Peter VERHAERT was full professor Analytical Biotechnology and Innovative Peptide Biology at Delft University of Technology [Netherlands; 2005 – 2016] before founding his company ProteoFormiX (www.proteoformix.com). His Flemish research startup resides at [email protected], the J&J Innovation Center on the Campus of Janssen Pharmaceuticals in Beerse [Belgium; 2017].

Peter is recognized worldwide as one of the pioneers in Peptidomics, Peptides in Biology being the common theme in his >35 years of research.

Prior to taking up his academic position in Delft and ultimately starting his own research company in Beerse, Peter's international career already combined academic and industrial positions:
He obtained an MSc in Biology (Zoology Group) and a PhD in Comparative Neurobiology at the University of Leuven, where he held a position as assistant professor [Belgium; 1983-1987].
He then took on a postdoc position at the Laboratory of Toxicology and Biochemistry in the Biology Department of the University of Waterloo [Canada; 1988].
Upon returning to the University of Leuven, he became an associate professor in Histology and Biological Mass Spectrometry [Belgium; 1988-1999].
After an industrial sabbat year at the Flemish Biotech Innogenetics in Ghent [Belgium; 1998-1999], Peter was appointed group leader Proteomics at the Dutch Pharma company Organon (now MSD) in Oss [Netherlands; 2000-2004].

His other professional activities include:
• Co-founder and president of the European Pharmaceutical Proteomics Laboratories (EPPL) [2000-2004];
• Proteomics expert at the Flemish Institute of Biotechnology (VIB) [2000-2004];
• Visiting professor Biomedical Proteomics at the Biomedical Research Institute at the Faculty of Medicine of Hasselt University [Belgium; 2004-2014];
• Editor-in-chief of the Elsevier Open Access Journal EuPA Open Proteomics [2013-2016]
• Co-director of the Center of Excellence in Biomedical Mass Spectrometry (CEBMMS) at the Faculty of Medicine (Clinical Sciences Department) of Lund University [Sweden; 2016];
• Appointment as honorary professor Mass Spectrometry Histochemistry at the Maastricht Multimodal Molecular Imaging Institute (M4i) of Maastricht University [Netherlands; 2017].

The lack of biomarkers still prevents the discovery and development of therapeutics and diagnostics for several serious diseases. Some of the latter can only be correctly diagnosed under the microscope by scrutinizing tissue sections of biopsy or even autopsy material.

Histopathologists all over the globe archive precisely annotated samples preferably in FFPE (formaldehyde-fixed paraffin-embedded) tissue banks. These represent a virtually unlimited resource of accurately diagnosed and stratified patients of all (stages of) diseases, which unfortunately today remains largely underexplored in biomarker research.

What if there would be a molecular discovery technology that could detect and identify biomarker candidates from the very same FFPE tissue sections?
What if this would be a label-free multiplex technology?
What if this technology would work on material stored for decades?
What if this technology could be spatially resolved?
What if this technology could generate molecule specific images that can be overlaid with other imaging modalities?
What if this technology would have single cell resolution in combination with single cell sensitivity?
What if this technology could localize molecules which are specifically produced and released from cells?
What if this technology would be multi-omics?

In this webinar I will argue that a technology already exists today that appears to combine all of the above.

Mass spectrometry histochemistry (MSHC), which combines atmospheric pressure MALDI with high resolution top-down MS, deserves this extra attention, as it may be(come) a welcome complement (or even alternative) to current LC-MS/MS biomarker discovery strategies that analyze extracts of tissues and body fluids.

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. Joyce Liao has more than ten years of clinical and management experience in laboratory medicine. She was a medical laboratory scientist in the newborn screening lab and obtained her Ph.D. degree in Clinical Medicine. She completed postdoctoral fellowship training in Clinical Chemistry at the University of Washington and Seattle Children’s Hospital. She is a board-certified Clinical Chemist and now served as an Associate Director at Harborview Medical Center, focusing on toxicology and mass spectrometry testing. She continues to focus on the translation of the analytical power of mass spectrometry to real clinical applications. Her interests include toxicology, mass spectrometry, and laboratory utilization.

Dr. Stieglitz is currently an Assistant Professor at The Ohio State University Wexner Medical center and Co-Director of Clinical Chemistry and Toxicology. She received her PhD from Emory University and completed a postdoctoral fellowship in Clinical Chemistry at the University of North Carolina before joining Ohio State. She is board certified in Clinical Chemistry by the American Board of Clinical Chemistry. Her interests are in mass spectrometry-based clinical toxicology testing in adults and newborns.

Once live with mass spectrometry-based testing, clinical laboratories face the challenge of ensuring adequate data review and accurate resulting. Inevitably, labs will encounter patient results that raise the question - should I report this? This interactive discussion will attempt to address issues related to questionable patient results including those with (i) unknown interferences that might impact the accuracy of the results, (ii) low internal standard recovery, and (iii) potential carryover. The discussion will be led by three individuals currently overseeing clinical toxicology mass spectrometry testing. Examples of challenges they have faced and (occasionally) approaches they have found useful will be presented as a starting point for discussion.

Jennifer Van Eyk, PhD, is an international leader in the area of clinical proteomics and her lab has focused on developing technical pipelines for de novo discovery and larger scale quantitative mass spectrometry methods. This includes multiple reaction monitoring (MRM, also known as SRM) and most recently data independent acquisition. Dr. Van Eyk's laboratory is well known for the extreme technical quality of the data generated, rigorous quality control with tight %CV while applying these to key clinical questions. The aim is to maximize throughput and reproducibility in order to move targeted and robust discovery methods into large population healthy continuous assessment and clinical grade assays focusing on brain and cardiovascular diseases.

The throughput and reproducibility of LC-MS has facilitated the development of biologically important protein assays that are facilitating precision medicine adoption.

Mari DeMarco, PhD, DABCC, FCACB, is a Clinical Chemist at Providence Health Care, the Research Director of Providence Research, and a Clinical Associate Professor in Pathology and Laboratory Medicine at the University of British Columbia in Vancouver Canada. Dr. DeMarco completed her PhD in the Biomolecular Structure and Design program at the University of Washington, and a clinical chemistry fellowship at Washington University School of Medicine.

With a strong interest in bridging basic biomedical science, analytical chemistry and laboratory medicine, Dr. DeMarco’s research group focuses on building new biofluid tests for direct translation into patient care. A particular area of interest is advancing protein-based clinical diagnostics for neurodegenerative disorders, such as Alzheimer’s disease. The goal of this program of research is to ensure that these new tools make the challenging jump from research into healthcare.

Originally Presented at MSACL 2022.

Want to run a new test in your clinical lab that takes multiple days to prep, has a complicated (and costly) calibration scheme, and a detection approach so selective it could miss the analyte of interest? If that doesn’t sound appealing, you would be in the majority! While the analytical advantages of mass spectrometry resulted in it decisively displacing ligand binding methods as the gold standard approach for protein quantitation, making progress on the routine testing front has taken additional effort. Here we look at how re-evaluating the status quo in clinical proteomics has helped us take leaps forward and implement protein mass spectrometry to improve patient care.

Leroy "Lee" Edward Hood is an American biologist who has served on the faculties at the California Institute of Technology (Caltech) and the University of Washington. He is currently Professor and Chrief Strategy OFficer at the Institute for Systems Biology. Dr Hood has developed ground-breaking scientific instruments which made possible major advances in the biological sciences and the medical sciences. These include the first gas phase protein sequencer (1982), for determining the sequence of amino acids in a given protein; a DNA synthesizer (1983), to synthesize short sections of DNA; a peptide synthesizer (1984), to combine amino acids into longer peptides and short proteins; the first automated DNA sequencer (1986), to identify the order of nucleotides in DNA; ink-jet oligonucleotide technology for synthesizing DNA and nanostring technology for analyzing single molecules of DNA and RNA.

Dr Hood believes that a combination of big data and systems biology has the potential to revolutionize healthcare and create a proactive medical approach focused on maximizing the wellness of the individual. He coined the term "P4 medicine" in 2003.

The vision of this project is that we will develop the infrastructure to employ a data-driven approach to optimizing the health trajectory of individuals for body and brain. We have two large populations (5,000 and 10,000) that have validated this approach for body and brain health, respectively. These studies have led to us pioneering the science of wellness and prevention. This project will require the acquisition of key partners for execution, which will be delineated. We are approaching the Federal Government for funding, as we did for the first Human Genome Project. This project will lead to striking new knowledge about medicine, it will catalyze the initiation of start-up companies and it will catalyze a paradigm shift in healthcare from a disease orientation to a wellness and prevention orientation. This will catalyze the largest paradigm shift in medicine, ever.

Dr. Lee is a clinical pathology resident in the Department of Laboratory Medicine at Yale School of Medicine. He received his MD from the Albert Einstein College of Medicine and his PhD in Immunology from the University of Glasgow, where he conducted research in T cell receptor sequencing and mathematical modeling of T cell dynamics. His current research interests include developing computational approaches for analyzing high-throughput single-cell B cell and T cell repertoire profiling data and understanding the immunological mechanisms of alloimmunization to red blood cell antigens. He also involved in projects applying machine learning techniques to clinical laboratory data. He will be staying at Yale for his transfusion medicine fellowship and postdoctoral research fellowship.

Dr. Durant is an Assistant Professor of Laboratory Medicine and informatics researcher at the Yale School of Medicine. He is the medical Director of Chemical Pathology and Laboratory Information Technology (IT) at Yale-New Haven Hospital, and the Associate Director for the ACGME Chemical Pathology Fellowship. He conducts applied laboratory medicine research with a pragmatic focus on quality care initiatives, laboratory outcomes, statistics, machine learning, and artificial intelligence applications in the context of pathology and clinical medicine. His primary research interests are in clinical informatics and using novel data management technology to better derive insight into the quality and overall operations for laboratories and patient care. Ongoing projects involve the investigation of stream processing of interface data for the purposes of automated sample identification for subsequent biobanking. Machine learning related projects include the use of 'very deep' convolutional neural networks for automated classification of digital images acquired in the clinical laboratory.

We will be talking with Thomas Durant and Edward Lee about recent advances in machine learning (ML) for mass spectrometry (MS) data analysis. The primary focus will be the alignment of these two fields (ML and MS) and how this offers a promising synergy that can be used to optimize workflows, improve result quality, and enhance our understanding of high-dimensional datasets, as well as their inherent relationship with disease biology. We will also dig deeper to understand a basic overview of ML and an ML-based experiment. Overall, we will have a opportunity go through the fundamental principles of supervised ML, outline the steps that are classically involved in an ML-based experiment, and discuss the purpose of good ML practice in the context of a binary MS classification problem.

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My research focuses on developing multimodal chemical instrumentation from a chemometric perspective, improving high spatial resolution mass spectrometry imaging capabilities, and applying semi-targeted complex mixture analysis methodologies. I'm interested in the development of new chemical imaging instrumentation because I see an increasing need for imaging instruments that produce high quality data that can can be easily interpreted by clinicians and applied scientists. To that end, I am working to build multimodal instruments, develop experiment methodologies, and create data analysis pipelines that are able to produce higher-quality chemical information more rapidly and with fewer steps than existing imaging instruments and workflows.

Graphics are what grab attention at your poster, what people see when they skim your paper, and what they remember from your presentation. Although it is possible to create professional quality graphics using a variety of approaches and software, there are only a few that provide flexibility to be useful across all scientific disciplines. Many of these are expensive, are not available on all popular operating systems, or use proprietary file formats. In this interactive MSACL Early Career Network event, you will learn how to use free and open source graphics software, specifically Inkscape and GIMP, to produce high quality scientific graphics that meet scientific journal requirements. We will cover (1) importing and saving different graphic file formats; (2) recoloring, cropping, and layering raster graphics; (3) editing and annotating plots; (4) creation of simple scientific workflow diagrams and schematics, and (5) assorted software “tips and tricks” aimed at the demands of scientific graphics.

Daniel C. Liebler, Ph.D. is an internationally-recognized research leader in the fields of proteomics, cancer proteogenomics, chemical biology and toxicology. With over 30 years experience at the interface of analytical technology, chemical biology and disease research, Dr. Liebler led multidisciplinary programs at the University of Arizona and Vanderbilt University School of Medicine funded by the National Institutes of Health, industry and private philanthropy. At Vanderbilt, Dr. Liebler's team laid the groundwork for the integration of proteomic technologies into cancer therapeutics and diagnostics. Dr. Liebler left Vanderbilt in 2016 to launch Protypia, which provides drug target and system analysis to leading pharmaceutical and biotechnology companies in therapeutic development.

