the Midwest Association for Toxicology and Therapeutic Drug Monitoring. He has over 50 peer-reviewed publications, 14 book chapters, and over 75 abstracts/presentations at various national meetings.

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

Learning objectives include:
1. Be able to define what Toxicology 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?

Anthony Newman, who is making the presentation today, is a Senior Publisher with Elsevier, and is based in Amsterdam. Currently responsible for sixteen laboratory medicine and biochemistry journals, he joined Elsevier over 30 years ago and has been Publisher for the last 20+ years. Before then he was the marketing communications manager for the biochemistry journals of Elsevier. By training he is a polymer chemist and was active in industry before leaving London and moving to Amsterdam in 1987 to join Elsevier.

Conducting the research is not enough – you must also publish it - or else, in effect, it never happened!
The art of writing scientific papers is not usually taught, and so has to be learned, without much readily available resources. This workshop remedies that. The various tips and tricks shared in the workshop will be helpful to novice post-doc authors, all the way up to experienced researchers.

Knowing the best way of structuring your paper when writing it and the most appropriate journal to send it to
really helps in getting your paper accepted. Apart from these areas, the workshop will also focus on method description to aid reproducibility, figure design, references, publication ethics, understanding the peer review process including appropriate response to referees comments, and concluding with a Q&A session with help from the JMSACL Editor-in-Chief Alan Rockwood.

Understanding how editors and publishers think and what they expect, and knowing how the peer review process works, is an invaluable insight into the publishing process. This should help you get your papers published more easily so that you are one of the 30% accepted authors, not one of the 70% rejected ones.

Craig E. Wheelock is an Associate Professor in the Department of Medical Biochemistry and Biophysics at the Karolinska Institute, Sweden, where he serves as director of the Integrative Molecular Phenotyping Laboratory (www.metabolomics.se). He is also a Distinguished Visiting Professor of Metabolomics at Gunma University, Japan. Following post-doctoral work on lipid mediators at the University of California Davis, he conducted additional post-doctoral studies at the KEGG laboratory in Kyoto University, Japan. In 2006, he was awarded a Marie Curie Fellowship to relocate to the Karolinska Institute. Research in his group focuses on molecular sub-phenotyping of respiratory disease, with a particular area of interest in investigating the role of eicosanoids and other lipid mediators. The overall aim is to develop personalized molecular profiles that can be associated with an individual’s lifestyle, environmental exposure and susceptibility to disease onset. He has been a founding Board Member of the Nordic Metabolomics Society since 2017, a Board Member of the International Metabolomics Society from 2016-2020, and serves on the European Respiratory Society (ERS) Advocacy Council as the Director of Scientific Relations with the EU. When not balancing his time between Sweden and Japan, he enjoys teaching his kids to kayak and play nicely with others.

"Mass Spectrometry has demonstrated to be a powerful analytical tool for the study of multiple diseases! This month, we will talk with Prof. Craig Wheelock about the application of MS-based approaches in the understanding of the pathophysiology of inflammatory respiratory diseases. His group is focused on the targeted analysis of lipid mediators (e.g., eicosanoids, sphingolipids) and investigating their role in the etiology of inflammatory disease.

Join our Career Fireside chat to learn from Prof. Craig Wheelock about his projects as well as his stories, lessons and advice on career paths in mass spectrometry. This is an interactive event and there will be an opportunity to chat and network with Craig and other attendees."

Mr. Huidong Gu is a Principal Scientist in the Clinical Biomarker Immunoassays and Mass Spec Department at Bristol-Myers Squibb Company. For the past 17 years, Huidong has been working in the area of LC-MS/MS bioanalysis of small molecules, biologics and biomarkers with over 30 peer-reviewed publications. Huidong developed a novel approach for calculating and mitigating isotopic interferences in LC-MS/MS quantitative analysis. This approach has a significant impact in the area of microdosing absolute bioavailability studies using LC-MS/MS analysis of both the oral dosed non-labeled drug and the IV microdosed stable labeled drug. His recent work of in-sample calibration curve (ISCC) with multiple isotopologue reaction monitoring (MIRM) technique allows the instant and accurate measurement of biomarkers, biotherapeutics and small-molecule drugs in biological samples without using external calibration curves. This methodology can bring unique values of eliminated external calibration curves, simplified the workflows and improved throughput in the areas where absolute quantitation and overall sample turnaround still remain great challenges.

External calibration curves are commonly used in LC-MS/MS quantitative bioanalysis. In this presentation, a novel methodology of In-Sample Calibration Curves (ISCC) using Multiple Isotopologue Reaction Monitoring (MIRM) of a SIL-analyte for instant LC-MS/MS bioanalysis will be discussed. The theoretical isotopic abundances of a SIL-analyte in its MIRM channels can be accurately calculated based on the isotopic distributions of its daughter ion and neutral loss. The isotopic abundances in these MIRM channels can also be accurately measured with a triple quadrupole mass spectrometer. By spiking a known amount of the SIL-analyte into each sample, an ISCC can be established based on the relationship between the calculated isotopic abundances and the measured LC-MS/MS peak areas in each sample for the quantitative bioanalysis. With this novel MIRM-ISCC-LC-MS/MS methodology, instant, accurate and reliable LC-MS/MS bioanalysis of biomarkers, biotherapeutics and small molecule drugs can be achieved without using external calibration curves. Moreover, this methodology can bring unique values of eliminated external calibration curves, simplified workflows and improved throughput in the areas where absolute quantitation and overall sample turnaround still remain great challenges. The potential applications in quantitative proteomics, clinical laboratories and other areas will also be discussed.

Isotope Abundance Calculator
https://www.sisweb.com/mstools/isotope.htm

Cam has recently discovered mass spectrometry imaging and found a home with data analysis. He hopes to continue MSI development and exploration through the completion of his undergraduate degree and pursue analytical chemistry in graduate school. Cam enjoys time in the outdoors when not camping out behind a computer screen.

Mass spectrometry imaging returns large dimensionally complex datasets. Traditional analysis in imaging utilizes a mindset focused on target molecule identification that parses data with a narrow view of molecular exploration. These data analysis methods are specifically focused on exploring differences between a traditional organic acid matrix when compared to using nanoparticles for MSI, which results in very different ionization of small molecules. Analysis methods have taken a shotgun approach using both supervised and unsupervised machine learning to reveal critical trends in MSI datasets. A workflow is being prepared which enables select regions of interest to be compared using powerful machine learning algorithms to offer a holistic approach to data analysis and class comparison.

Kate's primary job is as an educator at a Primarily Undergraduate Institution (PUI). In her spare time, she works with students on mass spectrometry imaging projects.

Mass spectrometry imaging (MSI) is a powerful analytical method for the simultaneous analysis of hundreds of compounds within a biological sample. Despite the broad applicability of this technique, there is a critical need for advancements in methods for small molecule detection. Some molecular classes of small molecules are more difficult than others to ionize, e.g., neurotransmitters (NTs). The chemical structure of NTs (i.e., primary, secondary, and tertiary amines) affects ionization and has been a noted difficulty in the literature. In order to achieve detection of NTs using MSI, strategies must focus on either changing the chemistry of target molecules to aid in detection or focus on new methods of ionization. This presentation will introduce a new method of ionization, using gold nanoparticles (AuNPs), and the bigger picture of NPs for MSI.

Dr. Benjamin Owusu is the Technical Director, Clinical Chemistry at Laboratory Corporation of America (Labcorp), Burlington, NC. He did his postdoctoral clinical fellowship at the University of Washington School of Medicine. Dr. Owusu earned his PhD degree in Biochemistry and Molecular Genetics at the University of Alabama at Birmingham (UAB). He obtained his Bachelor of Science degree in Biochemistry (first class honors) at the University of Ghana, where he also served as a Teaching Assistant. 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. Dr. Owusu is a recipient of multiple academic/research awards and honors. His research over the years span across cancer, cardiovascular, hematological, and endocrinological diseases. In addition to clinical service in diagnostics and research, Dr. Owusu is also passionate about teaching and mentoring, particularly in STEM education.

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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.

Shane Ellis completed his Undergraduate studies (B.Nanotechnology) and PhD in the field of ambient ionisation mass spectrometry and lipidomics the University of Wollongong, Australia. In 2012 he began a post-doctoral positional at the FOM-Institute AMOLF where he worked on the development of innovative active-pixel detectors for charged particle detection with applications in imaging mass spectrometry and ion mobility spectrometry. From 2014-2019 he was an Assistant Professor within the M4I Institute (Maastricht University, The Netherlands) where he led the Instrumentation and Application Development Group. His research develops and applies state-of-the-art mass spectrometry imaging methods to reveal localised biochemical processes within complex tissues and how they altered with disease. His group has developed a variety of innovative methods that significantly enhance the sensitivity and spatial resolution of MSI experiments and enabled precise and comprehensive structural identification of the many molecules detected by MSI. This research was supported by numerous Dutch and European grants. In 2020 he returned to Australia as an ARC Future Fellow and started a new mass spectrometry imaging group within the new Molecular Horizons Institute where he continues to further develop and apply mass spectrometry imaging technologies and apply them to challenging biological and chemical problems.

Dr Shane Ellis's group develops and applies mass spectrometry imaging (MSI) technologies to study the distributions of various molecular species throughout tissues and cells. His research covers both the development of new instrumentation to improve the performance of MSI (e.g., sensitivity, spatial resolution and molecular coverage) as well as the application of MSI to studying altered molecular processes occurring in diseased tissues and the spatially-resolved classification of such tissues. A particular focus is in the field of lipidomics, where he applies state-of-the-art MSI technologies to visualize and understand altered lipid biochemistry occurring in diseased tissues and cells.

Pieter Dorrestein uses mass spectrometry to eavesdrop on the molecular conversations between microbes and their world. To produce the image, researchers swabbed every surface in the room, including the people, several hundred times, then analysed the swabs with mass spectrometry to identify the chemicals present.

Kiana is currently a post-doctoral researcher in the Dorrestein Lab at UCSD. She is applying a reference data-driven approach to generate food readouts from metabolomics data acquired from clinical biospecimens. These readouts, proxies for diet consumption, are used to investigate interactions between diet, disease, and the gut microbiome. Her primary clinical focus is Inflammatory Bowel Disease (IBD), but she is also involved in other projects such as Alzheimer’s disease. Kiana received a PhD in Clinical Medicine Research from Imperial College London where she studied metabolomics and microbiomics. Her research at Imperial focused on uncovering metabolic/bacterial signatures associated with altered human development, such as adverse pregnancy outcomes and Autism Spectrum Disorder.

Untargeted metabolomics experiments suffer from large proportions of unannotated molecules. Using a reference data-driven approach, we increase the spectral annotation rate by assigning potential sources to molecular features. We have applied this approach using a food reference database to generate diet readouts from clinical samples. Surveying the food-associated compounds detected in clinical samples, we can differentiate patients with specific diet types, such as predominantly animal protein- versus plant-based diet. In addition, we can identify specific foods associated with clinical outcomes in disease cohorts. With its broad applications, we envision this approach becoming invaluable in nutrition research as well as many other fields once additional reference datasets become available.

A chemist by training, Renee is now the Chief Growth Officer for SciBase, which is the Yelp of scientific literature. She trained as a founder in programs such as YC Startup School and Founder Gym, completed a dual MBA program at Cornell University and Queen's University, and studied venture capitalism at The Wharton School. She has experience in industry as Senior Scientist and Senior Manager of Business Strategy and Operations at Janssen BioPharma.

Ken Hallenbeck earned a Ph.D. in pharmaceutical sciences from the University of California, San Francisco, and now is an early drug-discovery researcher. He loves to think and write about the future of scientific research. He serves on the board of directors of ReImagine Science, a nonprofit that empowers and connects scientist advocates, and is the life sciences lead at TerraPrime, a consulting firm that works with start-ups that aim to disrupt the scientific publication and education ecosystems.

It has happened to all of us: a paper comes out describing results related to your lab work. You scroll down to the methods to see what they did - a few days or weeks later, you try to replicate the result in your own lab. It doesn’t work.

