Dr. Tim Van Den Bossche is currently working as postdoctoral researcher in the CompOmics lab of Prof. Lennart Martens in the field of microbial community proteomics, commonly known as metaproteomics. Here, he led the first-ever, community-driven, multi-site experiment that compared the effects of different state-of-the-art metaproteomics analysis pipelines (wet-lab and computational), and also compared the results with the taxa obtained from metagenomic and metatranscriptomic experiments - commonly known as the CAMPI study. With this momentum, he co-founded the Metaproteomics Initiative (www.metaproteomics.org) to further help accelerate the metaproteomics field. Next to this benchmark study and his work in the Initiative, he develops bioinformatics tools to metaproteomics data analysis.

Through connecting genomic and metabolic information, metaproteomics is an essential approach for understanding how microbiomes function in space and time. The international metaproteomics community is delighted to announce the launch of the Metaproteomics Initiative (www.metaproteomics.org), the goal of which is to promote dissemination of metaproteomics fundamentals, advancements, and applications through collaborative networking in microbiome research.

We will discuss past, present and future of this project as well as possible clinical implementations.

Academics are more likely to suffer from mental health disorders yet are less likely to seek treatment. Stigma is one of the highest ranked barriers to help-seeking for mental health problems. Sharing faculty stories is a powerful mechanism to reduce stigma, promote more open communication, and foster cultural change around mental health issues. Olya did her MD, PhD, and postdoc in translational medicine and mass spec. Currently she works as a scientific communications officer and devotes her spare time to academic mental health advocacy.

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.

Most mass spectrometry imaging (MSI) is performed one pixel at a time at a rate below 1,000 pixels per second. Recently, researchers at the M4i institute at Maastricht University developed an MSI technique called fast mass microscopy [1] which acquires many mass spectra in parallel and is capable of imaging at over 1 million pixels per second. This improvement of >1,000 times imaging speed opens new opportunities for MSI in clinical applications as experiments that would otherwise take months can now be done in less than an hour. This seminar will focus on fast mass microscopy and strategies for its future clinical translation.

[1] Körber, A., et al. Anal. Chem. 2022 94 (42) 14652-8

Dr. Li obtained his B.Sc. degree in Chemistry from Zhejiang (Hangzhou) University, China, in 1983, and his Ph.D. degree in Chemistry from the University of Michigan, Ann Arbor, USA, in 1989, under the direction of Professor David M. Lubman. After graduation, he joined the Department of Chemistry at the University of Alberta, Edmonton, Alberta in July 1989. He was an Assistant Professor from 1989 to 1994 and an Associate Professor from 1994 to 1999. He has been a Full Professor since July 1999. He has also been an Adjunct Professor of Biochemistry Department, Faculty of Medicine, since January 2008. He holds a Visiting Professorship at Zhejiang University supported by K. P. Chao’s Hi-Tech Foundation for Scholars and Scientists since 2006. He is a co-PI of The Metabolomics Innovation Centre (TMIC) mainly supported by Genome Canada. He was a co-PI of the Human Metabolome Database (HMDB) Project; his laboratory generated the HMDB MS/MS spectral library of the endogenous human metabolites that has been widely used by the metabolomics community for unknown metabolite identification based on spectral matches. Dr. Li was a visiting scientist at Hewlett Packard Research Lab (now Agilent), Palo Alto, CA (on sabbatical leave) from July 1998 to June 1999. He served as Director, Alberta Cancer Board Proteomics Resource Lab from February 2000 to December 2005. He served as Chair, Analytical Chemistry Division of Chemistry Department from July 2007 to June 2019. He serves as a Co-Director of TMIC since July 2019. He is a founder of Nova Medical Testing, Inc., a university spin-off company focusing on developing mass spectrometry based analytical solutions for medical and health diagnostic applications, including targeted diagnostic-panel analysis and global biomarker analysis.

Dr. Li is an elected fellow of the Royal Society of Canada (Academy of Science) (2019) (watch this video on Youtube). He is a Canada Research Chair in Analytical Chemistry (Tier 1, 2005-2012; renewed for 2012-2019). He has won several awards including McBryde Medal (2001) from the Canadian Society for Chemistry, Faculty of Science Outstanding Research Award (2002), McCalla Professorship (2002-2003), and Killam Annual Professorship (2004-2005) from the University of Alberta. He received the Young Explorers Prize from the Canadian Institute for Advanced Research (CIAR), which was given to Canada’s top twenty researchers aged forty or under in science and engineering (2002) as chosen by a panel of international judges. He was the recipient of the Rutherford Memorial Medal in Chemistry from the Royal Society of Canada (2003). He received The F.P. Lossing Award from the Canadian Society for Mass Spectrometry in 2006, The Maxxam Award from the Canadian Society for Chemistry in 2009 and Gerhard Herzberg Award from the Canadian Society for Analytical Sciences and Spectroscopy in 2010. He was one of the seven researchers selected as Brightest Minds 2016 by Canadian Institutes of Health Research. He is a fellow of the Chemical Institute of Canada since 2001.

Dr. Li has published more than 300 research papers mainly in the area of analytical mass spectrometry. He has given many invited talks including Hong Kong Polytechic University Distinguished Lecture in 2011, Distinguished Lectureship on Cerebrating the 50th Anniversary of Hong Kong Baptist University Faculty of Science in 2011, and Thermo Fisher Scientific Distinguished Scientist Lecture at the University of Montreal in 2013.

Dr. Li is currently an editor of Analytica Chimica Acta, an international journal on analytical chemistry with an Impact Factor of 6.558 in 2020 (2005-present). He is a member of the editorial advisory boards for Current Analytical Chemistry (2004-present), Journal of Advanced Research (Elsevier) (2014-), Biophysics Reports (Springer) (2015-), and Chemical Data Collections (Elsevier) (2015-). Dr. Li was a member of the editorial advisory boards for Journal of the American Society for Mass Spectrometry (2001-2006), Canadian Journal of Chemistry (2004-2006), Clinical Proteomics (2011-2016), and Analytical Chemistry Insights (2006-2018). He was a member of Analytical Chemistry’s A-Page Advisory Panel (2006-2008).