In this discussion, Dr. Dan Liebler, President of Protypia, Inc., will highlight his research on MS proteotyping of human cancers in oncology therapeutic development using mass spectrometry.

Quantitative Analysis of the TIGIT/DNAM1 and PD-1/PD-L1 Axes in Primary Non-Small Cell Lung Cancers (NSCLC) and Lymph Node Metastases

Matt Westfall1, Salisha Hill1, Ryan D. Morrison1, Daniel C. Liebler1*, and Alexander Haragan2*

1 Protypia, Inc, Nashville, TN, USA
2 Royal Liverpool University Hospital, Department of Pathology, Liverpool, UK

New therapies targeting immune checkpoint (IC) proteins have revolutionized oncology therapeutics, but heterogeneous expression of IC proteins between individuals and tumor types complicates development of cancer immunotherapies. Although typically framed in the context of companion diagnostics, the need to reliably quantify drug targets is critical in the preclinical and clinical development of new drugs, especially for the design and interpretation of clinical trials. Quantification of drug target status can inform interpretation of target abundance and outcomes. Targeted mass spectrometry (MS) uniquely enables sensitive and precise measurement of IC proteins, coregulators and immune cell markers. MS measurements can be performed in formalin-fixed, paraffin-embedded (FFPE) samples and are multiplexed, thereby enabling simultaneous analysis of multiple IC proteins, immune cell markers, and related pathway markers in the same sample.

New immunotherapeutics targeting the IC protein TIGIT are in clinical development with PD-1/PD-L1 inhibitors for solid tumor indications, but without reliable TIGIT protein biomarkers to guide trial design and interpretation. We used targeted mass spectrometry (MS) to precisely quantify TIGIT, DNAM1, PVR, PVRL2, PD-1, PD-L1, and PD-L2 in 97 primary non-small cell lung cancers (NSCLC) and matched tumor draining lymph node metastases (TDLN). Only 56% of NSCLC cases expressed TIGIT, which was quantifiable almost exclusively in TDLN. TIGIT, DNAM1 and PVR abundance varied over approximately 25-fold and they were co-expressed only in some tumors. PD-1/PD-L1 axis proteins were quantified in virtually all samples over an even broader abundance range than TIGIT/DNAM1 axis proteins. Combined quantitation of TIGIT/DNAM1 and PD-1/PD-L1 axis proteins may indicate the sufficiency of the target system to respond to combined anti-TIGIT anti-PD-1/PD-L1 therapeutics.

Learn More
• Protypia, Inc.
• [email protected]

Publications of Interest
• New publication: Available soon
• Analysis of Immune Checkpoint Drug Targets and Tumor Proteotypes in Non-Small Cell Lung Cancer

Learn More About Thermo Scientific Mass Spectrometry Solutions
• Technical Note: Plasma Protein Profiling
• Biologist’s Guide to Modern Techniques in Quantitative Proteomics
• Thermo Scientific Quantitative Proteomics
• Product Page: Thermo Scientific Orbitrap Mass Spectrometry
• Join the Clinical Research Community!

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

Amanda Hummon earned her A.B. in chemistry at Cornell University in 1999 with honors. She completed her graduate studies in analytical chemistry at the University of Illinois, Urbana-Champaign, in the laboratory of Prof. Jonathan V. Sweedler. Her thesis work focused on the development of mass spectrometric and bioinformatic strategies to predict and identify neuropeptides. She received her Ph.D. in 2004. Amanda participated in the annotation of the newly sequenced honey bee genome as a post-doctoral fellow in the laboratories of Prof. Gene E. Robinson and Prof. Sandra L. Rodriguez-Zas at the University of Illinois from 2004-2005. The focus of her research was constructing a methodology to utilize detected gene products to decipher an unannotated genome.

From 2005-2009, Amanda was a Sallie Rosen Kaplen Post-Doctoral Fellow at the National Cancer Institute in the laboratory of Dr. Thomas Ried. During her time in the Ried lab, she utilized RNA interference screening techniques followed by microarray analysis to elucidate genes that regulate the viability of colorectal cancer cells.

In 2009, she began her independent career as the Walther Cancer Assistant Professor in the Department of Chemistry and Biochemistry at the University of Notre Dame and was promoted to the Charles L. Huisking Associate Professor in 2015. She has been recognized with a NSF CAREER award (2014), a Society for Analytical Chemists of Pittsburgh Starter Grant Award (2011), and a Rising Star Award from the American Chemical Society (2016). Amanda moved her research program to the Department of Chemistry and Biochemistry at The Ohio State University in January 2018 and was awarded the Presidential Early Career Award for Scientists and Engineers (PECASE) in 2019. In 2020, she was awarded a Fulbright Scholar Award and will spend a semester as a Visiting Professor at the Maastricht MultiModal Molecular Imaging Institute at Maastricht University in the Netherlands.

Emily Sekera earned her B.S. in chemistry at Rochester Institute of Technology in 2015. She then completed her graduate studies in analytical chemistry at University at Buffalo, in the laboratory of Prof. Troy D. Wood studying disease states using -omics based techniques and high resolution mass spectrometry. She is currently a postdoctoral researcher working under Dr. Amanda B. Hummon investigating at the intersection of cancer biology and analytical chemistry.

Fernando Tobias is currently a postdoctoral scholar in the Hummon Research Group. His current research focuses on several projects involving lipidomic, proteomic, glycomic, and MS imaging studies on the effects of chemotherapeutic in colorectal cancer. He obtained his Ph.D. degree working in the Cologna Research Group at the University of Illinois at Chicago conducting. He conducted lipidomic studies by LC-MS and MS imaging to elucidate biochemical changes in several neurodegenerative diseases.

Nicole Beller received her B.S. in Biochemistry from Wayne State University in 2018. That same year she joined the Ohio State University where she earned her M.S. in Chemistry. Nicole is currently a fourth year graduate student working under the guidance of Dr. Amanda Hummon. Nicole's current research focuses on bottom-up proteomic analysis of pulse-chase SILAC labeled three-dimensional multicellular spheroids.

The Hummon lab studies colorectal cancer by mass spectrometry. In this session, they will describe on going work in the lab to examine molecular distributions in primary colon tumors and 3D cell culture models by mass spectrometry.

Chris Shuford, Ph.D., is Associate Vice President and Technical Director for research and development at Laboratory Corporation of America in Burlington, North Carolina. Chris received his B.S. in Chemistry & Physics at Longwood University and obtained his Ph.D. in Bioanalytical Chemistry from North Carolina State University under the tutelage of Professor David Muddiman, where his research focused on applications of nano-flow chromatography for multiplexed peptide quantification using protein cleavage coupled with isotope dilution mass spectrometry (PC-IDMS). In 2012, Chris joined LabCorp’s research and development team where his efforts have focused on development of high-flow chromatographic methods (>1 mL/min) for multiplexed and single protein assays for clinical diagnostics.

The Michael S. Bereman Award for Innovative Clinical Proteomics recognizes recent innovations in clinical proteomics from early- and mid-career scientists. The awardee is honored at the annual meeting of MSACL, where they will be invited to give a lecture. Nominees will be reviewed annually by a rolling award committee.

The 2021 Awardee of the Michael S. Bereman Award for Innovative Clinical Proteomics is Christopher Shuford, Ph.D. for groundbreaking work on calibration and sensitivity.

Dr. Shuford will accept this award with a presentation : Breakthrough or Bust? Thyroglobulin Measurement by LC-MS/MS.

Proteolysis-aided workflows can effectively eliminate autoantibody complexes and allow for interference-free protein quantification by mass spectrometry with surrogate peptides. Owing to the prevalence of autoantibodies in thyroid cancer patients and associated interference among immunoassay platforms, the purported poster child for mass spectrometry-based protein measurements has been Thyroglobulin (Tg). However, many other factors contribute to the utility of measurement procedures for tumor makers such as Tg, including throughput, ruggedness, trueness, and sensitivity. This presentation will focus on these limitations – real or perceived – as it pertains to application of mass spectrometry measurements for Tg.

This year's Michael S. Bereman Award for Innovative Clinical Proteomics is proudly sponsored by Agilent with an MSACL Open Educational Grant Fund donation of $10,000. The MSACL Open Educational Grant program provides awards to early and mid-career community members to fund conference and short course attendance.

I grew up in San Diego, CA and Arlington, VA. I attended Santa Clara University where I received a B.S. in chemistry. I joined the MD PhD program at UCSD in 2007 and completed a PhD in Biomedical Sciences with a specialization in Anthropogeny. I continued at UCSD for residency training in internal medicine and completed a year as chief resident in 2019-2020. In June of 2020, I started my Endocrinology Fellowship. I plan to pursue a career in academic medicine that combines clinical endocrinology with outcomes research in Vitamin D metabolism.

Using the MrOS database and mass spectrometry, we demonstrate that 1,25(OH)2 Vitamin D, 24,25(OH)2 Vitamin D, and their associated metabolite ratios are associated with gut microbial diversity in older community dwelling men. Notably, 25(OH) Vitamin D levels did not show this association. We also demonstrate that firmicutes which frequently produce butyrate are associated with higher levels of activated Vitamin D. Overall, the project demonstrates that quantifying Vitamin D metabolites may provide more clinically relevant measures of Vitamin D metabolism.

Vitamin D metabolites and the gut microbiome in older men

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.

I am a researcher in the Thomas lab working on identifying PARP inhibitor-induced autophagosome-associated proteins to determine the means of resistance during PARPi treatment in high-grade serous ovarian cancers.

I am a PhD student in the Microbiology, Immunology, and Cancer Biology (MICaB) program at the University of Minnesota. The goal of my research is to study the molecular mechanisms of PARP inhibition in HGSOCs containing BRCA1/2 mutations and comparing these responses to wild-type BRCA1/2 ovarian cancers. By studying the differential responses that HGSOCs have on PARP inhibition at the level of the proteome, we can ascertain which type of HGSOCs would benefit most with PARP inhibition with minimal risk of relapse. Finally, studying changes in the proteome upon PARP inhibition will reveal other sets of genes besides BRCA1/2 that are involved in homologous recombination dysfunction.

I received my Ph.D. in Biology from Kongju National University in South Korea. During my Ph.D. program, I studied in the Medical Proteomic Research Center at the Korea Research Institute of Bioscience and Biotechnology (KRIBB). In Medical Proteomics Research Center, KRIBB, I performed proteome-based approaches for mining the molecular targets and susceptibility markers of various diseases such as cancers, senescence, neurodegenerative disorder, leukemia, psoriasis and rheumatism and investigated the molecular mechanisms for deeper understanding of diseases. After I received my Ph.D., I obtained as position of a Postdoctoral Researcher in the Division of Molecular and Cellular Biology at the Hormel Institute, University of Minnesota. At the Hormel Institute, I was a proteomics and mass spectrometry specialist, and I have worked on studying the analysis of protein modification and proteome quantification for drug discovery and molecular targeting in a variety of cancers for medical research as well as on structural analysis of protein complexes with cross-linking mass spectrometry. In addition, I have studied the epigenetic modifications to understand the regulatory mechanism of epigenetic marks in the chromatin and cancer biology fields. Currently, I am a Researcher 5 in Dr. Stefani Thomas Lab at University of Minnesota. My research is focused on ovarian cancer biology using discovery and targeted mass spectrometry-based proteomics.

I am a graduate student at the University of Minnesota in the department of Biochemistry, Molecular Biology, and Biophysics under the mentorship of Dr. Stefani Thomas. My initial project is focused on a mass-spectrometry based approach to evaluate the utility of HDAC and PARP inhibitors in ovarian cancer treatment with an emphasis on determining how epigenetic modifications confer treatment sensitivity in the context of homologous recombination proficiency or deficiency. Overall, I believe my current research plan will support the development of biomedical breakthroughs improving treatment opportunities for patients with this lethal gynecological malignancy.

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.

The Thomas lab applies discovery and targeted mass spectrometry-based proteomics methods to elucidate the biology of ovarian cancer. The common theme among the current research projects in the lab is the determination of protein-based signatures of sensitivity to ovarian cancer treatment. We are excited to share summaries of the following research projects during the Lab Showcase: "Proteome-level determinants of response to PARP inhibitor treatment in ovarian cancer," "HDAC inhibitor sensitization of high-grade serous ovarian cancer cells to PARP inhibitor treatment," "Development and validation of targeted mass spectrometry assays to detect ovarian cancer protein biomarkers," and "Longitudinal proteome alterations in high-grade serous ovarian cancer patient-derived xenografts."