What happens next? If you are a computational biologist, you might pop over to Stack Overflow or search the internet for common errors. But this is lab research, and there are a million things to test: Are the reagents old? What kind of instrument did the authors use and how does it compare? Were there nuances in the preparation steps that weren't recorded in the Methods?

Unfortunately, post-publication dialogue about lab research is difficult. Reports of irreproducible experiments can be taken as personal attacks on the author, or shots at the quality of the editors of the publishing journal. Most likely, the differences are perfectly logical details that were lost in translation from lab to manuscript and back to lab. How can the scientific community work together to translate those details more effectively? The internet has rewritten the rules of print publishing over the last 3 decades - why hasn’t it had the same impact on post-publication discussion?

There are four main challenges to post-publication peer review:

1. Incentives. Scientists want issues of reproducibility and post-publication dialogue to be addressed, but a lack of incentive inhibits many from engaging. They rightfully ask: "Will this help me get a postdoc position? How about a job? Will this increase my standing in the scientific community?" Any platform that seeks to be effective must align both self-interested and nobler motives.

2. Political realities. Science may position itself as an objective pursuit of truth, but research scientists know that's not always the way it works. How likely is a graduate student to publicly criticize her professor's work, even when her point is valid? A failure to recognize the prominent role that these dynamics play in human behavior will limit any solution’s effectiveness.

3. Balancing new & old. While the proliferation of open-access journals represent a tremendous step in the right direction, the vast majority of scientific knowledge still resides in traditional channels, or is left entirely unpublished. An ideal solution would allow the publishing of new work while building on the existing base of knowledge.

4. Critical mass. If you were the second person ever to visit Yelp and you saw one review of one restaurant on the other side of the country, how likely would you be to visit the site again (let alone contribute your own review)? Any new platform must reach a critical mass of users, readers, and content before it can achieve its goals.

There are several existing platforms for constructive post-publication conversations. Some succeed addressing a few of these challenges, but none have been widely adopted. If the research sciences want to truly address the reproducibility problem, we need to allow and incentivize post-publication review and dialogue. At the same time, discussion platforms need to protect users who may be opening themselves up to professional retaliation. Lastly, we believe any post-publication platform needs to be fast, easy to use, and accessible. While this might require an expansion of what is considered peer review, such an expansion is long overdue. Scientists have brief halfway conversations about their experiments daily - why couldn’t such conversations happen online, hosted somewhere that places these snippets of scientific discourse into a broader context?

At SciBase, we have built a platform to address all of these concerns directly. SciBase hosts crowdsourced reviews of chemistry and life sciences papers, letting the reviewer decide the level of detail they have the time, freedom, or desire to share. A categorized 5-star review system captures the basic message while allowing reviewers - if they so choose - to provide comprehensive justification for their scoring. Optional anonymity gives a microphone to voices that might otherwise be quashed, but moderators ensure that content is constructive and scientific, and data science approaches can be used to detect bad actors. Users can score each other’s reviews to help provide community moderation.

And what are the incentives? Foremost, the chance to promote your research and engage enthusiasts and critics in a structured fashion, all while directly addressing the reproducibility problem. SciBase has built a way for authors to provide additional insight into their own work. As authors, we know that the final version of a paper often excludes information we wish we could communicate to the broader field. Whether they are tips and tricks, or experiments we attempted that didn’t work, SciBase is a place to share those valuable details. SciBase also partners with companies looking for scientific talent to identify users that have written high-quality reviews. This recruitment strategy is orthogonal to the traditional use of publications as career currency. On SciBase, your review content is your CV. This levels the playing field and allows companies to identify candidates based on their engagement, rather than their success in the game of chance that traditional publishing can be.

SciBase is an experiment. The hypothesis? If we create a platform that facilitates and incentivizes scientific communication, we could succeed in creating a systemic change in the way science is conducted. As with any experiment, SciBase could fail. Post-publication review is a tricky problem that (we don't believe) anyone has gotten right yet, and - though we believe someone will get it right soon - it may not be SciBase. The only way to know is to try. Next time you publish or read a paper, considering looking it up on SciBase.co to begin the post-publication conversation. See you there!

Chad Borges is an associate professor at Arizona State University with appointments in the School of Molecular Sciences and The Biodesign Institute. He has a B.S. in chemistry and a Ph.D. in Analytical Toxicology. Though he has extensive experience in quantifying small molecules by mass spectrometry, his research interests currently reside in characterizing and quantifying protein post-translational modifications (PTMs) for biomedical purposes. This includes application of a new form of bottom-up glycomics known as glycan “node” analysis; developing molecular markers of biospecimen integrity; and quantification of PTMs as indicators of disease.

Exposure of blood plasma/serum (P/S) to thawed conditions (> -30 °C) can produce biomolecular changes that skew measurements of biomarkers within archived patient samples, potentially rendering them unfit for molecular analysis. Since freeze-thaw histories are often poorly documented, objective methods for assessing molecular fitness prior to analysis are needed. This presentation will described the concept, methodology, validation and performance characteristics of a 10-µL, dilute-and-shoot, intact-protein mass spectrometric assay of albumin proteoforms called “Delta-S-Cys-Albumin” that serves as an endogenous marker of P/S exposure to thawed conditions based on the inexorable ex vivo S-cysteinylation (oxidizability) of albumin. The multi-reaction chemical mechanism that drives changes in albumin S-cysteinylation is known and the rate law for it was established and accurately modeled in P/S—enabling back-calculation of the time at which unknown P/S specimens have been exposed to the equivalent of room temperature. Results from blind challenges and two unanticipated case studies that revealed unexpected integrity problems in sets of nominally pristine P/S samples will be presented.

Nevan Krogan, PhD, is a molecular biologist, UC San Francisco professor, and director of the intensely interdisciplinary Quantitative Biosciences Institute (QBI) under the UCSF School of Pharmacy. He is also a senior investigator at the Gladstone Institutes.

He led the work to create the SARS-CoV-2 interactome and assembled the QBI Coronavirus Research Group (QCRG), which includes hundreds of scientists from around the world. His research focuses on developing and using unbiased, quantitative systems approaches to study a wide variety of diseases with the ultimate goal of developing new therapeutics.

Nevan serves as Director of The HARC Center, an NIH-funded collaborative group that focuses on the structural characterization of HIV-human protein complexes. Dr. Krogan is also the co-Director of three Cell Mapping initiatives, the Cancer Cell Mapping Initiative (CCMI), the Host Pathogen Map Initiative (HPMI) and the Psychiatric Cell Map Initiative (PCMI). These initiatives map the gene and protein networks in healthy and diseased cells with these maps being used to better understand disease and provide novel therapies to fight them.

He has authored over 250 papers in the fields of genetics and molecular biology and has given over 350 lectures and seminars around the world. He is a Searle Scholar, a Keck Distinguished Scholar and was recently awarded the Roddenberry Prize for Biomedical Research.

Jacqueline Fabius obtained her undergraduate degree from Hamilton College in Comparative Literature and Spanish. She worked in media and management consulting for 11 years prior to joining the United Nations and later UCSF in the role of the Chief Operating Officer for the Quantitative Biosciences Institute, where she heads a number of initiatives including establishing relationships and collaborations as well as media and communication strategy for the institute. In alignment with QBI’s mission to bring young investigators and women scientists to the forefront at QBI, she started the Scholarship for Women from Developing Nations. Her focus is facilitating communication and networking across wide audiences ranging from scientists to lay audience.

The novel coronavirus SARS-CoV-2, the causative agent of COVID-19 respiratory disease is evolving during the current pandemic. New variants show enhanced replication and the potential to evade therapeutic antibodies. In the near future, variants may even evade first generation vaccines. The currently approved direct acting antiviral remdesivir targets the viral RNA-dependent RNA polymerase which is subject to rapid evolution as it is encoded by the viral RNA genome. In order to develop therapeutic approaches which act in a pan-coronavirus manner we and our colleagues at the QBI Coronavirus Research Group (QCRG) have mapped the human proteins (host factors) which multiple Coronaviruses rely on for replication. Through a rapid drug repurposing effort we have identified zotatifin, a clinical eIF4A inhibitor as a host factor targeted therapeutic. Zotatifin which is based on the natural product rocaglamide A works as a molecular glue to trap eIF4A on its target, the (+) RNA viral genome. Other examples of targeting essential host factors, including those for immune evasion will be discussed.

Liquid chromatography mass spectrometry-based proteomics has been widely used for protein biomarker discovery and validation. When transitioning from discovery proteomics to targeted protein biomarker quantification, the MRM-based LC/MS method plays an important role in clinical research. To ensure analytical reproducibility and robustness, implementing standard flow-based triple quadrupole LC/MS system has tremendous benefit when involving a large cohort. This webinar will discuss the analytical performance under standard-flow and low LC flow conditions using the Agilent 6495 triple quadrupole LC/MS system.

For Research Use Only. Not for use in diagnostic procedures.

Learning Objectives:

· Quantitative sensitivity, precision and accuracy of standard flow-based dynamic MRM method for targeted protein biomarker analysis using the Agilent 6495 LC/TQ

· Successful transfer of PromarkerD method for diabetic kidney disease research from nanoflow to standard flow

· When sample limited, a low flow LC system, Evosep One, coupled to Agilent 6495 LC/TQ could be used for high throughput studies

For Research Use Only. Not for use in diagnostic procedures.

Michelle Colgrave is a Professor of Food and Agricultural Proteomics in the School of Science at ECU, Australia. She is the Future Protein Lead in CSIRO Agriculture and Food, based at the Queensland Bioscience Precinct in Brisbane, Australia. Prof Michelle Colgrave is using mass spectrometry (MS) and proteomics to help identify key proteins that will benefit Australia's livestock and plant industries and improve human health. Prof Colgrave is working to identify novel proteins and characterise their function and post-translational modifications. Prof Colgrave is a Chief Investigator on the ARC Centre of Excellence for Innovations in Peptide and Protein Science.

Richard Lipscombe is the Founding and Managing Director of Proteomics International. Richard is a protein chemist by training having completed his chemistry degree at Oxford University and a Doctorate in Immunology at London University. Richard moved to Perth in 1995 and managed the Protein Analysis Facility at the University of Western Australia, before stepping out of academia to co-found Proteomics International in 2001.
Richard's career has focused on industry based research and the translation of innovative technology into commercial products and services. He holds several patents and, almost uniquely, has taken a protein biomarker from concept to commercial diagnostic test, with the company's pioneering prognostic test for diabetic kidney disease, PromarkerD, now in the clinic.

From down under, this time we bring you two successful scientists bridging academia and industry: Prof. Michelle Colgrave and Dr. Richard Lipscombe. Prof Colgrave of Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australia focuses on applications of mass spectrometry based proteomics in food and agriculture, while Dr. Lipscombe heads Proteomics International Laboratories Ltd (PILL), an Australian company in the field of clinical mass spectrometry and diagnostics. Come and e-meet these two grand individuals in the Australian mass spectrometry field!

Note the date and time:
Sydney - 2PM Thursday March 26
Auckland - 4PM Thursday March 26

Renee Ruhaak holds a PhD from the Leiden University Medical Center (LUMC, supervisor Prof. M. Wuhrer) and did a post-doc at UC Davis in the lab of Prof. C.B. Lebrilla prior to joining the department of Clinical Chemistry and Laboratory Medicine at the LUMC. She is currently an assistant professor with a research focus on the application of mass spectrometry within the clinical setting. This entails both development and implementation of quantitative protein mass spectrometry, as well as the role of mass spectrometry in metrology and test standardization.

Quantitative protein mass spectrometry is a promising, yet complex technology that enables precision diagnostics. It allows for the multiplexed and direct quantitation of analytes at the molecular level, potentially including identification of proteoforms. Therefore, MS based tests are now proposed more and more often. Yet, quantitative protein mass spectrometry is a complex technique, which has hampered its applications. To ensure efficient test development, novel tests should target clinical gaps in the contemporary clinical pathways, and each of five key elements of test evaluation, as identified by the European Federation for Clinical Chemistry and Laboratory Medicine should be considered. Here we present our experience in the development and application of quantitative protein mass spectrometry, and aim to take away the concerns that have kept laboratory medicine from implementing this promising technology.