Metabolomics is a relatively newcomer of the Omics family for large-scale characterization of small molecules of biological systems. A key step in metabolomics is to determine metabolic differences among different samples. We want to detect and quantify as many metabolites as possible, ideally covering the entire chemical space of the metabolome. High-coverage metabolome analysis will benefit many research areas, including disease biomarker discovery, population-based health analytics and clinical applications. This presentation will focus on the discussion of current challenges and potential solutions for translating global metabolomics into clinical applications.

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.

Setting up a clinical mass spectrometry lab presents a host of challenges with a great deal of attention understandably paid to developing and validating high quality assays. Rarely do laboratorians consider the reimbursement aspect of the testing they are setting up. This is unfortunate given the importance financial success has in determining whether or not an organization will invest in such testing. Reimbursement and appropriate billing is especially important to consider when it comes to more complex testing such as urine toxicology; appropriate billing of this testing is essential to ensure labs get adequately reimbursed and stay in compliance with applicable laws and regulations. This CONNECT webinar will focus on lessons learned establishing urine toxicology testing from the billing aspect. It will include an overview of how such testing should be billed, mistakes that are often made when establishing such testing, and the tools available to labs to help ensure testing is properly billed (and more likely reimbursed). Ample time will be given to ensure the audience can share their own struggles in this area and can ask questions about the topics raised.

View recordings of Josh's series on Getting going with Mass Spectrometry - his real time journey of setting up Mass Spec testing in a Clinical Lab.

1. Getting going with mass spectrometry: Josh installs a mass spectrometer


2. Getting going with mass spectrometry: Josh learns chromatography


3. Getting going with mass spectrometry: Josh analyzes peaks


4. Getting going with mass spectrometry: Josh attempts method validation


5. Should I report that?? Dealing with Unexpected Results in Clinical LC-MS/MS Testing

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 JLABS@BE, 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.

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.

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."

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.

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.

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).

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.

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 Ísbert is a postdoctoral researcher at Vanderbilt University where she works on mapping the whole molecular atlas of the kidneys using IMS and microscopy.. She earned a PhD in Pharmaceutical Science from the University of Iceland in 2021, with work on the project being conducted in London as a collaboration with Imperial College London. The thesis topic was metabolic identification in FFPE breast cancer using DESI-MSI.
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 one of the leads 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.

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.

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.

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.

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

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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

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. 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.

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.

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

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

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

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

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

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

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

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

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

John R. Yates is the Ernest W. Hahn Professor in the Departments of Molecular Medicine and Neurobiology at The Scripps Research Institute. His research interests include development of integrated methods for tandem mass spectrometry analysis of protein mixtures, bioinformatics using mass spectrometry data, and biological studies involving proteomics. He is the lead inventor of the SEQUEST software for correlating tandem mass spectrometry data to sequences in the database and developer of the shotgun proteomics technique for the analysis of protein mixtures. His laboratory has developed the use of proteomic techniques to analyze protein complexes, posttranslational modifications, organelles and quantitative analysis of protein expression for the discovery of new biology. Many proteomic approaches developed by Yates have become a national and international resource to many investigators in the scientific community. He has received the American Society for Mass Spectrometry research award, the Pehr Edman Award in Protein Chemistry, the American Society for Mass Spectrometry Biemann Medal, the HUPO Distinguished Achievement Award in Proteomics, Herbert Sober Award from the ASBMB, and the Christian Anfinsen Award from The Protein Society, the 2015 ACS’s Analytical Chemistry award, 2015 The Ralph N. Adams Award in Bioanalytical Chemistry, the 2018 Thomson Medal from the International Mass Spectrometry Society, and the 2019 John B. Fenn Distinguished Contribution to Mass Spectrometry award from the ASMS. He was ranked by Citation Impact, Science Watch as one of the Top 100 Chemists for the decade, 2000-2010. He was #1 on a List of Most Influential in Analytical Chemistry compiled by The Analytical Scientist 10/30/2013 and is on the List Of Most Highly Influential Biomedical Researchers, 1996-2011, European J. Clinical Investigation 2013, 43, 1339-1365 and the Thomson Reuters 2015 List of Highly Cited Scientists. He has published over 950 scientific articles with >125,000 citations, and an H index of 174 (Google Scholar). Dr. Yates served as an Associate Editor at Analytical Chemistry for 15 years and is currently the Editor in Chief at the Journal of Proteome Research.

Developments in mass spectrometers over the last decade have been numerous, but there are some clear trends. The drive to increase confidence in the identification of peptides and post-translational modifications pushed the development of high-resolution and high-mass accuracy instruments, most notably Orbitrap and time-of-flight (TOF) mass analyzers. Improvements in mass resolution in these instruments resulted in an increase in the mass range for effective analysis, precipitating greater interest in the “top down” proteomics which now could be performed without expensive high-field magnets previously required for ion cyclotron resonance MS of intact proteins. Additionally, the emergence of biological therapeutics has fueled a greater need to characterize intact proteins to verify structure, sequence, and modifications. Fragmentation of the amide bonds in intact proteins requires more robust methods than fragmentation of peptides to obtain sequence information. Two methods in particular—electron transfer dissociation (ETD) and ultraviolet photodissociation (UVPD)—have been used to achieve more efficient fragmentation of intact proteins, especially when used in combination. These substantial improvements in MS capability have led to greatly improved prospects for top-down MS.