Maria Fedorova studied Biochemistry at Saint-Petersburg State University, Russia and obtained her PhD at Faculty of Chemistry and Mineralogy, Leipzig University, Germany. She worked as a group leader at the Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, at the University of Leipzig. In August 2021 Maria group moved to the Center for Membrane Biochemistry and Lipid Research, University Hospital and Faculty of Medicine Carl Gustav Carus at TU Dresden.

Her research is focused on development and implementation of lipidomics and bioinformatics solutions to address complexity and plasticity of lipid metabolism in variety of biological systems. In particular, Maria aims for a deeper understanding of pathophysiology of metabolic and inflammatory disorders, including obesity, insulin resistance, type II diabetes and cardiovascular disorders. Another focus of Maria’s research is the development and application of mass spectrometry-based methods for the analysis of the epilipidome, which is a subset of the lipidome formed by lipid modifications aiming to increase the regulatory capacity of biological systems. Her group examines the role of modified lipids specifically in signalling processes, regulating physiological and pathological events at the cellular and organismal levels.

During her PhD at the University of Leipzig, Michele characterized alterations in milk proteome and lipidome upon processing and seasonal changes by mass spectrometry. Now she is starting her PostDoc in Fedorova group. Using various analytical techniques including mass spectrometry, she wants to understand the role of lipid metabolisms in ferroptotic cell death.

I started my research career as a chemist in the lab of Prof Oleg Shadyro at the Belarusian State University in Minsk, where I have been working on investigating new routes of free-radical degradation of biomolecules, paying special attention to lipids. Being now a Master's student in the Dr Maria Fedorova group, I pursue my path in lipid research and focus on the in-depth characterization of the lipid peroxidation process in obesity and in vivo models of ferroptosis by means of LC-MS/MS-based lipidomics and epilipidomics.

Zhixu Ni is a postdoc researcher at the Fedorova research group. Originally coming from analytical chemistry background (MSc, Leipzig University, Germany), Zhixu Ni transitioned to data analysis and software development during his PhD study on MS based lipidomics. Zhixu Ni’s main research interest is the dysregulation of enzymatically and non-enzymatically modified lipidome and metabolome in metabolic disorders with a strong focus on the high throughput LC-MS lipidomics data analysis and integration of multi-omics data. He is the main developer of several open source lipidomics tools including LipidHunter2, LPPtiger, LipidCircos, and LipidLynxX.

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.

Presentations include:
Maria Fedorova, “Lipid Metabolism: Analysis and Integration”: Maria will describe the research aims of her group focusing on understanding plasticity of lipid metabolism in physiological and pathological conditions. She will outline the work her group did on development and implementation of LC-MS and bioinformatics tools to describe human reference lipidomes, to map lipid alteration as well as concept of epilipidomics regulations in biological systems.

Michele Wölk, “LC-MS solutions to access remodelling of lipid metabolism in ferroptotic cell death”: Michele will present LC-MS methods used in our group to map lipidome plasticity under various stress conditions. In particular, she will introduce her project on time-resolved mapping of lipidome plasticity in ferroptotic cell death.

Palina Nepachlovich, “Hunting for oxidized lipids in biological samples”: Palina will describe MS based methods developed in our lab to identify and quantify diversity of oxidized lipids in complex biological samples. She will show an example of epilipidome profiling in human obesity.

Zhixu Ni, “Bioinformatics tools for lipidomics and epilipidomics”: Zhixu will present a bioinformatics pipeline he developed over last years to support high-throughput processing of LC-MS datasets. He will provide brief overview of software (LipidHunter, LPPtiger, LipidLynxX) used for identification of native and modified lipids, as well as solutions for large data integration.

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.

Boone M. Prentice received his B.S. degree in Chemistry with Honors and Distinction from Longwood University (Farmville, VA) in 2008 with minors in Biology and Mathematics. At Longwood, he conducted electroanalytical research focused on developing biosensors under the supervision of Professor Melissa C. Rhoten. He attended graduate school at Purdue University (West Lafayette, IN) under the mentorship of Professor Scott A. McLuckey and received a Ph.D. in Chemistry in 2013. His Ph.D. research focused on ion trap mass spectrometry (MS) instrumentation development as well as gas-phase ion/ion and ion/molecule reactions involving biopolymers. Boone then worked as a postdoctoral research fellow in Professor Richard Caprioli’s laboratory at Vanderbilt University (Nashville, TN) where he studied matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) instrumentation and applications. Specifically, he worked on Fourier transform ion cyclotron resonance (FT-ICR) and time-of-flight (TOF) MS systems and applied IMS to the study of diabetes, cancer, drug delivery, and infectious disease. Boone joined the Department of Chemistry at the University of Florida as an Assistant Professor in the fall of 2018. His research focuses on developing next-generation bioanalytical mass spectrometry to better understand the molecular basis of health and disease.

Imaging mass spectrometry is a powerful technology that enables the visualization of biochemical processes directly in tissues by combining the molecular specificity of mass spectrometry with the spatial fidelity of microscopic imaging. Especially when studying lipids, there are many isobaric and isomeric molecules that complicate spectral analysis, with each isoform having a potentially unique cellular function. While traditional tandem mass spectrometry (MS/MS) approaches can distinguish amongst these compounds in select instances, this is often not the case. Our group is developing gas-phase reactions that afford the ability to provide improved molecular specificity without manipulating the sample. These gas-phase transformations are fast, efficient, and specific, making them ideally suited for implementation into imaging mass spectrometry workflows to enable novel structural identification and separation based on chemical reactivity. While traditional analytical analyses oftentimes simply use the mass spectrometer as a detector of molecular mass, we instead use the mass spectrometer as a reaction vessel to perform unique gas-phase transformations to provide unparalleled levels of chemical resolution.

Steve graduated from Imperial College of Science and Technology (Imperial College London) with a joint honours degree in Chemistry and Biochemistry before completing a PhD in Biochemistry at the University of Cambridge. Subsequently, he was an Elmore Medical Research Fellow in the Department of Biochemistry in Cambridge University.
His research team in University College Dublin (UCD; www.ucd.ie) is currently developing multiplexed protein biomarker measurements using multiple reaction monitoring mass spectrometry to support the translation of novel multiplexed blood protein biomarkers to clinical diagnostic tests. He founded the UCD spin out company, Atturos (www.Atturos.com) in late 2016 and was awarded UCD's Innovator of the Year in 2018. Atturos aims to develop and deliver advanced diagnostic tests to support better decision making for better patient outcomes.

In 2017 he was the lead organiser of the 16th Human Proteome Organisation (HUPO) World Congress, which was held in Dublin and included a Gala Dinner at which former US Vice-President Joe Biden was guest speaker.

Steve is currently Professor of Proteomics and Senior Fellow, UCD Conway Institute and past President of HUPO (www.hupo.org)

The challenges of developing new protein biomarker tests and delivering them to use for patient benefit will be presented. In the context of a recently initiated EU IMI consortium, particular emphasis will be placed on analytical validation of new multiplexed protein biomarker assays and their use in multi-centre evaluation and validation studies to support the development of new tests in psoriatic disease. Patient engagement and use of patient centric sampling devices for effective test delivery will be introduced.

B.S. in Analytical Chemistry, Masaryk University, Brno, Czech Republic.
Ph.D. in Bioanalytical Chemistry, Brigham Young University, Provo, Utah.
Nearly three decades of HPLC, CE, CE-MS, and LC-MSMS method development and validation experience in academic, pharmaceutical, and clinical laboratory environments.

The popularity of LC-MS/MS-based methods for clinical testing continues to rise. However, despite their superior analytical specificity, these methods may still suffer from interference affecting method accuracy and precision, and hence negatively impacting patient care.

The following topics and issues will be addressed:

• Sources of guidelines for interference testing in method development/validation and routine testing (CLSI, CAP, SWGTOX)

• What is analytical interference and where does it come from?

• How do we define acceptable interference levels?

• How do we test for interference in LC-MS/MS?

• When do we test for interference?

• The use of internal standard in mitigating interference

• How do we monitor for interference?

Examples of interference issues in various methods and how they were resolved will be shown throughout the entire session.

Charlotte Teunissen’s drive is to improve care of patients with neurological diseases by developing body fluid biomarkers for diagnosis, stratification, prognosis and monitoring treatment responses. Studies of her research group span the entire spectrum of biomarker development, starting with biomarker identification, often by –omics methods, followed by biomarker assay development and analytical validation, and lastly, extensive clinical validation and implementation of novel biomarkers in clinical practice.
She has extensive expertise with assay development on state of the art technologies, such as mass spectrometry and antibody-based arrays for biomarker discovery, ultrasensitive immunoassays, and in in implementation of vitro diagnostic technologies for clinical routine lab analysis. She is responsible for the large well-characterised biobank of the Amsterdam Dementia cohort, containing >5200 paired CSF and serum samples of individuals visiting the memory clinical of the Alzheimer Center Amsterdam (a.o. controls, patients with Alzheimer, Frontotemporal, Lewy Bodies).To ensure the quality of the biosamples, the group studies pre-analytical effects, which are key to implementation. Charlotte is leading several collaborative international biomarker networks, such as the Society for Neurochemistry and routine CSF analysis and the Alzheimer Association-Global Biomarker Standardization and Blood Based Biomarkers consortia. She is the coordinator of the Marie Curie MIRIADE project, aiming to train 15 novel researchers into innovative strategies to develop dementia biomarkers (10 academic centers + 10 non-academic centers), and the JPND bPRIDE project, that aims to develop targeted blood based biomarker panels for early differential diagnoses of specific dementias and is a collaborative project between 7 European and 1 Australian centers.

The development of disease-modifying therapies against neurological diseases such as Alzheimer’s disease (AD) requires ?biomarkers reflecting the diverse pathological pathways. Cerebrospinal fluid (CSF) is a widely used matrix to identify and develop novel biomarkers for dementias. It reflects the ante-mortem biochemical alterations occurring in the brain, whereby it can provide the diverse pathobiological fingerprint of different dementias.

Our strategy is to employ array based proteomics to identify novel biomarkers, considering the high- throughput of the discovery process and the versatility to develop smaller panels using immunoassay technologies. Here we measured 665 proteins in 797 cerebrospinal fluid (CSF) samples from patients with mild cognitive impairment with abnormal amyloid (MCI(A?+): n=50), AD-dementia (n=230), non- AD dementias (n=322) and cognitively unimpaired controls (n=195) using proximity ligation-based immunoassays. Nested linear models identified >100 CSF proteins dysregulated in MCI(A?+) or AD compared to controls, as well as between AD and non-AD dementias. Distinct CSF profiles associated to different biological processes were identified along the symptomatic AD continuum. Proteins dysregulated in MCI(A?+) were primarily related to oxidative stress and energy metabolism, while those specifically dysregulated in AD dementia were related to cell remodeling, vascular function and immune system. Classification modeling unveiled different and translatable biomarker panels that discriminate specific clinical groups with high accuracies (AUCs>0.85). The proteins and panels identified in this study may provide novel pathophysiological targets and biomarker tools covering the heterogeneous nature of AD.

Dr Catarina Horro Pita possesses a BSc in Chemistry and Environmental Chemistry and a PhD in Synthetic Organic Chemistry. After concluding her PhD, she initiated her professional career as a Synthetic Chemist, prior to moving into Analytical Chemistry and Bioanalysis. She has been working in the field of Bioanalysis for 15 years, holding both scientific and managerial positions. Catarina currently works as a PK Project Manager at A4P Consulting. During her career, she has gained significant experience in the development, validation and management of LC-MS/MS assays for the analysis of both xenobiotic compounds and small molecule biomarkers. In addition, due to her expertise in Organic Chemistry, she also has an extensive knowledge of derivatization techniques for the improvement of LC-MS/MS methods.

Derivatization is a simple chemical reaction, often used in Bioanalysis to transform a “not so ideal” candidate for LC-MS/MS analysis into a molecule with enhanced phys-chem properties, which leads to improved detectability of the compound.

The objective of this presentation is to describe some of the most commonly used derivatization procedures and explain the benefits and drawbacks of these techniques.

When performing analysis by LC-MS/MS, the ideal analyte should be chemically stable and have moderate retention on the LC column. The molecule should also be ionisable under ESI or APCI conditions and have an efficient fragmentation upon collision. In addition, the target compound should be selectively separated from other xenobiotics or endogenous products present in the extracted matrix. When the analyte does not meet all of the above criteria, derivatisation can be used to modify its chemical structure and address these issues.