Reelvant Publication

Checklist for Identifying Unmet Clinical Needs

Joshua is currently the Chief of Chemistry at NortonHealthcare. He earned his PhD in chemistry from Carnegie Mellon University. He conducted postdoctoral research at Massachusetts Institute of Technology before completing a two-year clinical chemistry fellowship at University of Washington and 4 years as Assistant Professor at Weill Medical College. Joshua has special expertise developing and overseeing mass spectrometry assays in the clinical laboratory.

In the thrilling conclusion of this four part series, Josh encounters issues with his vacuum manifold, decides to forgo sample preparation, and attempts to validate a dilute-and-shoot mass spectrometry method. Problems are encountered. This session will outline the studies conducted and planned in order to complete validation of a mass spectrometry method in a CAP-accredited, clinical laboratory. While accuracy and precision and reportable range will be addressed, particular attention will be paid to the additional validation studies that should be conducted (matrix effect, injector stability, interferences, etc).

At the conclusion of this talk, participants should be able to…
1. List some of the studies that are essential when validating a mass spectrometry assay
2. Define acceptance criteria for mass spectrometry validation studies
3. Recognize some of the challenges that can be encountered with dilute-and-shoot assays

We are looking forward to our next FeMS Mass Spec Mixer coming up in March! Please join us on March 4th at 4pm PDT | 7pm EST | March 5th 11am AEST to hear from 3 more awesome transition-ers: Cameron Naylor, Saanghamitra Majumdar and Wout Bittremieux!

All are welcome, employers are encouraged!

Alicia Williams (PhD, Rutgers University) is a teaching instructor in the Graduate Writing Program at Rutgers University, where she works with graduate students from all disciplines on articles, grant proposals, and dissertations. While her degree is in English literature, she has a background in writing mentorship and editing in Chemistry. With colleagues at Rutgers she is working on a book called Spatialization: A Graduate Writing Pedagogy.

This workshop will talk about manuscript writing, its organization, and concept communication. We will internalize several accessible guiding principles of good science writing by revising various breeds of bad examples (focusing on manuscripts in mass spectrometry).
This workshop is appropriate for anyone in the scientific community who has an interest in writing effectively. Both native English speakers and non-native English speakers are more than welcome.

Slide Deck (PDF)

List of Connectors (PDF)

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.

Manfred Wuhrer is Professor of Proteomics and Glycomics and head of the Center for Proteomics and Metabolomics at the Leiden University Medical Center, The Netherlands. With his research he focuses on the development of mass spectrometric methods for glycomics and glycoproteomics, and their application in clinical research and biotechnology. Clinical applications cover the fields of rheumatoid arthritis, inflammatory bowel disease, autoimmune hepatitis, diabetes, colorectal and pancreatic cancer, longevity, as well as various infectious diseases.

Mikhail Savitski studied mathematics and physics at Uppsala University, where he also did his PhD in ion physics/mass spectrometry. After his PhD he worked at Cellzome as Group Leader in the Analytical Sciences department. Since 2016 he works at EMBL heading a research group as well as the proteomics core facility. He develops novel proteomics technologies and uses them to study post-translational regulation. He is an author of 87 peer reviewed publications including corresponding author papers in Nature, Cell, Science.

Mass spectrometry has demonstrated to be a powerful analytical tool for the study of SARS-CoV-2, contributing to our ability to understand and tackle the impact of COVID-19. During January and February, we will be interviewing scientists working in COVID-19 research using mass spectrometry, to learn about their projects and scientific career. Join our next COVID-19 Career Fireside chat to learn from Prof. Manfred Wuhrer and Dr. Mikhail Savitski about their COVID-19 projects, as well as their stories, lessons and advice on career paths in mass spectrometry.

Joshua is currently the Chief of Chemistry at NortonHealthcare. He earned his PhD in chemistry from Carnegie Mellon University. He conducted postdoctoral research at Massachusetts Institute of Technology before completing a two-year clinical chemistry fellowship at University of Washington and 4 years as Assistant Professor at Weill Medical College. Joshua has special expertise developing and overseeing mass spectrometry assays in the clinical laboratory.

Dr. Min Yu is the assistant professor, associate director of clinical chemistry and the director of clinical toxicology laboratory of the Department of Pathology and Laboratory medicine at the University of Kentucky. Dr. Yu earned her medical degree at the Nanjing Medical University in Nanjing, China, where she also completed her graduate education in pharmacology (MS). Dr. Yu received her PhD degree in Molecular and Environmental Toxicology from University of Wisconsin-Madison. She completed her clinical chemistry fellowship training at the University of Virginia and then became a Diplomate of the American Board of Clinical Chemistry. Her professional area of interests includes laboratory tests harmonization and utilization, drug of abuse testing and clinical toxicology. In addition, she is actively involved in conducting clinical and translational research on evaluation of biomarkers for diagnosis and prognosis of diseases. Uniquely, she is taking advantage of the open-source computational tools (machine learning, for example) to gain new insights from the laboratory data. Her work has been published in peer- reviewed journals and has been presented to the national and international meetings.

Continuing on with mass spectrometry misadventures, this session will discuss our efforts to begin analyzing and evaluating mass spectrometry data. Unlike conventional immunoassays which provide simple (and often incorrect!) results, mass spectrometers provide a plethora of data for every peak- qualifier ions, internal standard areas, retention times, peak shapes, etc. This data, often termed metadata, can help clinical laboratories evaluate their peaks to ensure that they are reporting accurate results. Unfortunately, the process of evaluating this metadata can be a doubting challenge. This session will discover our efforts to move ahead with implementing manageable processes for evaluating the metadata necessary to ensure accurate results.

At the conclusion of this talk, participants should be able to…

1. Ask questions related to their own efforts to implement monitoring/assessing metadata
2. List the metadata that must be evaluated to ensure accurate results
3. Prepare quality assurance metrics for their laboratories utilizing metadata

At the conclusion of this talk, participants should be able to…

1. Ask questions related to their own efforts to implement monitoring/assessing metadata

2. List the metadata that must be evaluated to ensure accurate results

3. Prepare quality assurance metrics for their laboratories utilizing metadata

Our research integrates the role of new technologies, workflow and software for the analysis of molecules of biological interest. The overall goal is to develop innovative analytical tools and solutions that will benefit the detection and understanding of disease, and the discovery and development of appropriate therapeutics. All aspects of analytical sciences from sample collection to assay validation are considered in our research where mass spectrometric detection plays a central role. In addition to the application of separation sciences (GC, LC, SFC) combined to mass spectrometry, disruptive approaches based on MALDI or ion mobility for high throughput, multiplexed and low cost analyses of biomarkers and pharmaceuticals are investigated.

Our scientific interests include: separation sciences, sample preparation, automation, bioanalysis, metabolism, metabolomics, analytical proteomics, toxicology, high resolution mass spectrometry, ion mobility mass spectrometry, data independent acquisition techniques (SWATH), MS/MS spectra interpretation, ionization, data analysis and mass spectrometry imaging.

The general topic of interest in our research group is the study of the mechanisms involved in photooxidative damage to biological systems, particularly in the human eye. Photooxidative damage is implicated in a number of ocular disorders such as age‐related cataract formation and age‐related macular degeneration (AMD; the leading cause of blindness in older adults). Light damage to biological systems may not manifest itself on a macroscopic level for decades, but the damage is initiated by short‐lived, electronically excited species that participate in Type I or Type II oxidative chemistry. We use a wide variety of experimental methods to study these systems, including laser‐based time‐resolved spectroscopy. By determining the sequence of events that leads to tissue injury and identifying the reactive species along the reaction pathway, we may be able to develop methods to slow down or stop these processes.

In collaboration with Prajkta Chivte and Zane LaCasse

Currently, the “gold standard” for Covid-19 diagnostic testing utilizes RT-PCR to detect the viral nucleic acid. This method is highly specific for selected viral genes and, with recent advances in methodology, saliva testing instead of nasopharyngeal swab sample collection is becoming more widely available. However, due to the global use of PCR testing, there are intermittent shortages of the necessary reagents and the average turnaround times for results are approximately two days. In collaboration with MAP sciences and ChemQuant Analytical Solutions, we are developing a new Covid-19 diagnostic test that utilizes MALDI ToF mass spectrometry to analyze protein profiles from human water gargle samples. Because the method detects all proteins in a sample, signatures from the viral proteins as well as the human immune response can be observed in a single measurement. In August 2020, we collected and analyzed ca. 550 samples from NIU’s student-athlete gateway testing program. This allowed us to develop the sample preparation method, data analysis and to compare the MALDI ToF results with PCR test results (Abbott RealTime). This population had a 14% positivity rate and 89% of the positive individuals were asymptomatic. At the end of Nov. 2020, we collected samples at a drive-thru testing program administered by the Illinois Department of Public Health. This population sampled a much wider range of ages and disease status and has allowed us to greatly refine the data analysis.

The new test is rapid and low cost and has a limit of detection comparable to the most widely available PCR tests. We have also recently established that the test has excellent specificity in that we are able to clearly distinguish SARS-2 from other viruses including four other coronaviruses (MERS, 229E, OC43 and NL63).

Dr. Kara Lynch is an Associate Professor of Laboratory Medicine at the University of California San Francisco, Co-Director of the Core Laboratory at Zuckerberg San Francisco General Hospital and Chemistry Director at UCSF Benioff Children’s Hospital Oakland. She is the co-director of the COMACC-accredited Clinical Chemistry Fellowship Program at UCSF. Her laboratory conducts studies aimed at identifying and quantifying endogenous and exogenous small molecules in biological specimens using novel diagnostic technologies, such as high resolution mass spectrometry, ion mobility mass spectrometry, ambient ionization mass spectrometry and thin-film interferometry. Her lab is involved in translational research studies evaluating the clinical utility of novel biomarkers or biomarker panels to diagnosis, treat and monitor disease. The methods developed in her laboratory are used to investigate perturbations in metabolic pathways caused by disease and drug use and translate the results into information that can be used in clinical practice.

Immunoassay urine drug screening has been the mainstay for the detection of drug exposure in patients for decades despite many limitations this approach presents. Positive samples are batched for confirmatory testing by LC-MS/MS targeted methods. Testing is limited to one matrix, a limited list of drugs/metabolites, and manual batch testing restricting interpretation, window of detection and timeliness of results to impact patient care. Utilization of alternative matrices, such as breath and oral fluid, is emerging for specific toxicological questions. Alternative analytical approaches, such as broad-spectrum drug testing with high resolution mass spectrometry, direct-to-mass spec testing with ambient ionization, and ion mobility mass spectrometry have the potential to change the landscape of drug testing in clinical laboratories. This talk will discuss alternative matrices and novel mass spectrometry-based approaches for drug detection.

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?

I currently hold an appointment at Queen’s University Belfast as a Vice-Chancellor’s Fellow (lecturer-equivalent position) where my group applies mass spectrometry and microbiology techniques to the direct-from-specimen diagnosis of pathogens and in the analysis of host-microbiome and early-life nutrition-microbiome interactions. I received my BSc (2011) and PhD (2015) from Aberystwyth University, Wales, UK in the area of molecular microbiology and metabolomics. I previously coordinated the work of the MicrobeID team within Professor Zoltan Takats’s research group at Imperial College London, which developed rapid evaporative ionisation mass spectrometry (REIMS) as a high-throughput platform to assign taxonomic and functional classifications to microbial isolates and to the direct-from-sample profiling of mixed microbial communities.

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

Learning objectives include:
1. Be able to define what Microbiology 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?

Dr Gus Grey is a senior research fellow in the Department of Physiology, University of Auckland, academic director of the Biomedical Imaging Research Unit and principal coordinator of the University’s Mass Spectrometry Hub. He completed his PhD in Auckland before pursuing post-doctoral research in the United States. While in the US he learnt MALDI imaging mass spectrometry at MUSC and Vanderbilt University. He returned to New Zealand at the end of 2009 and acquired MALDI imaging equipment which he now utilises in his own research. His lab aims to use this spatially-resolved technique to understand the basis of ocular lens tissue transparency, the biomolecular changes that take place in cataract formation, and use this knowledge to develop novel therapies to delay or prevent the onset of lens cataract. He also collaborates locally with other researchers to apply MALDI imaging to further understand the pathological processes involved in neurodegeneration, cancer, and even fruit development.