The Partnership for Clean Competition funds more than 70% of the world’s anti-doping research, but the organization is always looking for new researchers to apply for grants. If the opportunity interests you at all, please follow the PCC on Twitter(@PCCantidoping) or visit the PCC’s website and subscribe to the newsletter. That way you’re always up to date on new grant options. If you have research you think might be relevant to the PCC’s work, try measuring it against the organization’s research priorities, which you can find here. After all, you might be surprised by some of the fields that crossover into anti-doping. You can read about some of those fields here. If you’re interested in the overlap between mass spec and anti-doping specifically, you can read about it here. The PCC hopes to see an application with your name on it!

Slides (PDF)

Dr. Rosano is board certified in forensic toxicology by the American Board of Forensic Toxicologists and in clinical chemistry by the American Board of Clinical Chemistry. For over 35 years Dr. Rosano has been director of Clinical Chemistry and Toxicology at the Albany Medical Center Hospital where in 1993 he expanded toxicology services to include postmortem toxicology services for a 22 county region. During his career at the Albany Medical Center Dr. Rosano has progressed to tenured professor of Laboratory Medicine at the Albany Medical College where he has lectured and mentored medical and graduate students along with residents and fellows. In 2018 Dr. Rosano transitioned to toxicologist and director of the National Toxicology Center at the Center for Medical Science in Albany, New York and was promoted to Professor Emeritus in Laboratory Medicine at the Albany Medical College. His current focus is on court-ordered and addiction medicine casework and the advancement of clinical and forensic toxicology through innovations in high-volume definitive screening and applications of high-resolution mass spectroscopy.

Advancing analytical technology serves as the foundation of our toxicology practice and the explosion in pharmaceutical and illicit drug use now mandates the application of definitive testing technology in both our screening and confirmatory test protocols. While nominal mass GC-MS traditionally served as the analytical technology for confirmatory drug testing, the transition to liquid chromatography coupled with tandem mass spectroscopy has largely occurred and has brought with it an emerging application of high resolution mass spectroscopy. As definitive methods further the molecular identification and certainty of drug and metabolite confirmation work, our screening protocols in many areas of clinical toxicology still rely on presumptive methods with their high false negative rates and lack of selectivity. Conversion to definitive methods of screening with expanded drug panels is clearly needed but the challenges of high-volume screening with mass spectrometry has slowed the conversion to definitive screening across many areas of clinical toxicology. The hurdles on the way to definitive screening include automated sample preparation, rapid chromatography separation, analyte-specific matrix normalization, data management, alternative confirmatory methodology and interpretive reporting of findings. The presentation will focus on one laboratory’s journey and experience with definitive screening and confirmation protocols using a novel calibration technique for matrix normalization and application of high resolution mass spectroscopy for confirmation testing. Findings in addiction medicine and pain management casework will be presented and compared with the authors experience in court-ordered and postmortem casework.

Application of High-Resolution UPLC–MSE/TOF Confirmation in Forensic Urine Drug Screening by UPLC–MS/MS
Journal of Analytical Toxicology, 2019;43:353–363

Screening with Quantification for 64 Drugsand Metabolites in Human Urine using UPLC–MS-MS Analysis and a Threshold Accurate Calibration
Journal of Analytical Toxicology, 2017;41:536–546

Definitive Drug and Metabolite Screening in Urine by UPLC–MS-MS Using a Novel Calibration Technique
Journal of Analytical Toxicology, 2016;40:628–638

Dr. Robert B. (Chip) Cody received his Ph.D. from Purdue University in 1982 under the direction of Prof. Ben S, Freiser. After graduate school, he worked at Nicolet Instruments developing methods for Fourier Transform Mass Spectrometry until 1989 when he joined JEOL USA, Inc. where he is presently Product Manager for Mass Spectrometry. Among other achievements, Dr. Cody is responsible for developing the trapped-ion tandem-in-time MS/MS and MSn techniques, laser-desorption FTICR, and is coinventor of the DART ion source. He served as Vice-President for Arrangements for the American Society of Mass Spectrometry and was awarded the 2011 Anachem Award and a 2012 Purdue University Distinguished Alumni Award. He has over 100 publications and several patents, edited (with Marek Domin of Boston College) the book Ambient Ionization Mass Spectrometry, and is author of the Mass Mountaineer software suite.

It has now been 17 years since a patent was filed describing the Direct Analysis in Real Time (DART) ion source, yet no clinical applications of DART MS are currently in use. This is not to say that DART has no potential for clinical applications! As an ambient ionization method, DART has several attractive characteristics for clinical chemistry. DART analysis is rapid and robust, and can be applied to a wide range of analytes. In combination with a high-resolution and/or tandem mass spectrometer, DART can be quite sensitive and selective. Point-of-care applications are possible if DART is combined with a compact mass spectrometer.
Several promising DART applications have been reported. Because it produces a broad profile of small-molecule biomarkers, DART is well matched with chemometric analysis for speciation and classification. Two published feasibility studies have shown the potential for microbial identification using DART MS. The first (from CDC and GA Tech) used in-situ methylation and DART to identify bacterial fatty acid profiles. The second study found that free fatty acids from a simple extraction method could identify ten different pathogens. Another study from the Fernandez lab at GA Tech showed a DART method for ovarian cancer screening with statistics that showed 100% accuracy!
Clinical toxicology is another area of potential application. DART is well established for forensic drug screening. That same capability could be used to screen for drugs and toxins to guide treatment in victims of poisoning or overdose. With relatively simple sample handling methods, detection limits for drugs in body fluids are suitable for rapid screening. DART has demonstrated the potential for monitoring drug excretion kinetics and in at least one case, detection of biomarkers for disease conditions. In a recent study, we have found that DART can be combined with another ambient ionization method (Coated Blade Spray) to provide complementary data from minimal sample volumes.
So, why has DART not yet found a place in clinical chemistry? Commercially available laboratory systems have been on the market for 15 years, and portable systems are also now commercially available. Perhaps the answer is just a need for early adopters who are willing to carry out clinical validation studies, much as the VA DFS did for forensic drug screening.