A range of derivatization processes will be reviewed, indicating their bioanalytical applications and type of chemical reactions involved. In addition, examples of derivatization reagents and reaction conditions will be described.

Although the application of derivatization procedures can lead to an improved bioanalytical performance, these techniques also present a range of disadvantages, such as extended method development times, lengthy extraction procedures and increased method variability.

Despite all the recent technological improvements in the field of Bioanalysis, derivatization remains a very powerful tool to overcome problems associated with analyte instability, poor chromatographic performance, inadequate analyte ionization or unacceptable method selectivity. However, the application of derivatization procedures can often lead to an increase in assay complexity and may reduce method robustness. Therefore, both the advantages and disadvantages of these procedures should always be considered before their application to a bioanalytical method.

Ivayla Roberts is a doctoral researcher at the University of Liverpool in Prof. Kell system biology group. Originally coming from computer science background (MSc, Montpellier France) Iva transitioned to molecular biology research via a Translational Molecular Medicine MRes (Manchester, UK).
Iva’s research interests are metabolomics, mass-spectrometry, and the application of statistical and machine learning computational approaches to metabolomics.
Iva’s PhD is focused on metabolomics in COVID-19.

The diagnosis of COVID-19 is normally based on the qualitative detection of viral nucleic acid sequences. Properties of the host response are not measured but are key in determining outcome. Although metabolic profiles are well suited to capture host state, most metabolomics studies are either underpowered, measure only a restricted subset of metabolites (‘targeted metabolomics’), compare infected individuals against uninfected control cohorts that are not suitably matched, or do not provide a compact predictive model.

We here provide a well-powered, untargeted metabolomics assessment of 120 COVID-19 patient samples acquired at hospital admission. The study aims to predict patient’s infection severity (i.e. mild or severe) and potential outcome (i.e. discharged or deceased).

High resolution untargeted LC-MS/MS analysis was performed on patient serum using both positive and negative ionization. A subset of 20 intermediary metabolites predictive of severity or outcome were selected based on univariate statistical significance and a multiple predictor Bayesian logistic regression model. The predictors were selected for their relevant biological function and include cytosine and ureidopropionic acid (reflecting viral load), kynurenine (reflecting host inflammatory response), and multiple short chain acylcarnitines (energy metabolism) among others.

Currently, this approach predicts outcome and severity with a Monte Carlo cross validated area under the ROC curve of 0.792 (SD 0.09) and 0.793 (SD 0.08), respectively. A blind validation study on additional 90 patients predicted outcome and severity at ROC_AUC of 0.83 (CI 0.74 – 0.91) and 0.76 (CI 0.67 – 0.86). Prognostic tests based on the markers discussed in this paper could allow improvement in the planning of COVID-19 patient treatment.

Part 1: Importance of automated LC-MS/MS in a high robotized Central Laboratory: our opinion and experience at CDI, Milan, IT
Dr. Fulvio Ferrara, CDI Milan, IT

Part 2: Highway to automated mass spectrometry: from traditional LC-MS/MS to high troughput diagnostic solution
Prof. Gardana, Milan University, IT

Part 3: New method development in Mass Spec and expansion in Dx routine
Dr Giacomo Visconti, CDI Milan, IT

Part 4: MS Spectrometry and genetics/epigenetics synergic perspective: a new challenge to discover the passage to the “omics-land”
Dr.ssa Lucy Costantino, CDI Milan, IT

Serge Rudaz is Associate Professor at the University of Geneva where he leads the biomedical and metabolomics analysis (BMA) group. He's President of the Swiss Metabolomics Society (SMS), vice-president of the Competence Center in Chemical and Toxicological Analysis (ccCTA) and member of the management Board of the Swiss Centre for Applied Human Toxicology (SCAHT) Foundation. Serge Rudaz contributed to the field of analytical sciences with diverse activities, including invited lectures and invited/visiting professorships at various Universities; Lyon (France), Pavia (Italy), Guanzhou (China).

He is interested in steroids analysis, metabolomics, (UHP)LC and CE coupled to MS, advances in sample preparation, analysis of pharmaceuticals and counterfeits medicines, biological matrices, clinical and preclinical studies, including metabolism and toxicological analysis. He is a (co)author of over 10 book chapters and more than 320 peer-reviewed papers, with an H-index (Scopus) of 57. He was chair/co-chair of several national or international congress, such as Chimiométrie 2015, SEP 2017 and MSB 2020.

Web: https://epgl.unige.ch/labs/fanal/analyses-biomedicales

Historical compounds of interest are pharmaceutical substances, chiral products, and exogenous analytes. For several years, a major focus has been placed on the implementation of various strategy allowing the investigation of endogenous metabolites, including an extended steroid profiles (i.e. “steroidomics”). For that purpose, MS detection is generally used to offer improved the steroidome coverage. This has led to the development of various methodologies. Among them, an automated steroids annotation using a dedicated dynamic database involving retention time prediction from state-of-the-art in silico models was proposed. Numerous results were obtained using this steroidomics workflow which have provided valuable information for the early detection and diagnosis of various diseases and chemical exposures, whether it is to analyze data collected from biological samples such as plasma, seminal fluids, in vitro cell models, toxicological analysis or clinical studies. Following the exploratory step that can be achieved with the extended profile, the measurement of a selected sets of steroids using LC–MS in plasma could be now relatively rapidly achieved. Hence, the quantification of a limited number of steroid compound that are relevant for clinical, toxicological or anti-doping purposes could be done thanks to the internal calibration methodology. This targeted approach allows an absolute steroid quantification, which is crucial for a better understanding, diagnosis, prognosis and treatment of many endocrine alterations.

Jo Adaway is a Consultant Clinical Scientist at Manchester University NHS Foundation Trust. She is interested in developing LC-MS/MS assays for small molecules for endocrinology and neuroendocrine tumour applications and has recently branched out into protein quantification. She was awarded her PhD on Proteomic analysis of stem cell commitment in 2005 from the University of Manchester. She is Associate Editor for Annals of Clinical Biochemistry and honorary senior lecturer at the University of Manchester, where she lectures on chromatography, mass spectrometry and endocrinology.

You’ve successfully purchased a mass spectrometer for your clinical lab – what on earth do you do now? In this session, we will discuss the practicalities of what to do next, from training your staff and developing your first method, to integrating the technology into your lab. We will focus on basics that are really important to successfully running a mass spec service but which may not be included in other training programmes, including how to choose solvents, useful peripheral equipment and sources of information and support.

Steph graduated from the University of Lincoln, UK with a BSc (Hons) Forensic Science. She has worked at the LGC Fordham site since 2013 and is working as a Senior Scientist, in a Technical Specialist role. Her role includes method development of LC-MS/MS methods, training and mentoring others through method development, and instrument troubleshooting/maintenance. Steph is also a member of the Chromatographic Society. Outside of work Steph’s main passions are guinea-pigs and mountain biking.

When analysing patient samples the concentration of the analyte measured should mirror the concentration during sample collection; therefore consideration should be given to the pre analytical conditions of the samples. One such consideration in multi-analyte studies is the potential for interconversion between analytes, which can compromise this quantification, leading to potential overestimation of one analyte and underestimation of another. In this session the root causes of interconversion shall be discussed, from the reversible hydrolysis of lactones e.g. statin drugs to cleavage of ester bonds by esterases. We will be examining the entire life-cycle of a patient sample to allow identification of problem areas in a methodology. We shall examine how to create a robust and accurate method with particular focus on stabilisation protocols and practicalities for the clinical laboratory. How to calculate levels of interconversion shall be demonstrated and the ability to assess impact upon data discussed.

Associate Professor Emma Schymanski is head of the Environmental Cheminformatics (ECI) group at the Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg. In 2018 she received a Luxembourg National Research Fund (FNR) ATTRACT Fellowship to establish her group in Luxembourg, following a 6 year postdoc at Eawag, the Swiss Federal Institute of Aquatic Science and Technology and a PhD at the Helmholtz Centre for Environmental Research (UFZ) in Leipzig, Germany. Before undertaking her PhD, she worked as a consulting environmental engineer in Perth, Australia. She has over 80 publications and a book, and is involved in many collaborative software efforts. Her research combines cheminformatics and computational (high resolution) mass spectrometry approaches to elucidate the unknowns in complex samples, primarily with non-target screening, and relating these to environmental causes of disease. An advocate for open science, she is involved in and organizes several European and worldwide activities to improve the exchange of data, information and ideas between scientists to push progress in this field, including NORMAN Network activities (e.g. NORMAN-SLE https://www.norman-network.com/nds/SLE/), MassBank (https://massbank.eu/MassBank/), MetFrag (https://msbi.ipb-halle.de/MetFrag/) and PubChemLite for Exposomics (https://doi.org/10.5281/zenodo.4432123).

The multitude of chemicals to which we are exposed is ever increasing, with over 110 million chemicals in the largest open chemical databases, over 350,000 in global use inventories, and over 70,000 estimated to be in household use alone. Detectable molecules in exposomics can be captured using non-target high resolution mass spectrometry (HRMS), which provides a “snapshot” of all chemicals present in a sample and allows for retrospective data analysis through digital archiving. However, there is no “one size fits all” data or analytical method, and scientists cannot yet identify most of the tens of thousands of features in each sample, let alone associate them with health or disease, leading to critical bottlenecks in identification and data interpretation and thus clinical outcomes. Despite the size of the open chemicals databases, critical knowledge gaps still exist in them; environmental transformation products and metabolites forming a key part of these missing puzzle pieces. Defining the chemical space to search, the analytical methods to use, prioritizing efforts to find significant environmental chemicals, metabolites or biomarkers as well as filling the knowledge gaps are the key to transition non-target HRMS into routine applications such as the clinic. This involves reconciling complex samples with expert knowledge and careful validation in an automatable and reliable manner. This talk will cover European and worldwide community initiatives and resources to help connect environmental expert knowledge and observations towards generating clinical outcomes. Various open cheminformatics and computational mass spectrometry approaches including patRoon, Shinyscreen, MassBank, MetFrag and PubChemLite for Exposomics will be covered. Additionally, possibilities for disease-specific metadata retrieval to connect chemical observations with potential disease associations will be demonstrated, alongside how FAIRifying Transformation information in the NORMAN Suspect List Exchange and PubChem helps close database gaps and create new possibilities for dynamic suspect screening efforts. This talk will show how interdisciplinary efforts and data sharing can facilitate research in environmental sciences, metabolomics, exposomics and beyond, towards a not-to-distant furture where non-target HRMS could be used in the clinic. The very many contributors to these collaborative efforts will be acknowledged throughout the talk.

Introduction.
Breast cancer is a very serious problem worldwide. Breast cancer is accompanied by the metastatic lesion of the lymph nodes in 40-50% of cases. Currently, histology analysis is used during the surgery in order to verify the occurrence of metastasis in lymph nodes. Faster and more specific methods are urgently required for the identification of metastatic lesion in lymph nodes directly during the surgery.

Methods.
We present the new method based on the internal extractive electrospray ionization (iEESI) combined with high-resolution mass spectrometry analysis. It allows us to perform rapid (less than 5 minutes) molecular profiling of breast tissue and signal lymph nodes tissue with regard to presence of metastatic lesion. The distinctive feature of proposed ionization method allows the direct extraction of whole-volume biopsy tissue samples rather than just their surface. It makes it possible to substantially increase the sensitivity, accuracy and reproducibility of analysis compared with existing analogues. New analytical advancements were implemented which allow the sequential ionization of lipids, metabolites and proteins from the same single biopsy tissue sample.

Results.
Rapid diagnosis of the metastatic lesion of the signal lymph nodes upon invasive breast cancer on the biopsy tissue samples was performed in 50 patients. The signals of differential metabolites associated with the occurrence of lymphatic lesion were identified using high-resolution tandem MS analysis and reference LC-MS analysis. Bioinformatics approaches were developed in order to study the complex relationships between the identified metabolites. This led us to create of a molecular model of metastasis process.

Conclusions.
A minimally invasive method has been developed for the diagnosis of metastatic lesions of signal lymph nodes in invasive breast cancer based on direct mass spectrometric analysis. A mechanism for metastasis to the signal lymph nodes in breast cancer was proposed.
Novel Aspect.
A new method for mass spectrometric analysis of biopsy samples based on internal extractive electrospray ionization has been developed.

Acknowledgments.
The work was supported by Russian Foundation for Basic Research (Agreement ? 19-515-5502119).