Mark De Hora graduated from the National University of Ireland, Galway with a degree in Science in 1987. He began his career as a Biomedical Scientist in London in 1988 and worked in 4 different London Hospitals. He completed his MSc in Clinical Biochemistry in 1997 when he had his first exposure to GCMS. He began working in the West of England Newborn Screening and Biochemical Genetics laboratory in 2003 specialising in GCMS and LCMSMS investigations for inherited metabolic diseases. He moved to Auckland in 2011 with his family and works for the National Newborn Screening and Biochemical Genetics laboratory at the Starship Hospital in Auckland. Mark has completed the Fellowship of the Royal College of Pathologists Faculty of Science in 2016 and is currently enrolled for PhD programme looking at expanded steroid profiling in bloodspots using high resolution mass spectrometry.

Learn about biomedical imaging Mass spectrometry going on in academia from Dr. Gus Grey and dive deeper into clinical applications of MS with Mr. Mark De Hora in Auckland, New Zealand.

Note this session Date and Time:
Auckland - Jan 26, 4:00pm
Melbourne - Jan 26, 2:00pm
Beijing - Jan 26, 11:00am
Mumbai - Jan 26, 8:30am

Professor Jack Henion is Emeritus Professor of Toxicology at Cornell University where he was a member of the College of Veterinary Medicine commencing in 1976. Dr. Henion was co-founder of Advion BioSciences in 1993 where he served as President and CEO until 2006 when be became CSO of Advion, Inc. Dr. Henion carried out a wide range of research in many application areas involving GC/MS and LC/MS/MS techniques. Professor Henion has received three Doctor Honoris Causa (Honorary Doctorate) degrees in recognition of his international reputation in modern analytical techniques. These were awarded from each of the University of Ghent, Uppsala University and Albany University. During his tenure at Cornell Professor Henion conducted research and explored applications in many areas of liquid chromatography/mass spectrometry (LC/MS) employing atmospheric pressure ionization (API) sources. Professor Henion has published over 235 peer reviewed papers in the scientific literature, trained nearly 100 students, post-doctoral scientists, and trainees while receiving 12 patents for inventions developed from his work. He has also received a number of awards which recognize his contributions to analytical chemistry and entrepreneurship. More recently in April 2017 Dr. Henion received the Outstanding Contribution to Anti-Doping Science Award from the Partnership for Clean Competition (PCC) for his development of a novel Book-Type Dried Plasma Spot Card and in the Fall of 2017 Dr. Henion was the winner of the 2018 Bioanalysis Outstanding Contribution Award (BOSCA). In December 2019 Dr. Henion retired from Advion, Inc. and is now a consultant for Henion Enterprises.

The use of cannabis and cannabis-derived products by both young and older patients continues to increase. The COVID pandemic has forced people to remain home and be socially distance such that loneliness has increased both the use of alcohol as well as cannabis. A recent news report indicated cannabis sales has increased nearly 25% because of COVID-induced stress and social loneliness. The recent election added four additional states to those allowing legal use of recreational cannabis. There are also many anecdotal reports on the effectiveness of CBD and associated cannabis-derived products which has attracted a passionate following of those who believe using these products helps their ailments.

With these trends it should not be surprising that an increasing number of patients have cannabis-derived chemicals in their body fluids. Although patient ailments may or may not be attributed to cannabis compounds and their metabolites, the ‘wild, wild west’ nature of the current unregulated cannabis industry means there are often toxic substances in cannabis products that may be causing some of the patient symptoms. These include many pesticide residues that are derived from current grower practices, molds and the associated very toxic mycotoxins resulting from the warm, moist growing conditions within greenhouses, and a variety of heavy metals which bioaccumulate in the cannabis plant. A recent report indicated that 93% of the cannabis products tested by an iso 17025-certified laboratory had levels of pesticide contamination.

From the physician’s viewpoint many of the clinical signs of pesticide toxicity are common to other ailments. The purpose of this webinar is to highlight these issues and to suggest that physicians and clinical laboratorians be aware of the increasing number of patients whose ailments may be attributed to these cannabis-derived toxins and to have methods in place to test for these substances in the body fluids of patients.

Prof. Andrea Sinz is a member of the COVID-19 Mass Spectrometry coalition and she has been working on mass spectrometric Identification of SARS-CoV-2 Proteins from gargle solution samples of COVID-19 patients (Ihling C, Tänzler D, Hagemann S, Kehlen A, Hüttelmaier S, Arlt C, Sinz A. J Proteome Res. 2020; 19:4389-93). She is a full Professor of Pharmaceutical Chemistry at the Martin-Luther-University Halle-Wittenberg in Germany. The focus of her laboratory is the development of novel tools and workflows to promote the crosslinking/mass spectrometry (XL-MS) approach. She obtained her PhD in Pharmaceutical Chemistry from the University of Marburg, Germany. She received a degree in Pharmacy from the University of Tübingen, Germany. She was a post-doctoral fellow at the National Institutes of Health in Bethesda, MD, USA, where she became introduced into chemical cross-linking techniques and protein mass spectrometry. From 2017 to 2020, she was the president of the German Society for Mass Spectrometry and in 2016 she was recognised as one of the top 50 most influential women in Analytical Science.

Mass spectrometry has demonstrated to be a powerful analytical tool for the study of SARS-CoV-2, contributing to our ability to understand and tackle the impact of COVID-19. During January and February, we will be interviewing scientists working in COVID-19 research using mass spectrometry, to learn about their projects and scientific career. Join our first COVID-19 Career Fireside chat to learn from Prof. Andrea Sinz about her COVID-19 project, the COVID-19 MS coalition, as well as her stories, lessons and advice on career paths in clinical mass spectrometry.

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.

As a field, we have made great strides in quantifying proteins with LC-MS/MS. There has always been great hope that these advances will lead to the improved care of patients and there are now tangible examples. Our laboratory has had the honor of collaborating with laboratories around the world with the aim of getting it right. This presentation will highlight a few of those collaborations, touch on related efforts from other groups, and outline where we are headed next.

Kevin A. Schug is Professor and the Shimadzu Distinguished Professor of Analytical Chemistry in the Department of Chemistry and Biochemistry at The University of Texas at Arlington (UTA). He is also Director of the Collaborative Laboratories for Environmental Analysis and Remediation (CLEAR) at UTA. He received his B.S. degree in Chemistry in 1998 from the College of William and Mary, and his Ph.D. degree in Chemistry from Virginia Tech in 2002 under the direction of Prof. Harold M. McNair. From 2003-2005, he performed post-doctoral research at the University of Vienna in Austria with Prof. Dr. Wolfgang Lindner. Since joining UTA in 2005, his research has been focused on the theory and application of separation science and mass spectrometry for solving a variety of analytical and physical chemistry problems, in the fields of environmental, pharmaceutical, biological, and energy research. He has over 180 peer-reviewed publications and over 400 presentations, posters, and invited talks to his group’s credit. He has been the primary mentor and research advisor to more than 30 graduate and 60 undergraduate students. Dr. Schug has received several research awards, including the 2009 Emerging Leader Award in Chromatography by LCGC Magazine and the 2013 American Chemical Society Division of Analytical Chemistry Young Investigator in Separation Science Award. Recently, he was named to 2019 The Analytical Scientist’s Top 100 Power List of the best analytical chemists in the world. For his teaching, he received the 2014 University of Texas System Regents’ Outstanding Teaching Award and in 2017, was awarded the J. Calvin Giddings Award for Excellence in Analytical Chemistry Education by the American Chemical Society. He is a Fellow of both the University Of Texas System’s and U.T. Arlington’s Academy Of Distinguished Teachers.

A wide array of analytical instrumentation exist to perform quantitative and qualitative analysis on complex mixtures. The choice of chemical analysis tool, in conjunction with appropriate sample preparation, allows the lens to be focused on a particular sample dimension. Loosely, different sample dimensions can be equated to different classes of analytes contained in a sample. While, we ultimately will likely use very different strategies to characterize e.g. fatty acids vs. proteins in a biological sample, there is potentially value in monitoring each of these analyte classes for correlations with physiological changes that may results as part of a disease or some other abnormality. In fact, if one were trying to classify samples that were normal vs. abnormal, it could be argued that, while the monitoring of one sample dimension might be more diagnostic than another, monitoring and combining data from multiple sample dimensions would like provide additional information to aid the classification. This concept of chemical multi-fingerprinting (CMF) could ultimately help draw lines between different sample classifications, where they were previously difficult to discern. We are currently working to define useful strategies for the combination of multiple analytical techniques for CMF of various sample types. This includes the development of highly featured targeted and non-targeted methods using:
Headspace – solid phase microextraction (Arrow) – gas chromatography with parallel vacuum ultraviolet spectroscopy and tandem mass spectrometry detection (HS-SPME-GC-VUV/MS); and liquid chromatography – triple quadrupole and quadrupole – time-of-flight – mass spectrometry (LC-QQQ-MS and LC-QTOF-MS). Efforts are moving towards the incorporation of advanced machine learning techniques, such as capabilities for handling data sets with limited sample numbers. While a full workflow is still being delineated, data exhibiting the potential power of a CMF strategy has been collected for some complex systems, such as for differentiating craft beers and for classifying pathogenic bacteria exposed to different stressors.

Joshua is currently the Chief of Chemistry at NortonHealthcare. He earned his PhD in chemistry from Carnegie Mellon University. He conducted postdoctoral research at Massachusetts Institute of Technology before completing a two-year clinical chemistry fellowship at University of Washington and 4 years as Assistant Professor at Weill Medical College. Joshua has special expertise developing and overseeing mass spectrometry assays in the clinical laboratory.

Susan Abbatiello earned a B.A. in Chemistry at The College of the Holy Cross. She worked for 5 years at Genetics Institute (Andover, MA) in the Biopharmaceutical Characterization and Analysis group before returning to graduate school. Susan earned her Ph.D. in Analytical Chemistry at the University of Florida, working under advisement of Drs. John Eyler and Nigel G. J. Richards, focusing on the quantitation of a protein suspected to play a role in drug-resistant acute lymphoblastic leukemia. Susan worked as a post-doc in the Clinical Proteomics facility at the University of Pittsburgh for Dr. Thomas P. Conrads, where she continued efforts in targeted proteomics research with a focus on cancer. In 2008, Susan moved to the role of Scientist in the Proteomics Platform at the Broad Institute (Dr. Steven Carr), where she served as co-chair of the NCI CPTAC (National Cancer Institute Clinical Proteomics Technology Assessment for Cancer) working group to evaluate stable isotope dilution selected reaction monitoring for the quantitation of plasma proteins related to cancer. In 2014, Susan transitioned to the role of Triple Quadrupole Product Specialist at Thermo Fisher Scientific and took on the responsibilities of FAIMS Product Manager in 2015. In 2018, Susan transitioned to the role of Executive Director of the Barnett Institute for Chemical and Biological Analysis, overseeing the Mass Spectrometry Core Lab. In 2020, she accepted the position of Interim Director of the Barnett Institute, while continuing the MS Core Lab responsibilities.

Susan’s research interests include evaluation and making improvements in technologies for the targeted analysis and detection of biomarker candidates in blood, tissue, and cell samples. Her efforts have focused on improving accessibility and performance of mass spectrometric technologies and software, to help broaden its impact in basic, biomedical, and analytical research. Her work has resulted in over one dozen peer-reviewed publications as well as invited presentations at national conferences.

Susan has been a member of ASMS since 2002. She has participated in poster abstract evaluation and has organized and chaired oral sessions and served on the program committee for ASMS Conferences. Susan has been a short-course instructor for the ASMS short course “Practical LC-MS Troubleshooting and Maintenance” since 2013. She served as the Vice President of Arrangements for ASMS from 2017-2019. Susan is also a member of ACS, is a reviewer for Analytical Chemistry, Journal of Proteome Research, Nature, and is currently on the Editorial Board of Molecular & Cellular Proteomics.