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

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

Trueness and precision are the key quality attributes of a diagnostic assay and have to be proven in validation experiments throughout each assay development. CLSI does also acknowledge the importance of these criteria, having two guidelines in place, EP9 for method comparison, and EP5 for precision studies describing the design and the analysis of the corresponding experiments. The statistical methodology for both experiments is quite advanced and cannot be operated in a bread and butter software such as Excel. For method comparison studies a Deming regression is required and in some cases also a robust Passing-Bablok regression is state-of-the-art. Classical linear regression methods are not appropriate here, as measurement errors occur for both measurement methods. For precision studies, an appropriate variance-components design should be used and statistically analyzed accordingly.

The mcr R-package is a free available open source R package, which incorporates all analysis methods for method comparison studies, with special focus on the regression methods as Deming or Passing-Bablok regression.

The VCA package is the pendant for precision experiments, where different measurement designs can be analyzed. It is also freely available as open source R-package. Both R packages have been developed and are maintained by the Roche Diagnostics R&D biostatistics department.
The talk will cover the major aspects of the analysis requirements for method comparison and variance-components studies. In addition, we show the features of both R packages, their calculation capabilities as well as the graphical representation possibilities.

Jonathan Sweedler is the James R. Eiszner Family Endowed Chair in Chemistry, the Director of the School of Chemical Sciences, and has appointments in Neuroscience, Molecular and Integrative Physiology, Bioengineering and Medicine. His research interests focus on developing new approaches for assaying small volume samples, and in applying these methods to study novel interactions between cells. These analytical approaches include capillary separations, single cell mass spectrometry and mass spectrometry imaging. He has used these tools to characterize small molecules and peptides in a range of animal models across the metazoan and in samples as small as individual cells and cellular domains. Sweedler has published more than 500 manuscripts and presented 500 invited lectures. He is currently the Editor-in-Chief for Analytical Chemistry.

In the postgenomic era, one expects the suite of chemical players in a brain region to be known and their functions uncovered. Perhaps surprisingly, many neurochemicals remain poorly characterized and for those that are known, their localization, dynamics and function are oftentimes unknown. Mass spectrometry imaging (MSI) and single cell measurements using spatially targeted MS are highlighted. Using these approaches, we can measure lipids, fatty acids, neurotransmitters and neuropeptides, among others. For single cell measurements, the cells of interest are scattered across a microscope slide, the exact cell positions determined via optical microscopy, and mass spectra are acquired only at the cell positions. The single cell assays allow differences in the metabolome and peptidome from supposedly homogeneous populations of cells to be explored. By obtaining information from tens of thousands of individual cells, rare cells are found and unusual neurochemicals are discovered. Machine learning based approaches are highlighted to extract details on differences between targeted cellular populations.

While MS is one of the most information rich chemical characterization approaches, additional complementary information ranging including immunohistochemistry and vibrational spectroscopy aids in identifying cell types and in determining optimum follow-up studies. For select cells, follow-up capillary electrophoresis-mass spectrometry also is performed. Several applications of MSI and single cell mass spectrometry are highlighted from the discovery of unusual metabolites to characterizing the both known and previously unknown neuropeptides and hormones. Our overarching goal is to uncover the complex chemical mosaic of the brain and pinpoint key cellular players involved in a range of physiological and pathological processes.

Lingjun Li is a Vilas Distinguished Achievement Professor and the Charles Melbourne Johnson Distinguished Chair Professor of Pharmaceutical Sciences and Chemistry at the University of Wisconsin-Madison (UW-Madison). Dr. Li received her B.E. degree in Environmental Analytical Chemistry from Beijing University of Technology, China and her Ph.D. degree in Analytical Chemistry/Biomolecular Chemistry from the University of Illinois at Urbana-Champaign (UIUC). She did three-way postdoctoral research at the Pacific Northwest National Laboratory, Brandeis University, and UIUC before joining the faculty at UW-Madison in December 2002. Her research interests are in analytical neurochemistry, neuroproteomics and biological mass spectrometry. Dr. Li published more than 300 papers and has given over 200 invited talks. She was the recipient of the ASMS Research Award, NSF CAREER Award, Sloan Fellowship, PittCon Achievement Award, and ASMS Biemann Medal, and was named one of the Top 50 most influential women in the analytical sciences and featured in the 2019 and 2021 Top 100 Power List by the Analytical Scientist. Dr. Li is currently an Associate Editor for the Journal of the American Society for Mass Spectrometry (JASMS) and served on the Board of Directors for the US HUPO.

Mass spectrometric imaging (MSI) provides an attractive opportunity to detect and probe the molecular content of tissues in an anatomical context. This technique creates distribution maps of select compounds without the need for priori knowledge of target analytes. In this presentation, I will describe our efforts and recent progress in mapping and imaging of a wide variety of signaling molecules in several biological systems, highlighting the unique challenges and important roles of MSI in the areas of proteomics, peptidomics, and metabolomics.