Angela is interested in the development of highly sensitivity, high throughput, well validated mass spectrometry assays for steroid analysis. Application of these assays to answer important clinical questions is critical to her research. She feels the truly translational aspect of the work conducted at the Steroid Metabolome Analysis Core (SMAC) means the work is both analytically enjoyable and socially beneficial.
Angela has an analytical chemistry master’s degree from Swansea University (2005). In 2009 she received her PhD from Swansea University investigating steroid metabolism in the human endometrium using mass spectrometry. This was followed by post-doctoral work at the University of Birmingham working for Prof Wiebke Arlt, which cumulated in setting up the SMAC facility in 2016. The SMAC lab now conducts steroid research from wet lab based projects to clinical trials.

Translation of a test from the initial hypothesis to routine clinical use is a long and challenging journey. In this session I will discuss my experiences in the research laboratory focusing on the development of ‘urinary steroids metabolomics’ a combination of mass spectrometry and machine learning for diagnosis of adrenocortical carcinoma (ACC).

The journey starts with the hypothesis developed by Wiebke Arlt and Cedric Shackleton that urinary steroid excretion in patients with adrenal cancers would differ from those with benign adrenal adenomas (ACA). Initial studies were undertaken investigating 32 steroid metabolites using gas chromatography mass spectrometry (GC-MS). Through collaboration with computer scientists Michael Biehl and statisticians Alice Sitch and John Deeks, we were able to identify a malignant steroid fingerprint that differentiated ACC from ACA. When compared to current available imaging technologies, this urine steroid metabolomic assay demonstrated improved diagnostic sensitivity and specificity.

GC-MS is technically challenging and time consuming making it an expensive assay unsuitable for routine clinical use. Therefore, we selected the most relevant steroids when distinguishing between ACC and ACA and developed and validated a liquid chromatography tandem mass spectrometry (LC-MS/MS) assay for a subset of 15 steroids. Firstly, this was cross-validated to GC-MS to compare quantitation and diagnostic performance. Secondly, we prospectively validated the assay in a cohort of approximately 2000 unbiasedly recruited patients with adrenal tumours. Finally, we were able to determine the optimal stage in the patient pathway to place our assay to aid the diagnosis of ACC.
We are currently working towards the implementation of this assay into routine clinical biochemistry. It has taken us 10 years from the initial concept to its implementation, only possible through the work of a multi-disciplinary team. There have been many challenges on this pathway, I will discuss how we overcame these in this session.

Urine steroid metabolomics as a biomarker tool for detecting malignancy in adrenal tumors. Arlt W, et al. J Clin Endocrinol Metab. 2011 96(12):3775-84.

Urine steroid metabolomics for the differential diagnosis of adrenal incidentalomas in the EURINE-ACT study: a prospective test validation study. Bancos I Taylor AE, et al. Lancet Diabetes Endocrinol. 2020 8(9):773-781.

Gwen Wark is a consultant clinical biochemist employed within the Blood Sciences department of Berkshire and Surrey Pathology Services. She has worked at the Royal Surrey County Hospital in Guildford for over 22 years where she is now Director of the Supraregional Assay Service (SAS) Peptide Hormones Laboratory which specialises in the investigation of hypoglycaemia (includes a forensic case load) and the role of insulin-like growth factors and their binding proteins. Since 2002, she has also been the Scheme Director of the UK National External Quality Assessment Service (UK NEQAS) Guildford Peptide Hormones Scheme which covers the analytes insulin, C-peptide, gastrin, insulin-like growth factor-I (IGF-I) and insulin-like growth factor binding protein-3 (IGFBP-3). Since 2019, she has also been Director of the UK NEQAS Trace Elements schemes. She is involved in developing accuracy-based proficiency testing for all scheme analytes.

Gwen is also involved in promoting the development of reference methods/measurement systems. She is a member of the British Standards Institution (BSI) CH/212 committee which is responsible for standardisation in the field of in vitro diagnostics and reviewing/developing ISO standards. She is a member of the IFCC working group (collaboration with ADA and EASD) for the standardisation of insulin assays and a guest member of the NIDDK led C-peptide standardisation committee. In collaboration with the National Institute for Biological Standards and Control (NIBSC), she has been involved in the development of the WHO International Standards for IGF-I, insulin, C-peptide and proinsulin. She collaborated in the workshop that culminated in the ‘Consensus Statement on the Standardisation and Evaluation of Growth Hormone and Insulin-like Growth Factor Assays’ and also development of mass spectrometric assays for the measurement of IGF-I. Current LC-MS/MS assay development is focussed on developing further LC-MS/MS peptide assays for implementation into the routine laboratory e.g. insulin and C-peptide.

In the routine laboratory, the use of LC-MS/MS is becoming more widespread and is often used to overcome issues encountered with immunoassays. In this presentation, issues with peptide hormone analyses by LC-MS/MS and consensus statement recommendations will be discussed. Insulin and IGF-I will be used to highlight analytical approaches that be adopted to enable implementation of LC-MS/MS into the routine laboratory.

Dr. Uta Ceglarek, PhD, EuSpLM is senior scientist at the University Hospital Leipzig, Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics (ILM). She is board certified in Clinical Chemistry and Laboratory medicine (EuSpLM), in Toxicology and passed her postdoctoral lecture qualification in Clinical Chemistry and Laboratory Medicine.
Her research efforts are focused on the development of new mass spectrometric concepts for metabolome and proteome analysis in human body fluids and the investigations of metabolic alterations and lipid-modification in dyslipidemia, metabolic syndrome and cardiovascular diseases.

Over the past two decades clinical mass spectrometry becomes increasingly importance as analytical tool in routine diagnostics. LC-MS/MS offers a rapid, effective and economical way to analyze metabolic alterations of pre-defined target metabolites in biological samples. Recent developments open the way to implement quantification of proteins into clinical routine, too. Until now, access to clinical applications of LC-MS/MS have been restricted to specialist centers. The increasing availability of commercial assays, certified instruments, and a growing number of commercial solutions for mass spec lab automation will help to overcome this limitation.

However, for implementation into 24/7 patient care special requirements to laboratory diagnostic approaches have to be addressed. This presentation will give an overview to the current status aof LC-MS/MS applications like newborn screening, therapeutic drug monitoring, steroid analysis and quantitative protein analysis. Experiences from more than 20 years of implementation and maintenance of LC-MS/MS in our 24/7 diagnostic laboratory will be discussed. Perspectives for future developments in laboratory medicine directing to the clinical aim of predictive, preventive and personalized medicine by metabolomic and proteomic approaches will be depicted.

Lucia Grenga is a researcher in the laboratory of Innovative Technologies for Detection and Diagnostics at the French Alternative Energies and Atomic Energy Commission (CEA). She is interested in the development of tandem mass spectrometry‐based methodologies and their integration with other omics approaches for the characterization of clinically relevant microbiomes.

Proteomics offers a wide collection of methodologies to study biological systems at the finest granularity. Faced with COVID-19, the most worrying pandemic in a century, a collective mass spectrometry effort was launched to study COVID-19 and propose alternative solutions for the detection of SARS-CoV-2. Since then, proteomics researchers have made significant progress in understanding how its causative virus SARS-CoV-2 hijacks the host's cellular machinery and multiplies exponentially, how the disease can be diagnosed, and how it develops, as well as its severity predicted. Numerous cellular targets of potential interest for the development of new antiviral drugs have been documented. The main findings gathered by our group and other proteomists will be discussed while pointing out how they could represent game-changers in the COVID-19 battlefield and in deciphering the long-term consequences of the infection.

After successfully completing my Master in Pharmaceutical Care, I graduated as pharmacist in 2020. Mainly due to the interesting research performed during my Master’s thesis in the laboratory of Toxicology of prof. Christophe Stove, I decided to further pursue a career in science and research and started my PhD a few months after graduating. Currently, my work is mainly focusing on automation of microsampling-based analysis, including hematocrit prediction of dried blood microsamples (conventional dried blood spots and samples collected via volumetric absorptive microsampling) and the development of automated microsampling-based LC-MS/MS methods for the analysis of vitamins. Apart from research, I have also been involved in the organization of the last two Young Scientist Symposia of the European Bioanalysis Forum (EBF). I am (co-)author of 6 peer-reviewed publications.

I graduated in 2001 as a Master of Sciences in Chemistry at Ghent University. From 2001 to 2007 I did my PhD in the Laboratory of Analytical Chemistry at the Faculty of Pharmaceutical Sciences at Ghent University, followed by a post-doc in the same laboratory. Since October 2014 I'm a postdoctoral fellow at the Laboratory of Toxicology at Ghent University, where I am the quality manager and technical supervisor of the ISO17025 and ISO15195 accredited reference laboratory (Ref4U) section and the forensic service section of the lab. Besides this, I am the scientific secretary of the International Federation of Clinical Chemistry and Laboratory Medicine Committee for Standardization of Thyroid Function Tests.

I have expertise in development and validation of targeted GC or LC/MS (higher order reference) measurement procedures and their applications, with profound experience with method comparisons. Within the reference laboratory, the focus of the research activities is standardization and harmonization of thyroid function tests. Within the forensic applications, the focus is on determination of alcohol markers and new psychoactive substances. In 2020, I also participated in the development of a Sars-COV-2 LC/MS method.

Several biomarkers for alcohol (ab)use have been used throughout the years, including direct and indirect biomarkers. As indirect biomarkers show a low specificity and sensitivity for the detection of alcohol abuse, attention has shifted towards direct biomarkers such as ethanol itself and products derived thereof (ethyl glucuronide, ethyl sulfphate, etc.). Within the group of direct biomarkers, phosphatidylethanol (PEth) has been valued more and more since it increases the sensitivity of uncovering alcohol consumption and monitoring abstinence. With a half-life of 7-8 days, PEth provides a long detection window meaning it can take weeks for positive PEth values to drop below the decision limit for monitoring abstinence (20 ng/mL). Consequently, the question arises whether abstinence can be confirmed based on two consecutive PEth positive results.

In the first part of this session a detailed overview will be given of the abovementioned alcohol biomarkers. In the second part, the results of a large-scale PEth monitoring study will be discussed.

Methods
A large scale PEth monitoring study was set up in which over 500 participants agreed to stay sober for one month. During this period, they took 3 finger prick samples via self-sampling at home using volumetric absorptive micro sampling devices (VAMS, Mitra®, Neoteryx). PEth 16:0/18:1 was quantified using a validated liquid chromatography – tandem mass spectrometry method. A population-based algorithm capable of predicting abstinence with 95% probability was set up by fitting a linear mixed effect model to discern patterns in PEth elimination over time while accounting for intra- and interindividual variability in PEth scores. The latter was further incorporated in a 2-step decision tree, looking (i) whether or not PEth-values fall outside the prediction interval, and (ii) whether the slope between two PEth values is compatible with abstinence. Validation of this decision three was based on data of 74 people reporting to drink alcoholic beverages, alcohol free beverages or having eaten liquor-containing sweets.

Results
Allowing a cut-off of “4 units spread over 14 days”, the sensitivity and specificity of the decision tree was 89%. This is a realistic cut-off compared to other reports on detectability of a single dose intake of ethanol.

Conclusion
Monitoring the decrease in PEth, while the latter is still positive, can underpin claims of abstinence upon short term monitoring.

Christophe Stove graduated in 1999 as a Pharmacist at Ghent University. From 1999 to 2003 he did his PhD in the Laboratory of Experimental Cancerology in the Faculty of Medicine at Ghent University, followed by a post-doc in the Department for Molecular Biomedical Research in the Faculty of Sciences at Ghent University-VIB and -from Oct 2007 on- a Doctor-Assistant position in the Laboratory of Toxicology.

In February 2013 he became tenure-track assistant professor in the Faculty of Pharmaceutical Sciences and since October 2014 he is in charge of the Laboratory of Toxicology.

His activities include education, service (forensic toxicology and reference measurement services) and research. Research fields of special interest are alternative sampling strategies, the deployment of bio-analytical strategies for steering vitamin research and various aspects of G-protein-coupled receptors (GPCR’s).

Dr Richard Goodwin started research with MS imaging as postdoc in 2006 before moving to Uppsala University to work as an AstraZeneca post doc for Prof. Per Andrén. Richard now leads a global team of passionate imaging scientists that deliver expertise across AstraZeneca cutting-edge multidimensional imaging modalities. Deriving project insight and impact by connecting safety and efficacy endpoints using advanced tissue histology, molecular imaging, in vivo PET, MRI and much more. All connected by an integrated image analysis, digitization and AI. Passionate about collaboration and embedding new technologies and data analysis into the drug discovery process. Published over 75 publications while at AstraZeneca on the development and deployment of new technology in support of the portfolio. Honorary Professor at University of Glasgow.