On a personal note, Susan has been married to Russell Abbatiello for 23 years and they have a 10 year old daughter, Madeline, and a 7 year old son, James. They enjoy dressing up for Halloween as a family affair, and have attempted to replicate characters from Frozen, The Incredibles, Toy Story 4, and Despicable Me.

What do we want? Good chromatography! How do we get it? We don’t know! Columns, maybe?

Good chromatography is essential to any LC-MS/MS method. Setting it up is often one of the earlier steps in developing a new method. While it can be an iterative process, setting up good chromatographic conditions at the start can set you up for success later on. This webinar will discuss our laboratories efforts to setup chromatographic conditions for the analysis of ethyl-glucuronide and buprenorphine (plus metabolites). We will present what we tried, why it seemed like it a good/bad idea, and along the way talk through some basic chromatography concepts. The goal is for attendees to be more informed when they approach setting up their own chromatographic methods.

This session is the second in a 4 part series in which Dr. Hayden will invite attendees to witness in real time his journey bringing mass spec testing to a clinical lab. During these interactive sessions, attendees will be encouraged to help troubleshoot, and offer advice as desired.

You can watch the recording of the first session: "Getting going with mass spectrometry: Josh installs a mass spectrometer".

Subsequent sessions anticipated include:
Part 3. Getting going with mass spectrometry: Josh tries to do sample preparation
Part 4. Getting going with mass spectrometry: Josh analyzes peaks

Learning Objectives:

1. Define what good chromatography means for an LC-MS/MS method

2. State the situations where reverse phase or HILIC columns might be most appropriate

3. Explain the significance of various column factors (chemistry, length, particle size, etc)

4. Explain the value of mobile phase additives (formic acid, ammonium formate, etc)

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!

Mari L. DeMarco's (Clinical Associate Professor, Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada; Michael Smith Foundation for Health Research Scholar) clinical service focuses on development of novel mass spectrometry assays in support of the clinical laboratory at St Paul's Hospital, Providence Health Care. Her research lab develops strategies for quantitative MS workflows for protein biomarkers and leverages MALDI-TOF MS instrumentation for assay design and implementation.

Stephen Master received his undergraduate degree in Molecular Biology from Princeton University, and subsequently obtained his MD and PhD from the University of Pennsylvania School of Medicine. After residency in Clinical Pathology at Penn, he stayed on as a faculty member with a research focus in mass spectrometry-based proteomics as well as extensive course development experience in bioinformatics. After time as an Associate Professor of Pathology and Laboratory Medicine at Weill Cornell Medicine in New York City, where he served as Director of the Central Lab and Chief of Clinical Chemistry Laboratory Services, he took a position at the Children's Hospital of Philadelphia at Chief of Lab Medicine. One of his current interests is in the applications of bioinformatics and machine learning for the development of clinical laboratory assays. He would play with R for fun even if he weren't getting paid, but he would appreciate it if you didn't tell that to his department chair.

Infliximab (IFX) is an anti-TNF monoclonal antibody therapy used to treat autoimmune disorders such as Crohn’s disease and ulcerative colitis. For the significant portion of patients receiving IFX therapy who develops signs of loss of response to therapy, IFX therapeutic drug monitoring offers a rational approach to therapeutic decision making and is associated with improved outcomes (1,2).

Immunometric assays (ELISA, RIA, immunofluorometric) have been routinely used for the measurement of IFX in serum (3). Unfortunately, these assays demonstrate varying degrees of analytical and diagnostic concordance (3,4). Quantitation of IFX by LC-MS/MS has been implemented in clinical laboratories, and is faster and cheaper than traditionally used immunometric assays. In addition, mass spectrometry offers the potential to enable harmonization of testing between laboratories (5).

This session will describe: (1) the role of therapeutic drug monitoring of infliximab in guiding medical decision making; (2) the development and validation of an LC-MS/MS IFX assay at the St Paul’s Hospital Laboratory using the SCIEX Citrine platform; and (3) a web-based application for automated IFX reporting and QC review that was implemented at the Children’s Hospital of Philadelphia using the R statistical programming language. Taken together, this session provides a road map for clinical labs that are interested in implementing LC-MS/MS-based protein measurements on their own.

References:
1. Trasolini R and DeMarco ML. ‘Therapeutic drug monitoring of monoclonal antibody infliximab’ ASCP Case Reports, October, 2016.
2. Robert A. Mitchell, Constantin Shuster, Neal Shahidi, et al., ‘The Utility of Infliximab Therapeutic Drug Monitoring among Patients with Inflammatory Bowel Disease and Concerns for Loss of Response: A Retrospective Analysis of a Real-World Experience,’ Canadian Journal of Gastroenterology and Hepatology, vol. 2016, Article ID 5203898, 7 pages, 2016. doi:10.1155/2016/5203898
3. Niels Vande Casteele, Marc Ferrante, Gert Van Assche, et al., ‘Detection of infliximab levels and anti-infliximab antibodies: A comparison of three different assays’ Aliment Pharmacol. Ther 2012; 36:765-771
4. Bader, LI, Sol Solbert, SM, Kaada SH., et al., ‘Assays for Infliximab Drug Levels and Antibodies: A Matter of Scales and Categories’ Scand J Immunol 2017; 86:165-170

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.

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 2-Day Course with 7 total contact hours.

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.

Thursday

7:00 - 8:10am
Clinical tissue analysis: overview of workflows and diagnostic "blind spots" (BB) (70 min)

8:20 - 9:30am
Introduction to MALDI IMS (MR) (70 min)

9:40-10:50am
Advancements and applications using MALDI IMS (MR) (70 min)

Friday

7:00 - 8:10am
Introduction to ambient MS (CF) (70 min)

8:20 - 9:30am
Advancements and applications using AMS (CF) (70 min)

9:40-10:50am
Bringing IMS into the clinic: opportunities and challenges (BB) (70 min)

Slide Deck

Matthias is a proteomics expert with over 20 years of experience in mass spectrometry. He studied Chemistry in Freiburg, Germany, and Manchester, UK, did his PhD in Cellular Microbiology and Proteomics at the Helmholtz-Centre for Infection Research in Braunschweig, Germany and his post doctoral research at the Institute for Research in Immunology and Cancer in Montréal, Canada. In 2010, Matthias became Group Leader and Head of Proteomics at the MRC Protein Phosphorylation and Ubiquitylation Unit (MRC PPU) at the University of Dundee. In 2017, Matthias was appointed Professor of Proteomics at Newcastle University. Since 2019, he is a Wellcome Trust Investigator. His main biological interest is in phagosome and macrophage biology and particularly signalling events in innate immunity driven by phosphorylation and ubiquitylation. In recent years, his lab has additionally focused on using mass spectrometry for drug discovery. For this, the lab pioneered the usage of high-throughput MALDI TOF mass spectrometry for drug screening which has attracted significant industry interest.

Lisa M. Jones is an Associate Professor in the Department of Pharmaceutical Sciences at the University of Maryland. She received her BS from the Department of Chemistry at Syracuse University and her PhD in Chemistry from Georgia State University. She received postdoctoral training in structural virology at the University of Alabama- Birmingham and in MS-based protein footprinting at Washington University in St. Louis. Dr. Jones’s research interests include the use of the protein footprinting method fast photochemical oxidation of proteins (FPOP) coupled with mass spectrometry for the characterization of the higher order structure of proteins. In particular, her lab has further developed the FPOP method for in-cell (IC-FPOP) studies for proteome-wide structural biology. Biological applications of IC-FPOP include characterizing protein folding intermediates directly in the cell and drug target (both on and off targets) determination. The Jones lab has also extended the method for in vivo analysis (IV-FPOP) in C. elegans. This provides the ability to study protein structure in an animal model for human disease.

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 is on proteomics.

I grew up in rural Michigan and during these formative years greatly enjoyed flyfishing and woodworking. Putting the latter interest to practical use, I constructed several riverboats (for fishing) while in high school and college. Chemistry interested me, especially Analytical Chemistry, as it offered an avenue to continue “building”. Not boats, but chemical instrumentation. To escape the cold I joined the Chemistry graduate program at the University of Florida and worked with Willard Harrison. Professor Harrison didn’t just guide my research, he taught me how to write, present, and think like a scientist. He was a gentleman in every sense of the word. Upon graduation in 2002, I moved to Charlottesville, Virginia to join the laboratory of Professor Don Hunt. At Virginia I met John Syka. Don and John both shared a passion for science that was as infectious as it was inspiring. Together we worked to develop electron transfer dissociation (ETD). ETD worked just as we had hoped and the dissociation technique is now commonly used for proteomics and has been commercially introduced by no fewer than four major instrument vendors. In 2005 I moved to Wisconsin to start my own program. And though we have been productive and impactful with ~ 200 published manuscripts, I am most proud to have produced nearly 20 Ph.D. scientists, and our academic family continues to grow.

The sequencing of the human genome marked the beginning of a collective scientific expedition to understand complex organisms. Genes, of course, merely contain the instructions for which proteins will populate the cell. Untangling the multi-faceted networks that regulate complex organisms and their diseases will require innovative technologies to globally monitor many classes of biomolecules, including nucleic acids, proteins, and metabolites. High-throughput technologies for gene and transcript measurement are well-developed and broadly accessible, and, as such, have had a fantastic and transformative impact on modern biology and medicine. For numerous reasons, methods for global analysis of proteins and metabolites – crucial biological effector molecules – are less evolved and markedly less accessible. The overarching mission of my program is to (1) facilitate expedient, comprehensive analysis of proteins and metabolites by innovating new mass spectrometric technologies and (2) apply these techniques to advance biomedical research.

In this presentation I will describe numerous projects related to the development and application of high-throughput quantitative multi-omics. Examples include new proteomic methods and technologies to permit the deepest analysis of the human proteome to date and the discovery of thousands of alternatively spliced proteins and protein isoforms resulting from single nucleotide polymorphisms. In another example we use high throughput multi-omics to map the proteomes, lipidomes, and metabolomes of nearly 1,000 single gene knockout cell lines for large-scale functional mapping of genes. Finally, we use these same quantitative multi-omic technologies to study the molecular changes that occur during Covid-19 infection in a human cohort.

# 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.

Robert received his PhD in Analytical Chemistry from Virginia Commonwealth University applying top-down proteomics to characterize bacteria in the laboratory of Timothy Croley. Robert then transitioned to Boston Children’s Hospital as a postdoctoral fellow investigating multi-site phosphorylation dynamics using bottom-up and top-down proteomics under Hanno Steen. Next Robert pursued additional postdoctoral work in the laboratory of Steven Gygi in the Department of Cell Biology at Harvard Medical School (HMS) focusing on multiplexed proteomic strategies for phosphotyrosine signaling, selenocysteine containing protein networks and targeted proteomics. While in the Gygi Lab, Robert was a co-inventor of TOMAHAQ, a multiplexed targeted proteomics workflow. Robert then became the Director of Proteomics for the Laboratory of Systems Pharmacology (LSP) and joined the faculty at HMS at the rank of instructor. While at the LSP, Robert’s lab applied proteomics to numerous aspects of pharmacology including recently published work on covalent kinase inhibitors. Robert now leads the proteomics group within Hit Discovery & Optimization at Pfizer, where his group supports discovery programs in phenotypic screening, chemically-induced degradation, and the Centers for Therapeutic Innovation.

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.

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.

I will talk about how our first biomarker discovery was made and failed to be commercialized by us - but was commercialized by others.

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.

Marijuana is increasingly being used for both medical and recreational purposes. In the US, medical use of marijuana is legal in 33 states while recreational marijuana is available in 11 states. With more widespread use, there is growing concern about the effect of marijuana on driving performance.

The University of California-San Diego (UCSD) Center for Medical Cannabis Research (CMCR) recently completed a placebo controlled, double blinded study on the effects of smoked marijuana and driving performance. 200 subjects were randomized to smoking a joint containing placebo, 5.9% or 13.4% THC. Oral fluid, breath, and whole blood samples were collected along with driving performance on a simulator. THC and nine metabolites were measured using isotope dilution tandem mass spectrometry and the sensitivity and specificity of these compounds were examined using cutoffs commonly used by some state’s “per se” (by definition presumed to be impaired) laws.