Although high resolution accurate mass (HRAM) MSI platform offers unique advantages for mapping small molecule metabolites due to its high resolution and accuracy measurement, typical MALDI-LTQ-Orbitrap platform suffers from limited utility for large peptide and protein analysis due to its maximum m/z 4000. To overcome this challenge, we employed volatile matrices to produce multiply charged ions in MALDI source via laserspray ionization (LSI) and matrix assisted ionization in vacuum (MAIV) techniques on the MALDI Orbitrap platform. These new ionization techniques enabled substantial expansion of the mass range of the instrument and generated improved fragmentation efficiency compared to traditional MALDI-MS. To further enhance the chemical information extracted from in situ MALDI MSI experiments, we report on a multiplex-MSI method, which combines HRAM MSI technology with data dependent acquisition (DDA) tandem MS analysis in a single experiment. To improve the dynamic range and efficiency of in situ DDA, we introduce a novel gas-phase fractionation strategy prior to MS/MS scans, to decrease molecular complexity of tissue samples for enhanced peptidome coverage. In addition, the application of HRAM MALDI MSI to lipid analysis in a restenosis rat model and the utility of a novel subatmospheric pressure (SubAP)/MALDI source coupled with a Q Exactive HF hybrid quadrupole-orbitrap mass spectrometer for in situ imaging of glycans from formalin-fixed paraffin-embedded (FFPE) tissue sections and its translation to clinical cancer tissue microarray analysis will be highlighted. Finally, to further improve the sensitivity of MALDI MSI, a photoactive compound, 2-nitrobenzaldehyde is used to initiate a nanosecond photochemical reaction (nsPCR). This nsPCR strategy enables enhanced neuropeptide identification and visualization from complex tissue samples through on-demand removal of surrounding matrices within nanoseconds. The utility of this new approach for in situ analysis of endogenous biomolecules is evaluated and demonstrated.

Olga Vitek is a professor at Northeastern University. She joined Northeastern in the summer of 2014 with a joint appointment in the College of Science and the Khoury College of Computer Sciences. She was previously named the Sy and Laurie Sternberg Interdisciplinary Associate Professor at Northeastern University.

Prior to joining Northeastern, she was an assistant professor and then a tenured associate professor at Purdue University, with a joint appointment in the Department of Statistics and Department of Computer Science (2006-2014). She interned at Eli Lilly & Company in Indianapolis and held a position of post-doctoral associate in the Aebersold Lab at the Institute for Systems Biology in Seattle.

Vitek’s work develops statistical and computational methods for systems-wide molecular investigations of biological organisms. Her group works with high-throughput large-scale investigations in quantitative genomics, proteomics, metabolomics and ionomics. This research relies on mass spectrometry and other complementary technologies to characterize the components of the biological systems, their functional interactions, and their relevance to disease.The goal of Vitek’s research is to provide statistical and computational methods and open-source software for design of these experiments, and for accurate and objective interpretation of the resulting large and complex datasets.

Vitek is a recipient of the National Science Foundation CAREER Award. During her time at Purdue University, she was a University Faculty Scholar, as well as recognized with an Outstanding Assistant Professor Teaching Award, a Graduate Student Mentoring Award, and a Teaching for Tomorrow Award. She serves on the board of directors of the U.S. Human Proteome Organization.

Quantitative mass spectrometry-based proteomics aims to distinguish systematic variation in protein abundance (due, e.g., to a treatment or a disease) from nuisance biological and technological variation. Statistical mindset is key for doing so in both repeatable and reproducible manner. Frequently, statistical tasks are viewed as limited to detecting differentially abundant proteins. In reality, statistical components of reproducibility are substantially broader. They include all aspects of data processing (Which features should we use to quantify a protein? How should we combine the features into a protein-level conclusion?). They also include aspects of experimental design, from both biological perspective (Which proteins and samples, and how many, do we need to quantify?) and technological perspective (Are the assays appropriate for the task? Do the experimental steps run properly?). Answering these questions requires the availability of statistical methods, and but also of publicly available data that help understand the advantages and the limitations of the methodological choices. This talk will highlight the contributions of our lab to these components of reproducible research.

Dr. Muotri earned a BSc in Biological Sciences from the State University of Campinas in 1995 and a Ph.D. in Genetics in 2001 from University of Sao Paulo, in Brazil. He moved to the Salk Institute as Pew Latin America Fellow in 2002 for a postdoctoral training in the fields of neuroscience and stem cell biology. He has been a Professor at the School of Medicine, University of California in San Diego since late 2008. His research focuses on modeling neurological diseases, such as Autism Spectrum Disorders, using human induced pluripotent stem cells and brain organoids. He has received several awards, including the prestigious NIH Director’s New Innovator Award, NARSAD, Rock Star of Innovation from CONNECT, NIH EUREKA Award among others.

Structural and transcriptional changes during early brain maturation follow fixed developmental programs defined by genetics. However, whether this is true for functional network activity remains unknown, primarily due to experimental inaccessibility of the initial stages of the living human brain. We developed cortical organoids that spontaneously display periodic and regular oscillatory network events that are dependent on glutamatergic and GABAergic signaling. These nested oscillations exhibit cross-frequency coupling, proposed to coordinate neuronal computation and communication. As evidence of potential network maturation, oscillatory activity subsequently transitioned to more spatiotemporally irregular patterns, capturing features observed in preterm human electroencephalography (EEG). These results show that the development of structured network activity in the human neocortex may follow stable genetic programming, even in the absence of external or subcortical inputs. Our approach provides novel opportunities for investigating and manipulating the role of network activity in the developing human cortex. Applications for neurodevelopmental disorders and brain evolution will be discussed.

Mike's academic background spans across the fields of physics, biochemistry, electrical engineering, and medicine. During his residency he became interested in developing novel methods for immunohistochemical multiplexing using mass spectrometry leading to the development of MIBI during his postdoctoral work in the Nolan lab at Stanford University. Mike is now interested in optimizing MIBI and other mass reporter-based technologies further with the goal of identifying new transcriptional and translational signatures in solid tissue malignancies, and in allergic and other immunological disorders, that can be used to improve clinical diagnosis and treatment.