Drug discovery and development constantly asks scientists to unlock more from every patient biopsy or preclinical study. Questions around drug biodistribution and metabolism merge with studies examining efficacy and safety. Therefore, researchers as AstraZeneca are collaborating extensively with researchers do develop, deploy and integrate new imaging technologies that provide a holistic view of the hidden molecular landscape in tissues. This provides data volumes and complexity ripe for AI exploration. The presentation will cover the opportunities and challenges in utilizing molecular imaging endpoints to better understand complex disease and investigate therapeutic efficacy across the portfolio of a large pharmaceutical organization.

Nina Ogrinc finished her PhD at the University of Ljubljana, and the Department of Low and Medium energy Physics, at Jozef Stefan Institute, Slovenia.
In 2014, she joined the group of Prof. Ron Heeren (M4I) in Maastricht, Netherlands as a postdoctoral researcher. During this time, she was involved in the Marie Curie BRAINPATH consortium and actively engaged in a variety of projects developing and applying new mass spectrometry imaging tools for biomarker discovery (lipids, metabolites, peptides) in neurodegenerative diseases
Since October 2018 she is working at laboratory PRISM (Inserm U1192, University of Lille), under the direction of Prof Michel Salzet and Prof. Isabelle Fournier, on a highly innovative SpiderMass project, an instrument designed for guided surgery and real-time diagnosis in the surgical operating room. She is currently developing a multimodal platform for mass spectrometry and imaging techniques which will enable complex, low cost, rapid, molecular profiling for faster cancer diagnostics and biomarker discovery.

Introduction
Surgery of solid tumors is a difficult process and the quality of surgery is central for patient outcome. Despite important improvements in surgical practices, the completeness of tumor removal remains scarce and surgeons are still struggling in the decision making. The gold standard currently remains the collection of biopsies and examination by expert pathologist. This process is long and laborious while showing an important rate of wrong assessment. We recently introduced SpiderMass technology based on water-assisted laser desorption-ionization (WALDI) which enables to retrieve the necessary molecular information directly in-vivo and in real-time. Yet, the device was demonstrated for manual profiling of tissues. However, for intraoperative diagnostics and excision margins evaluation, the device must be integrated onto a robotic device to provide precise imaging of the defined area within the body.

Methods
The SpiderMass system is composed of a remote laser microprobe, a transfer line and the MS instrument. The laser microprobe is fibered and equipped with a handpiece and tuned to 2.94 µm. The desorbed material is transferred to a QTOF MS instrument through a tubing of several meters connected to the inlet of the MS instrument using a dedicated interface. For combined topological and molecular imaging, The SpiderMass system was coupled to a commercially available stiff 6D-axis precision MECA robotic arm (MECADEMIC, Montreal, Canada) with repeatability of 5 µm. The SpiderMass handpiece is attached to the robotic arm by a “home-made” 3D printed adaptor equipped with a distance sensor. The camera enables to get the topography of the object to be scanned and the molecular data is then plotted back onto the topographic surface. The new distance sensor enables the collection of topographical and molecular data simultaneously and can reach 1.6 pixels/s.

Results and Conclusion
We programmed the robotic arm to generate topographical and molecular information. This is achieved in two steps. First, the distance sensor is calibrated by measuring the distance between the LED and the center of the observed camera field. Then the investigated specimen is placed under the arm and the X, Y, and Z coordinates can be recorded point by point depending on the defined imaging area. Second, the arm was programmed to rescan the object while keeping the right focusing distance of the SpiderMass laser microprobe to generate the molecular data. Both acquired data were aligned in time and fused to plot the molecular distribution onto a topographic image. Preliminary tests were run at 500 µm resolution from a sponge piece which presents specific topography. Lipid standards were spotted at different places within the holes of the sponge and these specific signals were followed and monitored. Next the system was applied onto biological samples starting with model tissues including beef liver, apple core with seeds and then translated to skin biopsies. The system was further applied inside of the body of the mouse to demonstrate the potential of future in vivo imaging of organs. The first in vivo experiments were performed on a volunteer finger and organs of a mussel.

The integration of the Spidermass MS-based technology onto a robotic arm of high accuracy was shown to enable imaging surfaces in 3D by MS molecular-topographic imaging. These developments give a start to in vivo imaging and open a new way for the technology to get it integrated within the set of conventional surgical tools.

Dr. Michael Vogeser, MD, is specialist in Laboratory Medicine and senior physician at the Hospital of the University of the Ludwig-Maximilians-University Munich, Germany (LMU; Institute of Laboratory Medicine). As an Associate Professor he is teaching Clinical Chemistry and Laboratory Medicine. The main scope of his scientific work is the application of mass spectrometric technologies in routine clinical laboratory testing as translational diagnostics. Besides method development in therapeutic drug monitoring and endocrinology a further particular field of his work is quality and risk management in mass spectrometry and in clinical testing in general. Michael has published >200 articles in peer reviewed medical journals. Michael heads the Commission for In Vitro Diagnostics in the German Association of Scientific Medical Societies (AWMF).)

In vitro diagnostics in the European Union (EU) is facing fundamental change with the implementation of Regulation (EU) 2017/746 on in vitro diagnostic medical devices, known as IVDR. With its full entry into force from May 2022, the IVDR will affect a population of 447 million people in 27 countries. The regulation addresses - beyond commercially distributed products - devices manufactured in healthcare facilities. In many ways, it is not yet clear how the IVDR will actually impact in-house MS-based measurement procedures. This presentation will discuss recent documents and guidance and provide an update on the implementation process - which is the responsibility of member states. An IVDR-compliance checklist will also be presented.

Dirk Lefeber, Ph.D., is Professor at the Radboud University Medical Center, Translational Metabolic Laboratory, Department of Neurology. After a PhD in chemical and analytical glycosciences at Utrecht University, followed by a post-doctoral training in polysaccharide infectiology at Utrecht UMC, he took a position as staff member Glycosylation Disorders at the Radboud UMC to establish an independent research group. He completed a training to Laboratory specialist clinical genetics in 2008, founded the Radboudumc Expertise Center for Disorders of Glycosylation, formally recognized by the Dutch government, and received several awards, including the SSIEM award (2010&2016) and prestigious personal VIDI and VICI grants from the Netherlands Scientific Organisation. He has established the world-wide quality control scheme for CDG diagnostics within ERNDIM.

Congenital Disorders of Glycosylation (CDG) form a fast growing group of genetic defects, that are characterized by abnormal glycosylation of proteins and lipids. With already more than 140 different genetic diseases discovered in all glycosylation pathways, the need for better biomarkers is increasing. This includes diagnostic biomarkers with increased specificity and sensitivity, as well as biomarkers that can predict disease progression and therapy response.

This presentation will mainly focus on CDGs due to defects in protein N-glycosylation. Screening for defects in protein N-glycosylation is occurring broadly via analysis of plasma transferrin by isofocusing, HPLC or capillary electrophoresis. Increased specificity and sensitivity is obtained by high-resolution QTOF mass spectrometry of intact plasma transferrin, which allows for screening and CDG subtyping in a single diagnostic test. For example, diagnostic glycan profiles are obtained for intellectual disability due to MAN1B1-CDG and exercise intolerance due to PGM1-CDG.

More sophisticated glycomics and glycoproteomics techniques are being applied and developed for CDG gene discovery, by stratification of patient groups. Moreover, these technologies are applied to diagnose CDG defects that don’t affect transferrin glycosylation, such as SLC35C1-CDG. Defects in this GDP-fucose transporter can be diagnosed by glycosylation analysis of IgG. Although biomarkers for prognosis and therapy monitoring are not yet broadly applied in CDG, both of these -omics technologies are very promising to obtain individualized insights in treatment response in CDG, as will be discussed for PGM1-CDG and SLC35C1-CDG.

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.

Liz is a senior clinical trainee in Paediatric Endocrinology at Birmingham Children’s Hospital and an MRC clinical research training fellow working with Professor Wiebke Arlt at the Institute of Metabolism and Systems Research, University of Birmingham, UK. She is interested in translational interdisciplinary research; combining medical, biostatistics, mass spectrometry and machine learning domains for the eventual direct benefit of patients. Her research to date focuses on non-invasive testing for patients with inherited disorders of adrenal steroid biosynthesis.

Guinevere received her PhD on exploring prostate-specific antigen (PSA), the well-known biomarker for prostate cancer, and its glycosylation by capillary electrophoresis and mass spectrometry. Since 2022, Guinevere is appointed as an Assistant Professor (tenure track) in the Analytical Biochemistry group at the Univeristy of Groningen She currently works on further expanding a mass spectrometry-based PSA glycosylation assay which she developed during her PhD. In addition, she explores the possibilities for the in-depth analysis of glycans and intact glycoproteins for biomarker discovery for other diseases as well as for the characterization of biopharmaceuticals. In 2017, Guinevere joined the organization committee of the Netherlands Area Biotech (NLab) Discussion group of CASSS. In 2019, she became a member of the scientific committee of the glycomics session, and a member of the early career committee, of MSACL EU. Her research interests are focused on bringing together researchers from the field of biomarker discovery with clinical laboratory professionals, ensuring a better translation of potential biomarkers to the clinic. Moreover, she is dedicated to convincing her fellow colleagues that glycosylation is an important subject and should not be neglected just because it is rather complicated.

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.

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.

Christophe Stove graduated in 1999 as a Pharmacist at Ghent University. From 1999 to 2003 he did his PhD in the Laboratory of Experimental Cancerology in the Faculty of Medicine at Ghent University, followed by a post-doc in the Department for Molecular Biomedical Research in the Faculty of Sciences at Ghent University-VIB and -from Oct 2007 on- a Doctor-Assistant position in the Laboratory of Toxicology.

In February 2013 he became tenure-track assistant professor in the Faculty of Pharmaceutical Sciences and since October 2014 he is in charge of the Laboratory of Toxicology.

His activities include education, service (forensic toxicology and reference measurement services) and research. Research fields of special interest are alternative sampling strategies, the deployment of bio-analytical strategies for steering vitamin research and various aspects of G-protein-coupled receptors (GPCR’s).

Ólöf Gerður is a PhD student at Margret Thorsteinsdottir´s and Sigridur Klara Bodvarsdottir lab in Iceland. She is working on a collaborative project with Zoltan Takat´s lab at Imperial College London where she uses imaging mass spectrometry to identify biomarkers in breast tissue. Ólöf obtained her B.Sc. at University of Iceland in Biochemistry with focus on molecular biology. She achieved her M.Sc. at University of Copenhagen (Denmark) in Human Biology, with focus on cellular and molecular biology. She has 3 years experience working as a research assistant for both University of Iceland and University of Copenhagen as well as she did a short-term internship at the Danish pharmaceutical company, Lundbeck.
Ólöf is a current co-Chair of the MSACL Early Career Network (MSACL ECN).

Presented by MSACL EU Scientific Committee members, this address will provide an overview of the applications and technologies currently being used in Clinical Labs, and a clear view of the development pipeline. It will highlight applications expected to be available in the near-future, as well as emerging applications, and key contributors. Relevant talks, posters, and people present at the congress will be identified, enabling you to optimize your learning path and more effectively target potential network connections. Whether you are new to Clinical Mass Spectrometry, or a seasoned veteran, the State of the Science address should be on your agenda.

Dr. Markus Kostrzewa is currently the Senior Vice President of Microbiology & Diagnostics R&D, Regulatory Affairs and Scientific Affairs at Bruker. He completed his PhD in 1993 at the Justus-Liebig-University in Giessen Germany, and his post-doc at the institute of Human Genetics in 1997. He joined Bruker in 1998, where he developed DNA analysis by MALDI-TOF mass spectrometry, Clinical Proteomics methods, consumables and software for mass spectrometry profiling of body fluids and tissues, and microorganism identification by MALDI-TOF mass spectrometry, which is produced and marketed by Bruker under the brand name, MALDI Biotyper.

Already at the end of the last century, MALDI-TOF mass spectrometry protein profiles were proposed as specific fingerprints for microorganisms which can be used for their unequivocal identification by comparison of dedicated reference databases. Nevertheless, it took a further decade until the technology entered routine diagnostic laboratories, suddenly considered as a revolution in microbiology diagnostics. After introduction into the first routine laboratories, it took only a few. years until it became the new microbial identification standard.