There was no relationship between whole blood concentrations of THC and performance on a driving simulator. Smoking active drug produced a significant (p< 0.05) decrement in driving performance that lasted for 2-3 hours. The sensitivity and specificity of THC and metabolites as recent markers of marijuana varied according to the selected cutpoint.

Recognition of driving impairment will likely continue to depend on both officer observations and toxicology results.

Joshua is currently the Chief of Chemistry at NortonHealthcare. He earned his PhD in chemistry from Carnegie Mellon University. He conducted postdoctoral research at Massachusetts Institute of Technology before completing a two-year clinical chemistry fellowship at University of Washington and 4 years as Assistant Professor at Weill Medical College. Joshua has special expertise developing and overseeing mass spectrometry assays in the clinical laboratory.

The applications of mass spectrometry in the clinical laboratory continue to expand.
Unfortunately, not all clinical laboratories have mass spectrometers and there are substantial barriers to bringing in this instrumentation. This webinar will discuss some of these barriers and how we have been able to overcome them in our path towards setting up clinical mass spectrometry testing.

This session will serve as an introduction to a 4 part series in which Dr. Hayden will invite attendees to witness in real time his journey bringing mass spec testing to a clinical lab. During these interactive sessions, attendees will be encouraged to help troubleshoot, and offer advice as desired.

Subsequent sessions anticipated include:
1. Getting going with mass spectrometry: Josh learns chromatography
2. Getting going with mass spectrometry: Josh tries to do sample preparation
3. Getting going with mass spectrometry: Josh analyzes peaks

BONUS FUN ACTIVITY:
We are certain there is a very catchy title for this series. "The Real World: Clinical Mass Spec" and "Josh vs The World" didn't make the cut. If you think you have the perfect titles, let us know (Twitter handle @MSACL). Your ideas could be featured right here on MSACL Connect!

Ruth Andrew holds a Chair in Pharmaceutical Endocrinology at the University of Edinburgh and directs the Clinical Research Facility Mass Spectrometry Core. After qualifying as a pharmacist in 1990, she studied for a PhD in the field of pharmaceutical analysis, using gas chromatography mass spectrometry as an approach to profile catecholamines in hypertension. In 1994, she joined the Endocrinology Unit in the University of Edinburgh to develop further interests in mass spectrometry and establish its use in steroid profiling in cardiovascular disease. Since then Ruth has investigated the regulation of glucocorticoid metabolism and her group has focussed on the role of hepatic 5α-reductase in diabetes and in dynamic methods to quantify these metabolic pathways in vivo using stable isotope tracers. She leads a team specialising in small molecule quantitative analysis in support of translational medicine. She takes an active role in teaching both Honours students (Endocrine Physiology and Pharmacology, Clinical Biochemistry) and post- graduate students. She is a Committee member of the Society for Endocrinology, the Chief Scientist Office, FWO (Flanders), and the Commonwealth Commission and an Editor for the British Journal of Pharmacology, a Specialty Chief Editor for Systems Endocrinology (Frontiers in Endocrinology) and an Associate Editor with Talanta.

Dr. Adam Rosebrock is an assistant professor in the Department of Pathology at Stony Brook School of Medicine and the Stony Brook University Cancer Center. He has had longstanding interest in using “big data” to address fundamental biological questions. The focus of his research is on understanding the regulation of biochemical activities that underlie cell division, growth, and survival across diverse external states. The Rosebrock lab actively develops new experimental and analytical methods and builds genetic, hardware, and computational tools to enable high-throughput and high-content biology, with particular emphasis on quantitative mass-spectrometry metabolomics.

1994-​1999: Master in Biotechnology, ETH Zürich
1999-​2003: PhD, Institute of Biotechnology, ETH Zürich, Uwe Sauer and Prof. Jay Bailey
2004-​2005: PostDoc, Genome Technology Center, Stanford University, Prof. Peter Oefner and John Ross
since 2005: Principal Investigator, Institute of Molecular Systems Biology, ETH Zürich

PhD student
PhD in Epidemiology, Environment and Public Healthcare
University of Milan (Italy)

Project title: Childhood obesity and biomarkers: evaluation of the level of persistent organic pollutants and metabolic profile

Federal University of Rio de Janeiro - Ph.D. Natural Products Chemistry
Federal University of Rio Grande do Sul - Msc. Pharmaceutical Sciences
University National Mayor de San Marcos - Bacharel of Pharmacy and Biochemistry

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 is on data science in proteomics.

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.

David Pirman is currently an Associate Director at Agios working in the metabolism and proteomics group. He and his team support numerous drug discovery programs at varying stages across the portfolio. He completed his training under Professor Richard Yost at the University of Florida developing quantitative MALDI MS imaging methods. He then spent a year at MD Anderson Cancer Center working on cancer lipid metabolism followed by a postdoctoral position at Pfizer further studying metabolic disease and building metabolomics analytical capabilities. David has been developing and using mass spectrometry methods to study disease metabolism applied to the drug discovery setting for 8+ years.

Alla Kloss is a Scientific Director at Analytical Research and Development Department in PDS, NA Hub, Sanofi where she leads a Biomarkers and Advanced Analytical Development group. Her group has established and validated an in-house metabolomics/lipidomics platform which includes both commercially available and novel, developed internally, tools for discovery of translational biomarkers. This platform is successfully used for discovery and identification of metabolic biomarkers, development of phenotypic screens, target credentialing, as well as in later phases of drug development.
Alla has been at Genzyme/Sanofi for 19 years, supporting broad range of programs from early discovery to Manufacturing. She has lead Manufacturing Forensics efforts at AR&D and brought to successful resolution over 25 manufacturing investigations.
Education:
MS in Chemical Engineering from The Institute of Technology (St. Petersburg Russia).
PhD in Physical/Analytical Chemistry from University of California, Davis
Post Doctoral studies at the University of Illinois at Urbana-Champaign.

Join our Fireside Chat with Dr. David Pirman and Dr. Alla Kloss to learn about a career after your studies in metabolomics/lipidomics. This session will be interactive and offers opportunities to network.

Jody van den Ouweland is specialist in Laboratory Medicine and working as Laboratory Director at the Canisius-Wilhelmina Hospital, 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). Areas of clinical interest are diabetes, endocrinology and clinical biomarkers. 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 vitamins, steroids and amino acids. He is a member of the Dutch working group of Clinical Mass Spectrometry, member of the MSACL EU Scientific Board, and Editorial Board member of the Journal of Mass Spectrometry & Advances in the Clinical Lab.

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

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.

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. To identify the importance of specimen processing in acquiring accurate results.
2. To describe how interferents can impact mass spectrometric results.
3. To weigh the benefits and limitations of different specimen preparation approaches for mass spectrometric assays using a fit-for-purpose approach

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, is an Asst. Director of Clinical Chemistry & Laboratory Informatics at Nationwide Children's Hospital. His research focuses small molecule analysis by mass spectrometry in a clinical setting and hospital and clinical informatics.

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

Putting R Skills to Use in Clinical Laboratories
Dustin Bunch

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

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.

Speaker: Dr. Patrick Mathias
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.

Speaker: Dr. Dan Holmes
Dan Holmes will discuss end-to-end liquid handling, data and reporting automation for pooled SARS CoV-2 testing using R, R Shiny and other open source tools. The talk will discuss development, validation, workflow and user experience with an aim to increase testing throughput, improve staff experience and decrease the risk of error.

Ample time for discussion post-presentation will be available.

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

Dr. Carmen Wiley was the 2019 - 2020 President of AACC. Recently she returned to the clinical practice of laboratory medicine and serves as Clinical Medical Director at Incyte Diagnostics. In this role, she supports the new clinical lab facility located in Spokane Valley and acts as the Medical Director over the clinical labs at Providence Sacred Heart Medical Center, Holy Family, My Carmel, and St. Joseph’s.

Dr. Wiley holds a Bachelor’s degree in Chemistry from the University of Minnesota, a Master’s degree in Organic Chemistry from the University of Washington, a Doctoral degree in Organic Chemistry from the University of Washington, and was a COMACC Accredited Fellow at the Mayo School of Medicine. She is board certified by American Board of Clinical Chemistry (ABCC) and a Fellow of the Academy of the American Association of Clinical Chemistry (FAACC).

Most recently, she was the Chief Medical Officer of a start-up company based in Oakdale, MN. Previously, she was a Regional Manager of Scientific Affairs – Cardiac at Roche Diagnostics. In this role, she was responsible for leading and developing the Medical & Scientific Liaisons in their relationships with the medical/scientific community, with the objective of critical scientific exchange including medical/scientific education. Dr. Wiley played a key role in providing support to healthcare professionals as well as internal Roche scientific groups and local business teams. Dr. Wiley was the Scientific Director at PAML where she was responsible for the medical and scientific oversight of all laboratory testing and oversaw all aspects of PAML’s research and development program. Prior to that, Dr. Wiley was Co-Director of Chemistry, Immunology, and Point of Care at Providence Health and Services, Sacred Heart Hospital in Spokane, WA and the Head of Clinical Chemistry in the Division of Laboratory Medicine and Pathology at the Marshfield Clinic in Marshfield, WI.

Dr. Wiley, her husband of 21 years and two kids enjoy time spent with their three dogs. She loves hiking, camping, and knitting. She is a native to Minnesota, but now considers Spokane, WA her home.

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

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.

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.

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.

Join us for some informal networking and to hear from Michelle Reid, Aruna Vigneshwari, and L. Tamina Hagemann on the research they have been working on in their laboratories! Employers, be sure to join us to find your next perfect hire!

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.

David Tabb, born in the U.S. Midwest, surprisingly finds himself living in South Africa after a fifteen-year transition from assistant professor to associate professor to “full” professor. While in the United States, he conducted his research in a state university, a private research institute, a national laboratory, and a private university. Since 2015, he has enjoyed the moderate climate of Cape Town, where he is completing a five-year contract in tuberculosis biomarker research at Stellenbosch University. He has survived and occasionally thrived in the rich world of clinical proteomics, where he has specialized in the informatics of protein identification from tandem mass spectrometry. He was particularly fortunate to be a bioinformatics lead for the Clinical Proteomics Technology Assessment for Cancer (CPTAC) during the first ten years of that program’s operations. His hobbies include choral singing, computer upgrading, board gaming, and cat pestering.

Proteomics is a field in constant demand in academia, industry, and the clinical lab. With the rapidly changing technology in the proteomics world, bioinformaticians who have an intimate understanding of mass spectrometry as well as computational skills are much needed. Join our Fireside Chat with clinical proteomics bioinformatician, Dr. David Tabb to learn more about a career in bioinformatics from all angles.
This session will be interactive and offers opportunities to network.

*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.

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.

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.

Join the FeMS network (Females in Mass Spectrometry) with guest Michelle Reid for a discussion on mentorship and to learn about a new FeMS mentoring program. You may signup to participate in the mentoring program using the Mentorship Program signup form.

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!

More on FeMS: femalesinms.com

Please join us for another Mass Spec Mixer featuring presentations from Grad Students Transitioning to PostDocs: Ettore Gilardoni, Daniel Mouzo Calzadilla and Alexandra Iakab. There will be time for networking, all are welcome, employers encouraged!

Dr. Carmen Wiley was the 2019 - 2020 President of AACC. Recently she returned to the clinical practice of laboratory medicine and serves as Clinical Medical Director at Incyte Diagnostics. In this role, she supports the new clinical lab facility located in Spokane Valley and acts as the Medical Director over the clinical labs at Providence Sacred Heart Medical Center, Holy Family, My Carmel, and St. Joseph’s.

Dr. Wiley holds a Bachelor’s degree in Chemistry from the University of Minnesota, a Master’s degree in Organic Chemistry from the University of Washington, a Doctoral degree in Organic Chemistry from the University of Washington, and was a COMACC Accredited Fellow at the Mayo School of Medicine. She is board certified by American Board of Clinical Chemistry (ABCC) and a Fellow of the Academy of the American Association of Clinical Chemistry (FAACC).