Michael Angelo is an assistant professor in the Department of Pathology at Stanford University. He is board certified in clinical pathology and a recipient of the NIH Director’s Early Independence Award. Dr. Angelo received a BS in Physics from the University of Mississippi in 2002 and subsequently enrolled at Duke University, where he received an MD and PhD in Electrical and Computer Engineering in 2010. He trained in clinical pathology at UCSF and completed a postdoctoral research fellowship in the lab of Garry Nolan. His main research focus is creating and applying next generation instrumentation and methods for nanometer scale, multiplexed, quantitative imaging of genes and proteins in clinical tissue biopsies. With this in mind, his lab has developed a purpose-built instrument that utilizes high brightness primary ion sources and orthogonal time-of-flight mass spectrometry to rapidly image antibodies tagged with elemental metal reporters in intact tissue sections at sub-cellular resolution. Multiplexed ion beam imaging by time of flight (MIBI-TOF) permits simultaneous, rapid, and quantitative imaging of up to 42 metal-labeled antibodies at resolutions down to 250nm. This technology is being utilized in Dr. Angelo’s lab to characterize the phenotype and spatial organization of infiltrating immune cells in breast carcinoma, lung carcinoma, and melanoma. In addition to immune oncology, MIBI-TOF is being utilized to study immune tolerance in granulomatous inflammation, at the maternal fetal interface, and in solid organ transplantation.

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

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

Recent discoveries put metabolism into the spotlight. Metabolism not only fuels cells but also plays key roles in health and disease in particular in cancer, inflammation, and immunity. In parallel, emerging single-cell technologies opened a new world of heterogeneous cell types and states previously hidden beneath population averages. Yet, methods for discovering links between metabolism, cell states, metabolic plasticity and reprogramming on the single-cell level and in situ are crucially lacking. Our research aims to bridge this gap. First, I will explain how the emerging technology of imaging mass spectrometry can be used for the spatial profiling of metabolites, lipids, and drugs in tissues. I will present our cloud and Artificial Intelligence-powered platform METASPACE which is increasingly used across the world. In the second part of my talk I will focus on our method SpaceM for spatial single-cell metabolomics in situ. We applied SpaceM to investigate hepatocytes stimulated with fatty acids and cytokines, a model mimicking the inflammation-associated transition from the fatty liver disease NAFLD to steatohepatitis NASH. We characterized the metabolic state of steatotic hepatocytes and metabolic plasticity associated with the inflammation. We discovered that steatosis and proliferation take place in distinct cell subpopulations, each with a characteristic spatial organization and metabolic signatures. Overall, such methods open novel avenues for understanding metabolism in tissues and cell cultures on the single-cell level.

Dr. McMillin is a Professor (Clinical) at the University of Utah in the Department of Pathology and a Medical Director for Clinical Toxicology, Mass Spectrometry and Pharmacogenomics at ARUP Laboratories. She received her Ph.D. in Pharmacology and postdoctoral training in clinical chemistry from the University of Utah. Dr. McMillin is board certified by the American Board of Clinical Chemistry in Clinical Chemistry and Toxicological Chemistry. She also currently serves as a member of the Executive Board for the ARUP Institute of Clinical and Experimental Pathology and is actively involved in several external Professional Organizations.

Dr. Johnson-Davis is an Associate Professor (Clinical) at the University of Utah in the Department of Pathology and a Medical Director for Clinical Toxicology at ARUP Laboratories. She received her B.S. degree in Biochemistry from the University of California, Riverside and her Ph.D. in Pharmacology from the University of Utah. She was a postdoctoral research associate at the Center for Human Toxicology and she completed a postdoctoral fellowship in clinical chemistry at the University of Utah, Department of Pathology. Dr. Johnson-Davis is board certified by the American Board of Clinical Chemistry in Clinical Chemistry in Clinical Chemistry and Toxicological Chemistry and she is the Director for the Clinical Chemistry Fellowship Program at the University of Utah.

Alcohol use is widespread, and when used in excess, is associated with many negative health and social consequences. As such, detection of alcohol use/exposure is relevant to many clinical scenarios such as substance use disorder clinics, surgery qualification, chronic pain management and pregnancy. In this webinar we will provide an overview of the biomarkers commonly used to detect and monitor alcohol exposure. We will also describe approaches and limitations to detecting and measuring concentrations of alcohol metabolites in urine, whole blood, meconium and umbilical cord tissue by LC-MS/MS.

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.

Sarah Delaney, MSc, PhD, is a second year Clinical Chemistry Fellow at Mayo Clinic (Rochester, MN) currently serving as an Acting Director in the Clinical and Forensic Toxicology Laboratory. She completed both her MSc and PhD in the Department of Pharmacology and Toxicology at the University of Toronto. Before entering her PhD program, Sarah was active in the clinical chemistry community in her role as the clinical project coordinator for the Canadian Laboratory Initiative on Pediatric Reference Intervals (CALIPER) study at SickKids Hospital in Toronto. Her scientific interests include drug monitoring in pain management patients and neonatal/pediatric laboratory medicine.

Pain is one of the most common reasons people seek care and affects more Americans than diabetes, heart disease and cancer combined. Treatment is subjective as pharmacological interventions using opiates and opioids involve empirical adjustments based upon observed clinical outcomes including the presence of adverse drug reactions. Addiction and diversion of pain management medications is also a growing problem and a key concern for clinicians. Therefore, professional organizations and published recommendations include the use of laboratory tests, specifically urine drug testing. As a result, physicians are using a variety of urine drug tests to provide objective measures to effectively manage pain patients, assess compliance, and detect diversion. This session will focus on the use of mass spectrometry-based urine tests and discuss the advantages and limitations of these assays.

Following this session the participants will be able to:

Describe the advantages and challenges of mass spectrometry-based testing for pain management patients.
Successfully overcome some of the challenges associated with mass spectrometry-based urine drug testing for pain management patients
List some future opportunities for mass spectrometry-based pain management testing.

Expected Outcomes:
Detailed understanding of the advantages and challenges of mass spectrometry-based urine drug testing for pain management patients.