A prerequisite of success was the offering of a comprehensive system, a package consisting of the mass spectrometer including user friendly software for data acquisition, interpretation and report, reference databases, standard procedures, and consumables. Reliable service for the instrument and software, but also application support had to be offered to gain confidence of microbiologists and lab technicians in the novel technology. Regulatory approvals are prerequisite for diagnostic in most countries. This could only be achieved by companies who took over the central responsibility for the new diagnostic system.

Three main arguments made MALDI-TOF MS successful, being faster, better and more cost-effective than the previously applied techniques, i.e. biochemical and other phenotypical tests. Superior quality of MALDI-TOF based identification was demonstrated already with early versions of reference databases. Over the years, the libraries for different organism groups have been significantly expanded, today covering thousands of species from different microorganism groups. Species previously not considered to be pathogenic for humans have been detected as causative for infections, and even new microbial species have been discovered. Time to identification has been shortened by at least one day, and even more for slow-growing organisms and for microbes isolated directly from positive blood cultures. Although the initial investment for a MALDI-TOF instrument is considerably higher than for former standard identification systems, the very low running costs make it more cost-effective at least for medium and high throughput laboratories.

While MALDI-TOF is undisputed as the standard routine identification tool for microbiology laboratories, further applications have been proposed which might increase the value of MALDI-TOF MS for clinical microbiology. The considerable diversity in mass spectra that can be observed for many species was proposed for subtyping and epidemiology purposes. Several different approaches have been published for antibiotic resistance or even susceptibility testing. A first IVD-CE marked test for detection of a resistance mechanism has been introduced. Simple detection of specific marker peaks in the mass spectra enables detection of particular strains exhibiting antibiotic resistance. Other procedures comprise the observation of incorporation of isotope-labelled nutrients or the semi-quantitative determination of microbial biomass for susceptibility testing. Recently, besides proteins also lipids get into the focus of MALDI-TOF MS analysis as specific markers, for resistance detection as well as for identification or typing purposes.

My talk will describe the evolution of MALDI-TOF mass spectrometry in the microbiology lab, the conditions for its success and status of today, and I will give an outlook for its future potential.

Dr. Ginsberg is an Assistant Professor of Medicine at the University of California, San Diego. He is a nephrologist with funding from the NIDDK to study the relationship fo vitamin D metabolites and vitamin D binding protein with clinical outcomes. Additionally, he is the PI on a phase-1 trial evaluating advanced imaging techniques for diabetic nephropathy. He also directs the bone biopsy for histomorphometry program at UCSD.

Daniel Globisch studied Chemistry at the Technical University of Kaiserslautern (Germany) and the University of Southern Denmark, Odense (Denmark). He received his Ph.D. from the Ludwig-Maximilians-University Munich (Germany) with Professor Thomas Carell in 2011 and joined the laboratory of Professor Kim D. Janda at The Scripps Research Institute (CA, USA) for his postdoctoral studies. He started his independent career in 2015 at Uppsala University (Sweden) as a Science For Life Laboratory Fellow and was appointed as Associate Professor in 2017. He received tenure in December 2020. Daniel has been elected as a board member of the Nordic Metabolomics Society and is an Editorial Board Member for the metabolomics society journal Metabolites. The interdisciplinary nature of the research projects is focused on the elucidation of the metabolic interaction between the gut microbiota and their human host. His laboratory develops new Chemical Biology tools to extend the scope of metabolomics research for discovery of unknown biomarkers and bioactive metabolites.

One of the most exciting scientific developments in the past decade has been the understanding that gut microbiota profoundly impact human physiology. The complex consortium of trillions of microbes possesses a wide range of metabolic activity. This metabolic interspecies communication represents a tremendous opportunity for the discovery of unknown bioactive molecules as only limited information on this co-metabolism has been elucidated on a molecular level. Mass spectrometry-based metabolomics analysis is the method of choice for the analysis of known and discovery of unknown metabolites. Chemical Biology tools are still limited in metabolomics compared to other ‘omics research fields. Especially, the detailed and selective analysis of microbial metabolism remains a major challenge that requires specific techniques.

We have developed new state-of-the-art Chemical Biology methodologies for that exceed the scope of global metabolomics analysis. These unique metabolite analysis tools overcome limitations in metabolomics and were applied for the discovery of unknown metabolites in human samples to evaluate their potential as biomarkers. We have developed arylsulfatase-based metabolite analysis methods for specific identification of sulfated metabolites as this compound class represents a signature for microbiome-host co-metabolism. This analysis led to identification of more than 230 sulfated metabolites, exceeding the number of this metabolite class in common metabolomics databases. An optimized enzymatic method was applied for a dietary intervention study to investigate the dietary sulfatome. Several previously unknown and undetected metabolites are derived from specific microbiota metabolism. Based on our interested in phase II modifications, we identified a series of unexpected substrates for the common human N-acetyltransferase NAT2. Furthermore, we have also designed unique chemoselective probes immobilized to magnetic beads that allow for facile extraction of metabolites with increased mass spectrometric sensitivity by six orders of magnitude.

A native of Florida, Kelly completed her undergraduate studies in Chemistry at the University of Florida. After graduating with honors in 2009, Kelly joined the Department of Chemistry at Vanderbilt University as a graduate student. Her research in the lab of John A. McLean focused on the development of ion mobility-mass spectrometry (IM-MS) methods for the identification of metabolite, lipid, and peptide biomolecular signatures of disease from complex biological samples. After receiving her Ph.D. in 2014, Dr. Hines completed a one-year postdoctoral fellowship in the Mayo Clinic Regional Metabolomics Core where she established quantitative MS methods for lipidomics and protein metabolism using isotope labeling. In 2015, Dr. Hines joined the lab of Libin Xu at the University of Washington. Her work in the Xu Lab focused on the development of IM-MS methods for lipidomics, high-throughput IM-MS measurements of drugs and small molecules, and the significance of lipids in human diseases, environmental exposure and antibiotic resistance. Kelly has authored research publications in top-tier analytical chemistry and molecular sciences journals such as Analytical Chemistry, Journal of Lipid Research, and Molecular Cell. Kelly has been the recipient of several noteworthy awards, including a U.S. Pharmacopoeia Fellowship, the ACS Dan Su Travel Award, and several Young Investigator travel awards. She is most proud of being selected as a Finalist for the University of Washington Graduate School Postdoc Mentoring Award during her time at UW. Outside the lab, Kelly is an avid reader of fiction, a college football enthusiast and enjoys being outdoors.

I'm currently a second-year graduate student in the Hines lab at the University of Georgia. My focus now is looking into lipid composition variability caused by external growth factors or gene mutation using reversed-phase liquid chromatography mass spectrometry.

I graduated from Samford University in Birmingham, Alabama in spring 2020 with a bachelor’s degree in chemistry and biochemistry and joined UGA’s Chemistry Ph.D. program in the fall of 2020. As an undergraduate, I worked on organometallic research involving transition metal catalyzed synthesis reactions. Now as a member of the Hines lab, my research focuses on high-throughput flow-injection mass spectrometry and lipid isomer identification through determining carbon-carbon double bond location via ion-mobility.

Our goal is to better understand the ways in which lipids and small molecules contribute to diseases affecting human health and use this knowledge to develop diagnostic and prognostic tools based on molecular signatures of the disease. To achieve this, the Hines Lab develops and applies bioanalytical methods using ion mobility-mass spectrometry (IM-MS) to enhance the throughput and dimensionality of lipidomics and metabolomics experiments. One focus of the group is antibiotic resistance, where we are characterizing the metabolic alterations in antibiotic resistant pathogens and developing IM-MS methods for antibiotic susceptibility testing and small molecule screening.

Dr. Hamid's PhD studies in Prof. M. Samy El-Shall’s research laboratory in Virginia Commonwealth University were focused on studying ion-molecule kinetics, thermochemistry, and structures using drift tube ion mobility spectrometer measurements associated with quantum mechanics calculations. Then, Ahmed joined Purdue University to work under the supervision of Prof. R. Graham Cooks where he focused on the applications of mass spectrometry to various biological systems, in particular on differentiation of microorganisms using various ambient ionization techniques coupled to mass spectrometry which resulted in novel approaches in the ionization and the identification of bacteria and fungi with high prediction rates without sample preparation. To learn new skills, Dr. Hamid joined the team of Dr. Richard D. Smith in Pacific Northwest National Laboratory to work on the development of novel Structures for Lossless Ion Manipulations (SLIM) which allows previously unattainable ion mobility resolution and remarkable ion manipulations. Moreover, as a senior scientist in MOBILion Systems, Ahmed transferred and further developed the SLIM technology. In summary, Dr. Hamid has more than 14 years of experience researching in the fields of technology development and the applications of mass spectrometry and ion mobility spectrometry which resulted in more than 29 peer-reviewed publications in high impact journals and 7 patents.

CDC estimates that each year 48 million people get sick from a foodborne illness where 128,000 are hospitalized leading to 3,000 deaths. They are caused by pathogenic bacteria, parasites, or viruses that enter the body through the consumption of contaminated food or beverages followed by growth inside the host body. Therefore, rapid methods are crucial for the effective detection of foodborne pathogens in food products to provide safe food supply and to prevent outbreaks of foodborne diseases and the spread of foodborne pathogens. In addition, developing fast robust diagnosis techniques will increase the recovery rates of patients suffering from foodborne infections and will lead to reduced antibiotic resistance.

The membrane of these bacteria contains varying lipid composition that can be utilized as diagnostic biomarker for foodborne disease diagnosis. However, their full characterization remains analytically challenging due to their enormous structural diversity and complexity (e.g., varying acyl chain positions and/or double bond geometries). This presentation will demonstrate the advantages of interfacing liquid chromatography and structurally-based ion mobility with tandem mass spectrometry in the resolution of isomeric lipids. Moreover, this presentation will demonstrate the developments of ambient ionization techniques when coupled to high-resolution ion mobility spectrometry. We expect these developments to enable portable diagnosis devices that can be used for sensitive detection and superior separation power in the analysis of contaminated food samples and foodborne clinical samples without any prior sample preparation. This will enable high throughput analyses that is affordable and can be performed by less-skilled users, such as nurses and farmers.

Professor Vera Ignjatovic is a medical researcher focused on improving outcomes for children. She leads the Haematology Research team at the Murdoch Children’s Research Institute and is a pioneer in the field of paediatric thrombosis and haemostasis and specifically Developmental Haemostasis, the concept describing age-specific development of the haemostatic system. Her research highlights include: First to describe differences in fibrin clot structure in children compared to adults; and first to demonstrate age-specific differences in response to heparin. Vera is an international expert in plasma proteomics, an approach that she uses widely in her research.

In this session, we will discuss:

1. The role of networking for scientists,
2. What are the dos and donts of networking?,
3. Career paths and making the choice,
4. Leadership role and building collaborations,
5. Beyond science and community participation.

Hoda Safari Yazd is a Ph.D. candidate in analytical chemistry at the University of Florida and working under the supervision of Prof. Richard Yost and Dr. Timothy Garrett. She received her B.Sc. in chemistry from Sharif University of Technology in 2015 and her M.Sc. in computational chemistry from the same school in 2017. Hoda's research at UF primarily focuses on combining analytical chemistry tools and scientific programming for the metabolomic discovery of rare disorders. She is currently working on two projects; the first project concentrates on the detection of new biomarkers in meningiomas to improve early detection of this disease by employing machine learning as a tool on mass spectrometry-based metabolomics data. The second project is focused on the characterization of rare X-chromosome deletion disorders using metabolomics and lipidomics workflows by UHPLC-HRMS on neural progenitor cells. Hoda is one of the founding members and main organizers of the MSACL Early Career Network (MSACL-ECN).

Dr. Garrett has over 20 years of experience in the field of mass spectrometry spanning both instrument and application development. He received his PhD from the University of Florida, under Dr. Richard A. Yost, working on the first imaging mass spectrometry-based ion trap instrument. He has also developed MALDI-based approaches to analyze proteins in bacteria and small molecules in tissue specimens. His current interests include the translation of LC-HRMS, MALDI, DESI and LMJSSP in metabolomics to clinical diagnostics. He is an Associate Professor in the Department of Pathology at the University of Florida, and an Associate Director for the Southeast Center for Integrated Metabolomics (SECIM).

Hoda Safari Yadz and Tim Garrett, from the Garrett lab in Florida, join us today for a presentation and discussion of their work on the metabolomic and lipidomic characterization of an X-chromosome deletion disorder in neural progenitor cells, hosted by the JMSACL podcast group.