Most recently, she was the Chief Medical Officer of a start-up company based in Oakdale, MN. Previously, she was a Regional Manager of Scientific Affairs – Cardiac at Roche Diagnostics. In this role, she was responsible for leading and developing the Medical & Scientific Liaisons in their relationships with the medical/scientific community, with the objective of critical scientific exchange including medical/scientific education. Dr. Wiley played a key role in providing support to healthcare professionals as well as internal Roche scientific groups and local business teams. Dr. Wiley was the Scientific Director at PAML where she was responsible for the medical and scientific oversight of all laboratory testing and oversaw all aspects of PAML’s research and development program. Prior to that, Dr. Wiley was Co-Director of Chemistry, Immunology, and Point of Care at Providence Health and Services, Sacred Heart Hospital in Spokane, WA and the Head of Clinical Chemistry in the Division of Laboratory Medicine and Pathology at the Marshfield Clinic in Marshfield, WI.

Dr. Wiley, her husband of 21 years and two kids enjoy time spent with their three dogs. She loves hiking, camping, and knitting. She is a native to Minnesota, but now considers Spokane, WA her home.

Dr. Bystrom serves as Translational Laboratory director at Cedars-Sinai, where he is responsible for novel biomarker validation and commercialization. Prior to joining Cedars-Sinai, he directed research and development at Cleveland Heart Lab and commercialized a multiplex proteomic diagnostic test focusing on HDL functionality.

Dr. Jeanne Rhea-McManus completed her PhD in Genetics at the University of Georgia followed by a post-doctoral fellowship within the Department of Pathology and Laboratory Medicine at Emory University in Atlanta, Georgia. There she served as the Technical Coordinator and Assistant Director of the Emory Clinical Translational Research Laboratory and specialized in the development of mass spectrometry methods for use in patient care. Since 2014, Dr. Rhea-McManus has served as a Medical Officer for Siemens Healthineers where one of her primary roles is to ensure the safety, efficacy, and sustainability of products that are put on the market and used for patient care. In addition to this role, she also organizes the Siemens Healthineers Medical and Scientific Learning Exchange program which as been held annually since 2016 and serves to bridge the knowledge gap that exists between the training received by medical professionals and IVD manufacturers.

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!

Prof Roessner has obtained her Diploma in Biochemistry at the University of Potsdam and the John Innes Institute in Norwich, UK after which she pursued a PhD in Plant Biochemistry at the Max-Planck-Institute for Molecular Plant Physiology in Germany, where she developed novel GC-MS methods to analyse metabolites in plants. Together with the application of sophisticated data mining, the field of metabolomics was born and is today an important tool in biological sciences, systems biology and biomarker discovery. In 2003 she moved to Australia where she established a GC-MS and LC-MS based metabolomics platform as part of the Australian Centre for Plant Functional Genomics for which she led the node at the University of Melbourne. In addition, since 2007, Prof Roessner has been involved in the setup and lead of Metabolomics Australia (MA), a federal and state government funded national metabolomics service facility and now leads the MA node at the University of Melbourne. In 2013, Prof Roessner was awarded an Australian Research Council Future Fellowship to establish her own research program applying Imaging Mass Spectrometry for spatial metabolite and lipid analyses to understand root metabolism under salinity stress. Currently her research program uses metabolomics and lipidomics technologies to decipher how plant roots interact with beneficial microbes under abiotic stress conditions. In 2018, Prof Roessner took up the position as Head of School, School of BioSciences, University of Melbourne.

Join us for our next FeMS Happy Hour! We will be following our usual format with small group breakout room discussions followed by Ute Roesnner presenting on Resilience, and a time for Q&A and Discussion. All are welcome!

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 received his BS (1966) in Chemistry from Tulane University. He completed his MA (1972) in Chemistry at the University of North Carolina-Chapel Hill, served 5 years in the USAF, received his MD (1979) and PhD (1982) at the University of Utah and then completed a Clinical Pathology residency (1982) at the University of Virginia. In 1982 he joined the University of Virginia faculty. In 1991 he moved to the University of California, San Diego and is now Professor of Pathology. He has authored and co-authored over 80 scientific publications and presented at numerous international scientific conferences. Inspired by the 2007 ASMS Asilomar conference on clinical mass spectrometry, Dr. Herold co-founded MSACL. From 2008 to the present, he has served as CEO, Executive Board Chair and Global Scientific Coordinator of MSACL. MSACL's mission is to further the accumulation and sharing of expertise in mass spectrometry and other advanced technologies in the clinical laboratory through educational advancement. MSACL will continue building the foundation for the adoption of technology in the clinical laboratory, including data science, based on the belief that this will provide more accurate, precise and timely laboratory results at lower overall costs that will result in better patient care and outcomes.

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!

Dr. Stefani Thomas earned her BA in Biological Sciences from Dartmouth College and her PhD in Pharmaceutical Sciences from the University of Southern California. She pursued postdoctoral training in Dr. Robert Cotter’s Middle Atlantic Mass Spectrometry laboratory, conducted clinical proteomics research in the Center for Biomarker Discovery and Translation, and completed a Clinical Chemistry postdoctoral fellowship at Johns Hopkins University. She is currently an Assistant Professor, a faculty member of the Advanced Research and Diagnostics Laboratory (ARDL) and a member of the Masonic Cancer Center at the University of Minnesota. She is also the Associate Medical Director of the M Health Fairview West Bank Laboratory. Stefani's research laboratory applies discovery and targeted mass spectrometry-based proteomics methods to elucidate the biology of ovarian cancer and to identify proteome-level mechanisms of improved ovarian cancer treatment response.

Jacqueline Hubbard received her B.S. degree in Biochemistry from the University of Vermont. She then enrolled in the Biochemistry and Molecular Biology program at the University of California, Riverside (UCR) where she earned her M.S. and Ph.D. Following a one year postdoc at UCR, Dr. Hubbard completed a Fellowship in Clinical Chemistry at the University of California, San Diego Health. She is board certified in Clinical Chemistry by the American Board of Clinical Chemistry. In 2019, she took a position as an Assistant Professor in the Department of Pathology and Laboratory Medicine at the Geisel School of Medicine at Dartmouth and as the Assistant Director of Chemistry at Dartmouth-Hitchcock Medical Center. Her current focus includes developing and validating drugs of abuse confirmation testing.

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!

Nicholas is a fifth year PhD candidate in Molecular Biophysics with a focus in Computational and Systems Biology at The University of Texas Southwestern Medical Center under Dr. Prashant Mishra. His interest is in using isotope tracing mass spectrometry to perform metabolic flux analysis to investigate alterations in metabolism as a result of dysfunctional mitochondria.

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.

Even though our scientific lives have vastly moved to a virtual space, the clock keeps ticking and graduate school & post doc positions are ending for many. To help promote networking for those searching for jobs in this crazy time, Females in Mass Spectrometry (FeMS) would like to institute Transition Talks where ALL graduate students and post docs in MS-related fields within 1 year of transition are welcome to participate. Additionally, students looking for an internship may apply.

The Transition Talks will be 10 minute informal talks, followed by 5 minutes of questions, where the speakers:
>Introduce themselves
>Give an overview of their current research
>Explain their desired transition

Transition Talks will be presented virtually at FeMS Mass Spec Mixers, which will be held on the last Thursday of every month starting on 07/30/2020. Mass Spec Mixers will enable informal networking and connections between the speakers and the scientific community so that job postings can be quickly communicated to those on the market. Anyone who would like to grow their network is encouraged to attend!

If you are interested in giving a Transition Talk, please fill out the google form linked below and we will schedule you depending on the timeline of your transition and your preferred time.
Sign up to present a Transition Talk Here

We look forward to seeing you there!
Best,
FeMS

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.

Tiffany Payne is the Marketing Director for Clinical Diagnostic Analytical Instruments at Agilent Technologies. She studied mass spectrometry at the University of the Pacific under David Sparkman and holds an M.S. in Chemistry and Pharmaceutical Sciences. She started her career at Varían, Inc. as an Application Scientist and joined Agilent after their acquisition of Varían in 2010. Since joining Agilent Tiffany has held a number of marketing positions in Product Management and Segment Marketing.

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.

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.

Slides (PDF)

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.

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.

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.

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.

Compiled Posters

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

Compiled Posters

Zhicheng Jin received his PhD in analytical chemistry from Purdue University in 2010. He completed two postdoctoral trainings, one at Johns Hopkins University and one at Case Western Reserve University. He then worked at Cleveland HeartLab, now part of Quest Diagnostics, as a research scientist. Dr. Jin is currently a clinical chemistry fellow in the Department of Pathology and Genomic Medicine at Houston Methodist Hospital.

Graduated from the University of Wisconsin Lacrosse in 2007. Started my career at Mayo Clinic in 2007 as Clinical Laboratory Scientist. In 2010, I was promoted to a Technical Specialist I role in the Endocrinology lab which then became the Clinical Mass Spec Lab. In 2016 I transitioned to a Development Technologist I role and just recently I was promoted to a Development Technologist II within the Mass Spec Development lab.

I studied pharmacy and graduated from the Heinrich Heine University in 2016. Currently, I’m a PhD student at the institute of clinical pharmacy and pharmacotherapy. My research focuses on biomarker quantification using hybrid LBA/LC-HRMS assays.

An Investigation of Positive Bias in Our Mass Spectrometry-based 1?,25-dihydroxyvitamin D Assay
Zhicheng Jin
Houston Methodist Hospital
>> VIEW POSTER (PDF)

The determination of human active renin and prorenin by LC-MS: the impact of injection solvent composition and material on precision and signal intensity
Ilja Burdman
Institut of Clinical Pharmacy and Pharmacotherapy
>> VIEW POSTER (PDF)

A Direct Comparison of Mircoflow Liquid Chromatography versus High Flow LC-MS/MS Utilizing the Thyroglobulin Assay
Jennifer Kemp
Mayo Clinic

LCMS Method Development for Undergraduate Lab Curriculum by Analysis of Caffeine and Theobromine in Chocolate
Robyn Araiza
California State University San Marcos
>> VIEW POSTER (PDF)

Batch Cover Sheet (Judy Stone)

Medical School
MD - Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA

Residency
Clinical Pathology - Massachusetts General Hospital, Boston, MA (Chief Resident)

Fellowship
Transfusion Medicine - Harvard Medical School, Cambridge, MA

Board Certification
Clinical Pathology

Graduate Degree
PhD in Cell and Molecular Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA

Michael Kane is an Assistant Professor in Yale University's Biostatistics Department. He is interested in Scalable Statistical/Machine Learning, Statistical Computing, and Applied Probability.

Joseph is RStudio’s “Ambassador at Large” for all things R, editor of the R Views blog, and RStudio’s representative on the R Consortium’s board of directors. Joseph came to RStudio via Revolution Analytics and Microsoft where he was a data scientist, blogger and community manager. Before joining Revolution Analytics Joseph worked as a statistician for a small healthcare economics consulting firm, and before that he held a variety of technical, marketing and sales positions while working for startups that spanned multiple industries including government contracting, local area networks, disk drives and test equipment. Joseph studied Classics and Mathematics as an undergraduate at Franklin & Marshall College and earned an M.A. in Humanities and an M.S. in Statistics from the California State University.

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.

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.

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.

R is a freely available open-source programming language and a powerful statistical computing environment that is extremely popular among statisticians and data scientists. R is ideally suited for building customized applications for clinical operations, however many (real and perceived) hurdles exist in operationalizing R in healthcare in general, and in the labs in particular. This session is hosted by the organizers of R/Medicine, an annual conference aiming to promote the R ecosystem in clinical research and practice. This will be a highly interactive session aimed to share insights and experiences both of the discussants and participants, with the aim of facilitating the integration of the R ecosystem into clinical laboratory practice.

Hosted by R/Medicine

Panelists:

Stephan Kadauke, Assistant Professor of Pathology and Laboratory Medicine at the Children’s Hospital of Philadelphia, Chair of R/Medicine 2020

Michael Kane, Assistant Professor of Biostatistics at Yale University School of Public Health, past Chair of R/Medicine

Joseph Rickert, R Consortium, and RStudio, PBC

Lindsay Bazydlo, Associate Clinical Professor of Pathology, University of Virginia

Shannon Haymond, Associate Professor of Pathology, NorthWestern University

After completing this activity, participants will be able to:

1. Cite resources available for R and data science education tailored for clinicians and laboratorians.

2. Describe organizational, regulatory, and cultural challenges to integrating the R ecosystem into clinical practice.

3. Discuss best practices for building customized clinical laboratory-developed applications (“lab apps”) in R/Shiny.

Some R Resources

Alfonso Limon is the Chief Liaison of R&D for Oneirix Labs, a consulting company developing market-leading technologies resulting in high-value intellectual property. Previously, he was the Director of Research at Intersection Medical, leading groups developing optimal algorithms for the management of congestive heart failure. Alfonso earned a B.S. in Mechanical Engineering from San Diego State University, a M.S. in Mathematics from Claremont Graduate University and Ph.D. in Computational Science from their joint program.