Needs Assessment:
Urine drug testing is recommended by multiple clinical practice guidelines for use in the management of pain patients. Due to the lack of standardized laboratory test offerings, methodologies, and reporting formats coupled with incomplete knowledge surrounding the limitations of each type of laboratory test, incorrect interpretation by clinicians is possible. This webinar will discuss the strengths and limitations of using mass spectrometry-based testing for compliance monitoring of pain management patients. It will also discuss various strategies to overcome some of the challenges and future opportunities.

Christa Cobbaert is a Laboratory Specialist in Clinical Chemistry and Laboratory Medicine and heads the Department of Clinical Chemistry and Laboratory Medicine at LUMC, Leiden.
She is vice-chair of the International Federation of Clinical Chemistry Scientific Division Executive Committee and chair of the European Federation of Laboratory Medicine Working Group on Test Evaluation . She is an expert in metrology, i.e. the science of measurement, which is essential for global standardization c.q. harmonization of medical tests.

Introduction

Lipoprotein(a) (Lp(a)) is a lipoprotein particle that is causally related with atherosclerotic disease, myocardial infarction and aortic valve stenosis. The recent introduction of Lp(a) lowering medication has caused large interest in Lp(a) quantitation. The Lp(a) particle consists of an LDL particle to which an apolipoprotein (a) (apo(a)) protein is covalently bound via a disulfide bridge. Apo(a) contains a number of kringle IV repeats, a kringle V and a protease domain, and varies widely in size due to a size polymorphism in kringle IV-2. The Lp(a) particle holds a lipid core consisting of free cholesterol, phospholipids, cholesteryl esters and triglycerides, apoB and apo(a), and its concentration is traditionally expressed in mass units. Yet, apo(a) size heterogeneity and post-translational modifications such as N- and O-glycosylation of apo(a) affect the molecular mass of Lp(a) particles. We assessed the impact of defining the measurand at the molecular level using bottom-up proteomics, in relation to apo(a) size polymorphism and available PTMs.

Methods

The chemical composition of Lp(a) was assessed through literature study, and the masses of apoB and apo(a) were determined based on their amino acid sequence. A model for the molecular composition of Lp(a) was developed based on the assumption that the lipid composition of the particle is not affected by the apo(a) size polymorphism. The number of kringle IV-2 repeats reported in literature is 3-50, and chemical compositions were calculated for these values. Glycosylation patterns of both apoB and apo(a) were taken into account.

Results

The outcomes of the developed model correspond well with previously reported chemical compositions of Lp(a) [1,2]. An Lp(a) particle containing only three kringle IV-2 repeats per apo(a) is calculated to have a particle mass of 2,767 kDa with a lipid portion of 70% (w/w), apoB of 20% (w/w) and apo(a) of 10% (w/w). However, for a particle containing 50 kringles, the particle mass is 3,639 kDa with a lipid portion of 53% (w/w), apoB of 16% (w/w) and apo(a) of 31% (w/w). The huge mass variation of Lp(a) impedes Lp(a) standardization efforts, whereas molecular characterization of the apo(a) measurand and molar expression of apo(a) content may avert standardization problems.

Conclusions

The expression of Lp(a) particle concentrations in mass units is metrologically inappropriate and should be abandoned. Mass spectrometry using LC-MRM-MS allows molecular characterization of the apo(a) measurand and enables accurate quantitation in molar units, unaffected by the apo(a) size polymorphism and glycosylation. Future traceability of apo(a) to SI units can only be accomplished with an unequivocally molecularly defined protein measurand and the consistent use of molar units [3].

References
1. Kostner et al. J Lipid Res. 1999;40:2255-63.
2. Tsimikas et al. J Clin Lipidol. 2018;12:1313-23.
3. Cobbaert et al. Clin Chem Lab Med. 2018;56:1598-1602.

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).)

Background: So far, most publications reporting mass spectrometry-based measurement methods intended for diagnostic use describe in detail the method realization in one individual laboratory site - showing a very limited level of abstraction

Methods: To overcome this limitation we suggest a standardized approach to reporting LC-MS based methods, differentiating between fundamental characteristics of a measurement method on the one hand; and variable characteristics on the other hand. In this concept, fundamental characteristics are those that can be essentially translated into separate realizations too - e.g. the mode of ionization (e.g., electrospray in positive polarity) or the m/z ratio of monitored ions. They are intended to define in their entirety the identity of a measurement method. In contrast, variable characteristics are those that cannot realistically be standardized over time and space – e.g. the lot of a chromatographic column or of solvents, or the instrument specific geometry of the ion source that is highly manufacturer dependent, as well as instrument tuning settings.

Results: We have developed a preliminary set of 35 fundamental characteristics – defining a measurement procedure generically; these also include well-defined essential system performance characteristics – e.g. the required mass resolution, or a signal readout for the lowest concentrated calibrant. Furthermore, we suggest a set of 15 variable characteristics – which should be documented for each individual implementation and analytical run to achieve methodological traceability of individual results.

Conclusion: We recommend this novel standardized approach to method description for discussion and evaluation in the community.

Currently Folker is the Professor for regulatory affairs and quality management for medical devices at the University of Applied Sciences, Luebeck, Germany Drug and medical device regulatory affairs, standardization, quality management, conformity assessment, accreditation, laboratory medicine, in vitro diagnostic medical devices. His focus area of clinical/scientific work is drug and medical device regulatory affairs, standardization, quality management, conformity assessment, accreditation, laboratory medicine, in vitro diagnostic medical devices. Since 2005 until present experience as consultant, scientific expert, advisor for WHO, EU, PTB and other organizations in numerous international projects related to regulatory affairs, quality assurance, quality management, biosafety/biosecurity, accreditation/certification and standardization of medical/health laboratories.