X linked disorders are considerably rare and research analysing human samples is under-
represented. Research undertaken in this study used neural progenitor cells from an afflicted patient to begin exploring this rare disorder. While most experimental work focuses on the
neurodevelopmental impacts of X-chromosome associated diseases, this work demonstrates that
they should also be considered metabolic disorders owing to their perturbations on metabolite and
lipid biochemistry. This work aims to use mass spectrometry to improve our understanding of these
conditions and guide novel interventions by characterizing disease associated metabolic alterations.

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Joseph Jones has worked in the clinical forensic toxicology field for over 30 years for large workplace drug testing laboratories and boutique forensic laboratories that specialize in testing alternative specimen types and is currently the Chief Operating Officer and Executive Vice President of United States Drug Testing Laboratories. He has contributed to over 25 peer-reviewed scientific papers in the field of forensic toxicology and facilitated numerous workshops and presentations. Jones has provided drug testing expert testimony on behalf of LabCorp and USDTL in a number of venues including union arbitration, unemployment hearings, family court child custody, child abuse/neglect and capital murder cases. Jones has been certified by the National Registry of Certified Chemists at a Toxicological Chemist.

Andre Sukta joined USDTL in early 2013 as our Laboratory Supervisor, bringing more than a decade of forensic toxicology expertise with him.
Andre received his Bachelor of Science degree in Chemistry (Forensics concentration) in 2002 from Benedictine University, Lisle, IL. In 2009, he received his Masters of Science degree in Forensic Science from University of Illinois at Chicago. He has co-authored several peer-reviewed research articles, including papers in the Journal of Analytical Toxicology and Forensic Science International.
In 2002, Andre began his career in toxicology as a Forensic Scientist with the Illinois Racing Board Laboratory. Since then, he has worked with various toxicology groups, including University of Illinois at Chicago - College of Pharmacy, Indiana University - College of Medicine, and the Indiana State Department of Toxicology.
Andre Sukta is a member of the Society of Forensic Toxicologists (SOFT), where he serves as a director of the organization, and serves on the professional mentoring program committee. He is also a member of the National Safety Councils Alcohol, Drugs and Impairment Division, where he serves as the Cannabis and Health and Safety subcommittee chair. He is also a full member of the American Academy of Forensic Sciences (AAFS), Chicago Chromatography Discussion Group (CCDG), and Midwest Association of Toxicology and Therapeutic Drug Monitoring (MATT).

Prenatal exposure to ethanol has long been associated with several long-term negative health consequences for the newborn including physical, cognitive, social, and behavioral impairments. The prevalence of FASD in North America may be as high as 5% of the population which represents an enormous public health concern (Flannigan, Coons-Harding, Anderson, Wolfson, Campbell, Mela, & Pei, 2020). Early identification of those affected is critical to address the special needs of these children to improve their outcomes. Outside of maternal self-report, there are limited strategies to objectively identify PAE at or near the time of birth.

Current testing strategies to detect prenatal exposure to ethanol is limited in scope and utility Unfortunately, a rapid immunoassay test does not exist leaving us with a very expensive and time-consuming liquid chromatography tandem mass spectrometry screening method. The objective of this presentation is to demonstrate a newly developed and validated a method for the detection of ethyl glucuronide in umbilical cord tissue using Laser Diode Thermal Desorption-Tandem Mass Spectrometry. The Laser Diode Thermal Desorption (LDTD), allows for a significant decrease in time and expense when compared to the current methodology.

The method was developed and validated according to the guidelines of the Scientific Working Group on Forensic Toxicology. Briefly, Umbilical Cord Tissue was weighed out (0.5 g), deuterated internal standard is added and homogenized in 3 mL of deionized water. Following centrifugation, the supernatant was purified using a solid phase extraction technique. The final reconstituted extract (8 µL) was transferred to an AD LazWell Plate and dried in a recirculating oven at 35°C until dry. The plate was transferred to the LDTD and analyzed. We will discuss our validation results as well as our experience with the analysis of authentic specimens in our laboratory.

Dr Cristina Legido-Quigley is the Head of Systems Medicine at Steno Diabetes Center Copenhagen and an Associate Professor at King’s College London.
Her main area of interest is neurometabolism and how the brain copes with disease, as well as finding clinical tests for healthy aging, Alzheimer's, cognition, diabetes and metabolic diseases. Her discoveries span fatty molecules that are important for cognition, small molecules that in liver alert to tissue damage, together with modulating molecular pathways for improving the treatment of diabetes. She is also researching algorithms for better personalised diagnoses in the clinic.
She has been a group leader at King's College London since 2006. In 2018 she moved to Steno a hospital and research center in Denmark to pursue her interests in Systems Medicine. She shares her findings in scientific publications in the biotechnology and medical fields

Scientist passionate to improve patient care via novel biomarkers & precision medicine

I had the pleasure to learn from the best in the field in metabolomics, lipidomics and proteomics. My primary interest is translating these technologies into the clinical setting for improved, more personalized disease treatment.
My education is a combination of various experiences within technology, mass spectrometry and clinical applications:

MSE from the Technical University of Warsaw (Poland)
PhD from the Technical University of Denmark (Denmark)
Postdoctoral research at the University of Auckland (New Zealand) and University of Copenhagen (Denamrk)
Short-term visits at the University of Campinas (Brazil), University of Alberta (Canada), Max Planck Institute of Biochemistry (Germany)

His PhD project looks into individual metabolic response to diabetes treatments and investigate biomarkers that can be used to direct personalized treatment.

Dr Jin Xu is a Research Associate at King's College London. Her research focuses on the application of metabolomics and lipidomics to understand the underlying biology in Alzheimer's disease, together with the integration of multi-omics and clinical data to test early diagnostic panels.

I am a data scientist with a background in machine learning and computational sciences, and a specific focus in digital human health.

I am affiliated with the Systems Medicine research group at Steno Diabetes Center Copenhagen, where I work as a bioinformatics and biostatistics specialist to process, analyze, visualize and understand complex omics data from the small molecule profiling platforms managed by the team.

Postdoctoral researcher at Steno Diabetes Center. Currently working with the use of state-of-the -art mass spectrometry-based metabolomics to investigate gut-and-liver axis in alcoholic liver fibrosis, in collaboration with SDU through GALAXY project. Andressa did a PhD in the field of metabolomics at the University of São Paulo and University of Copenhagen. She worked 2 years as a postdoc in the department of Food Science at the University of Copenhagen.

Our research goal is to discover clinical tests for diagnostics and new disease treatments. We work on neuro and metabolic diseases and particulalrly in disease that affects the brain and the liver, like Alzheimer's Disease and Diabetes.

Our science is at the interface between chemistry and medicine and we are experts in biotechnology and the use of data science to allow the detection of thousands of small molecules / lipids in order to understand the underlying biology in disease.
We can get molecular data with mass spectrometry instruments and perform data analytics, including machine learning, to understand this biology. In order to translate results into the clinic we also work with clinical trials and evidence portfolios for EMA approval. This field of research can be called systems medicine, because it integrates -omic data and clinical data together to understand health.

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.

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.

Are you thinking about the next step in your career? About an international career move? Publishing your exciting scientific findings in an Open Access journal? Don’t miss our next career development event with Dr. Anne Bendt where we will talk about her career path in academia and how that led to her current role in the National University of Singapore and SLING. We will also talk about a wide range of topics including interviews, the importance of networking and collaborations as well as publishing at the JMSACL!

Dr. Xin Li is a research fellow at the Department of Urology, Graduate School of Medicine, Kyoto University where he got his Ph.D. degree. He is going to start to work at Peking University Third Hospital as a urologist in August 2021. Dr. Li is also proud to win the Young Investigator Grant in MSACL EU 2019 and to have a podium presentation of his research there. Recently, he has become a member of the Japanese Society for Biomedical Mass Spectrometry (JSBMS). While studying at Kyoto University he became interested in the clinical application of MALDI-TOF/MS, especially when using it in the urinary lipid analysis. Dr. Li and his supervisors, especially Dr. Kenji Nakayama who is an Asia Outreach Committee of MSACL and also one of the JSBMS council members, developed a simple relative-quantitative MALDI-TOF/MS system for urinary lipidomics, and they are applying it in the screening of urinary biomarkers for genitourinary disorders. Now, they are aiming at promoting the "qShot MALDI” system as a simple application for the MALDI analysis.

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS) has been used for lipid analysis since the 2000s. However, the poor reproducibility and quantitative ability hinder its application in clinical biomarker screenings. To improve the clinical usage of MALDI-TOF/MS, especially for quantitative detection of the urinary phospholipids (PLs) and lysophospholipids (LPLs), we have adopted three main strategies including the selection of a proper matrix, a specially designed plate, and a spike of ionization standards. This system, named “qShot MALDI” analysis, offers a quick, qualitative, and quantitative detection of urinary PLs and LPLs. Meanwhile, a clinical application of this system was conducted for screening urine lipidomic biomarkers for prostate cancer. The results indicated that the qShot MALID system had a good performance with rapid, convenient, and reproducible properties.

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?

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 a 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 biolayer 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 was most recently the LC-MS/MS Assay Development Specialist in the clinical chemistry laboratory at St Paul’s Hospital in Vancouver, BC, Canada where she was passionate about making challenging assays work for a busy clinical mass spectrometry laboratory. Grace has a BSc in Chemistry from The King’s University College and has spent the past 17 years doing hands-on LC-MS/MS lab work in bioanalytical and clinical laboratories. She is passionate about mass spectrometry and that this technology is utilized to help patients. Grace has a strong interest in troubleshooting - especially when an answer is found - and loves to share her knowledge and experience through teaching and training.

Mari DeMarco, PhD, DABCC, FCACB, is a Clinical Chemist at Providence Health Care, the Research Director of Providence Research, and a Clinical Associate Professor in Pathology and Laboratory Medicine at the University of British Columbia in Vancouver Canada. Dr. DeMarco completed her PhD in the Biomolecular Structure and Design program at the University of Washington, and a clinical chemistry fellowship at Washington University School of Medicine.

With a strong interest in bridging basic biomedical science, analytical chemistry and laboratory medicine, Dr. DeMarco’s research group focuses on building new biofluid tests for direct translation into patient care. A particular area of interest is advancing protein-based clinical diagnostics for neurodegenerative disorders, such as Alzheimer’s disease. The goal of this program of research is to ensure that these new tools make the challenging jump from research into healthcare.

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.

Dr. Adina Badea, PhD, DABCC, earned her BA in Chemistry from Wellesley College, and her PhD in Chemistry from the University of Illinois at Urbana-Champaign. She completed her clinical chemistry and toxicology fellowship at UCSF, where she worked under the supervision of Dr. Alan Wu and Dr. Kara Lynch on developing methods and finding new solutions to current challenges in clinical toxicology testing. Currently, she is Director of Toxicology at Rhode Island Hospital and Assistant Professor of Pathology and Laboratory Medicine at The Warren Alpert Medical School of Brown University, where she focuses on expanding the capabilities of the clinical toxicology lab using high resolution mass spectrometry. Her research interests include bringing state-of-the-art testing to the service of emergency medicine patients and to address public health crises with real-time comprehensive toxicology testing via collaborations with the local Poison Control Center and Department of Health.

# 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 Professor of Pathology and Medicine in the Johns Hopkins University School of Medicine. He is board-certified in Clinical Chemistry by the American Board of Clinical Chemistry. He serves as the Director of the General Chemistry Laboratory at the Johns Hopkins Hospital and the Clinical Pharmacology Analytical Laboratory within the Division of Clinical Pharmacology. Dr. Marzinke is Co-Principal Investigator (PI) of the HIV Prevention Trials Network (HPTN) Laboratory Center (LC) and is the Director of the Clinical Laboratory Core for the Johns Hopkins Center for AIDS Research. His primary research interests are in the areas of antiretroviral pharmacology, HIV prevention science, mass spectrometry, pharmacogenetics and precision medicine, and laboratory automation. Dr. Marzinke has an active research program and serves as a principal investigator (PI) or co-investigator on a number of grants. He has collaborated on research to better characterize the multi-compartment pharmacology of antiretroviral agents when administered using alternative drug delivery systems using liquid chromatographic-mass spectrometric approaches. He has published more than 180 peer-reviewed articles, and holds leadership positions in several societies.

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 & Co-Director Laboratory Informatics at Nationwide Children's Hospital. His research focuses small molecule analysis by mass spectrometry in a clinical setting 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.

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.