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

Learning objectives include:
1. Be able to define what Data Science is, why it matters, and why you personally should care. What is the clinical relevance?
2. Define any terminology that is specific to this field.
3. Describe how it works, what are the methods and workflows used when studying this field and/or how is it implemented in clinical labs.
4. Identify any challenges to implementation/adoption, where do the opportunities lie?

Dr. Yost is the University Professor and Head of Analytical Chemistry at the University of Florida. He is also director of the Southeast Center for Integrated Metabolomics (SECIM) and of NIH’s Metabolomics Consortium Coordinating Center (M3C). He is recognized internationally as a leader in the field of analytical chemistry, particularly tandem mass spectrometry (MS/MS). His research has been recognized with the ASMS Award for Distinguished Contribution in Mass Spectrometry, the MSACL Award for Distinguished Contribution to Clinical Mass Spectrometry, and the Florida Academy of Sciences Medal. Dr. Yost currently serves as President of the American Society for Mass Spectrometry (ASMS).

All are welcome to join the Early Career Network for an informal chat with mentoring legend, Dr Yost. Bring your career development related questions. This is a networking opportunity you won't want to miss.

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.

Join the FeMS network (Females in Mass Spectrometry) for a presentation from special guests Drs. Candice Ulmer, Michelle Reid, and Christina M. Jones, founders of Black People Meet @ASMS.

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.

Slide Deck (pdf)

Alan Rockwood, PhD, DABCC is Professor (Clinical) Emeritus of Pathology at the University of Utah School of Medicine in Salt Lake City, Utah, USA. Originally trained in Physical Chemistry, he performed research on the fundamentals of mass spectrometry and instrumentation development before focusing his career on Clinical Chemistry. He is certified by the American Board of Clinical Chemistry and has held a Certificate of Qualification in Clinical Chemistry from the New York State Board of Health. Currently, his primary area of research is the development of mass spectrometry-based quantitative assays for targeted analytes of clinical interest, including small molecules and more recently proteins and peptides. Additionally, he maintains a smaller research effort on fundamentals of mass spectrometry, particularly novel approaches for isotopic profile calculations. He has published >150 papers in peer reviewed journals.

Like many people in the field of Clinical Chemistry, I arrived here by an indirect route. In this presentation I give an account of the path I traveled to get here, discussing my development as a scientist and ultimately my embrace of Clinical Chemistry and Clinical Mass Spectrometry as career choice for the last half of my career journey, including some of the people who influenced or mentored me, a few stops along the way, and some of the lessons learned along the way, both from a scientific and a personal perspective. Included will be some projects and discoveries that I regard as successes as well as a few that were less successful, and lessons that can be drawn from both.

Slides (pdf)

Assistant Professor at the Maastricht MultiModal Molecular Imaging (M4I) institute, I have more than 8 years of experience in the MSI imaging fields and had the opportunity to gain insights on different aspects, including instrumental development, sample preparation and quantification. Since I have earned my PhD at the School of Pharmaceutical Sciences (University of Geneva), I am now devoted to demonstrate how MSI can be employed to improve the accuracy of cancer diagnostics. I am strongly motivated by the translational aspect between the development of innovative instrumentation and direct application to clinical research – with a special focus on intraoperative mass spectrometry – and by the close collaboration with the Surgeons and Pathologists of the Maastricht University Medical Center + (MUMC+), and with the RWTH Aachen in Germany.

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

Learning objectives include:
1. Be able to define what MS Imaging 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?

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.

This informal Practical Training session will include a presentation on Financial Considerations for Purchasing a Mass Spectrometer, as well as offer small group discussion and networking opportunities.

1. Describe the clinical and monetary benefits of purchasing a mass spectrometry system.
2. Identify different models for financing a mass spectrometry system purchase.
3. Participate in effective negotiations with vendors.

Dr. Drake earned his PhD in Biochemistry and Molecular Biology from the University of Kentucky in 1990. Over the course of his career, first as a faculty member at the University of Arkansas for Medical Sciences, then the Eastern Virginia Medical School, and finally for the past seven years at the Medical University of South Carolina (MUSC), Dr. Drake has published over 150 manuscripts in peer-reviewed journals, developed 4 patents, and edited 2 books. He has been Director of the MUSC Proteomics Center since 2011, and in close collaboration with Dr. Ball will serve as Director of the DDRCC Proteomics Core. The Core will provide highly specialized expertise and advanced instrumentation for the application of imaging mass spectrometry (IMS) technologies to gastrointestinal and liver research questions (includes both experimental and clinical projects).

Since 2002, Dr. Drake has developed multiple MS-based approaches for profiling clinical biofluids and tissues, and specializes in the analysis of glycans and glycoprotein biomarkers. In the past five years, his laboratory has developed a robust and highly novel IMS approach for the analysis of N-linked glycans in tissues. This method is of great utility as it can be used with any FFPE (formalin-fixed paraffin-embedded) or frozen tissue, ranging from clinical samples to tissues harvested from genetically engineered animal models. His glycan IMS approach continues to generate high-content N-glycome maps which provide detailed information on potential marker functions and localization in tissues. This in turn is facilitating further IMS method development for other types of glycan targets, such as O-glycans and heparin/chondroitin sulfate glycosaminoglycans, as well as glycoprotein post-translational modifications (PTMs).

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

Learning objectives include:
1. Be able to define what Glycomics 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?

Dennis works as a Clinical Biochemist, overseeing the Mass Spectrometry testing laboratory in Calgary for Alberta Precision Labs and has a cross appointment as a Clinical Assistant Professor at the University of Calgary. His research interests include lab assay design targeting drug metabolism and pharmacokinetics.

A follow up to the presentation from May 20, 2020 entitled “No Middleware? No Problem.” This interactive session will walk through the design and implementation of an R Shiny app able to summarize and display the quality metrics of your choice in the absence of a middleware. The dashboard example provides a method for streamlining QC data review from various analyzer types and vendors, across sites and lot numbers, all of which can be viewed remotely. The goal is to provide technical staff the opportunity to quickly get through monthly QC review, as well as identify analyzers which may be seeing shifts in QC running means between analyzers or lot numbers. Ready access to this data allows staff to get through routine QC review quickly, while also promoting better region-wide lab quality and inter-site continuity. Adaptation of this dashboard could also allow review of LC-MS quality metrics such as retention times, peak areas, and QC running means within and between batches. The goal of this workshop is to provide attendees the tools they need to implement R Shiny apps in their own labs and allow them to track whatever metrics are most important to them.

The file followed throughout the workshop

The Final_App showed in my original presentation

An updated version of Final_App with more streamlined coding (thanks to Sumedh) with is much easier to read

Bachelor Degree in Chemistry obtained from NC State University in Raleigh, North Carolina, with early research experience in Molecular Paleontology under the mentorship of Dr. Mary H. Schweitzer analyzing soft tissue extracts from a 66 million year old T. rex specimen. This early research experience inspired a passion for analytical sciences.

Upon Completion of B.S. Degree in 2006, continued Graduate School at NC State with a focus in Bioanalytical Chemistry and a Graduate Minor in Biotechnology under the mentorship of Dr. David Muddiman at the W. M. Keck FT-ICR Mass Spectrometry Laboratory, working on biological systems ranging from fungal crop pathogens to human embryonic stem cell biology, with methodological focuses on quantitative Top-Down and Bottom-Up Proteomic Methodologies. This exposure to applying new analytical methods to pursue questions related to human health inspired a decision to pursue research in that area further.

After completion of Ph.D. work in 2010, training continued as a Post-Doctoral Research Scholar in the division of Molecular Oncology at Washington University School of Medicine in St. Louis, MO, in the lab of Dr. Ron Bose, and with additional mentorship from Dr. Michael Gross, where quantitative proteomic and siRNA methods were developed to identify drug-resistance mechanisms in HER2 positive breast cancers. Further structural mass spectrometry methods were combined with molecular dynamics simulations to identify specific multimeric interactions between HER2 and HER3 kinases to illuminate structural relationships between tumor-driving mutations and unregulated signaling activity.

Upon completing post-doctoral work in 2013, moved to Cleveland, OH to become a Research and Development Scientist at Cleveland HeartLab, Inc., working with a dynamic team to develop diagnostic tests based on novel biomarkers to improve assessment of cardiovascular risk, and was promoted to current role Senior Research and Development Scientist in 2016.

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

Learning objectives include:
1. Be able to define what Proteomics 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?

Anne K Bendt studied Biology focusing on marine biotechnology (Greifswald University, Germany), followed by a PhD in Biochemistry (Cologne University, Germany) employing proteomics and transcriptomics. Driven by her fascination for infectious diseases, she joined the National University of Singapore (NUS) in 2004 to develop lipidomics tools for tuberculosis studies. She is now a Principal Investigator at the Life Sciences Institute, NUS, focussing on translation of mass spec technologies into clinical applications, and serving as the Associate Director of the Singapore Lipidomics Incubator (SLING) taking care of operations and commercialization.

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

Learning objectives include:

1. Be able to define what Lipidomics 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?

Theodore Alexandrov is a group leader at the European Molecular Biology Laboratory (EMBL) in Heidelberg, the head of the EMBL Metabolomics Core Facility and an Assistant Adjunct Professor at the Skaggs School of Pharmacy, University of California San Diego. The Alexandrov team at EMBL aims to reveal secrets of metabolism in time and space in tissues and single cells by developing experimental and computational methods. The team unites interdisciplinary scientists from biology, chemistry, and computer science as well as software and machine learning engineers. Theodore Alexandrov is a grantee of an ERC Consolidator project focused on studying metabolism in single cells, as well as of various other European, national, NIH, and industrially-funded projects. He has co-founded and scientifically directed the company SCiLS and has over 70 journal publications and patents in spatial omics.

PhD 2007, St. Petersburg State University, Russia
Postdoctoral research at the University of Bremen, Germany
Group leader, University of Bremen, Germany
Assistant Adjunct Professor, University of California San Diego, USA
Team leader at EMBL since 2014.

The METASPACE platform hosts an engine for metabolite annotation of imaging mass spectrometry data as well as a spatial metabolite knowledgebase of the metabolites from hundreds of public datasets provided by the community.

Karen holds an MBA from the Yale University School of Management and is founder and principal at Articulate Consulting. Karen has provided training in presentation development skills to professionals around the world from executives and managers to analysts, consultants, and graduate students. In addition, over her career as both a management consultant and a marketing professional for a Fortune 20 company, Karen has created a multitude of clear and compelling presentations to help senior executives and board members of large companies make better strategic decisions. She understands first-hand the challenges of creating presentations when the stakes are high and clients' expectations are even higher. Karen's style is both visionary and practical. She seeks to inspire others to have confidence in what they can accomplish with their presentations, and also to give them the concrete know-how and tools they need to immediately begin creating presentations that give them the influence they desire.

This is a one hour primer packed with actionable steps that will have a positive impact on how you communicate your science in presentations.

Karen will discuss secrets to unlocking success in your presentation storyboarding, visual design, and oral delivery.

Several aspects of Karen's full-length course will be covered, pulling from:

1. Storyboarding
Learn how to use storyboarding—the method used by the world’s largest management consulting firms and Fortune 500 companies—to structure your content so it's highly compelling.

2. Visual Design
Visual polish goes a long way in establishing the credibility of your ideas. Learn to design visually appealing, professional-looking slides—whether you consider yourself artistically inclined or not!

3. Oral Delivery
Discover the secrets to delivering your presentation in a way that fully engages your audience with your ideas so they leave energized and ready to take the next steps you want them to.