The current regulatory rules governing in vitro diagnostic medical devices (IVDMD) in the European Union are mainly represented by the European IVD Directive dating back from 1998. This directive does not cover devices with characteristics related to newer techniques and applications in current in vitro diagnostic testing. It also lacks conformity with current international guidelines and regulation systems with regard to a number of regulatory elements such as risk-based classification of IVDMD, clinical evaluation, identification and labelling of IVDMD and handling of requirements for “in-house testing” (referring to devices manufactured and used within one single health facility).


The new Regulation (EU) 2017/746 (“IVDR”) will have to be fully implemented by May 2022 and aims at solving these shortcomings. It will therefore significantly change the regulatory requirements for manufacturers and other stakeholders such as notified bodies and competent authorities. It will also largely impact medical laboratories with their different roles as users of IVDMD, as manufacturers of “in-house”- IVDMD and as institutions involved in performance/clinical evaluation of new devices.


This web session will give an overview on the chances and challenges derived from the IVDR with a special focus on medical laboratories.

Dr Grant earned a PhD in chromatographic and mass spectrometric technologies from the University of Swansea, Wales, United Kingdom. He continued his scientific training in various industrial settings, which have included senior scientist at GSK, principal scientist at Cohesive Technologies, technical director at Eli Lilly, and director of mass spectrometry at Esoterix Endocrinology.

Dr Grant has pioneered the use of direct injection technologies, chromatographic systems multiplexing, utility of automation, and new analytical platforms for application in bioanalytical applications. His research goals are focused upon improvements in speed, sensitivity, and quality of liquid chromatography with tandem mass spectrometric (LC-MS/MS) analytical systems and assays.

Dr Grant serves as clinical chemistry chair for the American Society of Mass Spectrometry and is a member of the American Association for Clinical Chemistry

Introduction

Internal standards are ideally a perfect mimic for analytes and correct for a multitude of analytical variance and bias, when designed and used correctly. Internal standards provide qualitative details that can elucidate confidence in results release apriori, such as enabling analyte peak selection (retention time) and expected peak shape (asymmetry). Internal standards are used quantitatively to correct for inter-sample recovery variance (absolute recovery and matrix effects), as such, much credence is afforded to their performance. In our experience over >15 years, many confounding and fundamental errors in these simple premises are observed. This has led to extensive determination of absolute agreement between analytes and internal standards, with some rather surprising outcomes.

Methods

Key experimental considerations and "cause-effect" will be detailed to establish when internal standards are behaving in a manner consistent with the analyte.

Session 1 will include: What level should I add IS at? what does the IS actually do? Qualitative details and error observations, quantitative assessment of binding equivalency (Reverse admixing - and when it can be misleading), drift over time using dynamic extraction and automation tools (and how to both elucidate and correct).

Session 2 will highlight examples of internal standardization failures such as the impact of excessive labeling, Isotopic contribution (from and to analyte), and when to use an "analog" internal standard - correctly.

Session 3 will detail expanded uses of Internal standards such as in-vitro redox correction (prior to receipt in the laboratory for sample analysis), results reporting outside the calibration range and how an internal standard can be used as a calibration system (and when not to!)

Results

The end result in each of these examples is an LC-MS/MS assay that is appropriate for use in patient management - in every scenario.

Conclusions & Discussion

You will take home a number of key developmental tools and practical solutions to get the most out of your Internal Standards and know when and hopefully how to correct implicit errors in their use to provide high quality actionable results using LC-MS/MS.

Dr. Clarke received his Ph.D. in Analytical Chemistry from the University of Nebraska in Lincoln in 2000, followed by a post-doctoral fellowship in Clinical Chemistry at the Johns Hopkins School of Medicine, ending in 2002. In addition, he received an MBA focused on medical services management from the Carey School of Business at Johns Hopkins in 2007. Following his post-doctoral fellowship, he remained at Johns Hopkins, where he is a Professor in the Department of Pathology, as well as the director of Point-of-Care Testing, Reference Toxicology, and Phlebotomy for the hospital. He also serves as the Vice-Chair for Quality and Regulatory Affairs in the Department of Pathology. His research interests include clinical mass spectrometry, method development and evaluation for therapeutic drug monitoring, clinical toxicology, point-of-care testing, and development/validation of biomarkers for use in drug management. Dr. Clarke has published as author or co-author over 170 peer-reviewed manuscripts or book chapters, and is the Co-Editor of the textbook Contemporary Practice in Clinical Chemistry.

Cases are reviewed that range from simple human error during routine production, to evolution of method protocols to add robustness, to process improvements implemented to cope with too many specimens from a large clinical trial. The perspective of troubleshooting as a filter that can uncover issues to then address with quality improvement processes is highlighted.

1. list basic approaches to LC-MS/MS trouble shooting

2. discuss common causes for LC-MS/MS assay problems

3. formulate strategies for LC-MS/MS troubleshooting, and converting them to QA processes.

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

Learn from the experiences gained at a large reference laboratory that was an early adopter of LC-MSMS and successfully executed high test volumes and sophisticated methods. Follow the painstaking inquiries necessary to solve devious and difficult cases that occurred with LC-MSMS testing for endocrine and other analytes. Quality measures that can detect or prevent subtle variance from normal method performance are reviewed.

1. outline an overall strategy for troubleshooting problems in a clinical mass spectrometry lab,

2. explain the relationship between record keeping and troubleshooting in a clinical mass spectrometry lab

1. resolve discrepancies in proficiency testing

2. find ways to monitor drugs with poor fragmentation patterns

3. monitor drugs which are nearly completely metabolized

4. establish comparative criteria for drugs not in proficiency tests

Judy Stone, MT (ASCP), PhD, DABCC has worked with LC-MS in diagnostic laboratories since 1999. Her clinical practice involved small molecule method development, instrument to instrument and instrument to LIS interfacing, LC-MS automation, monitoring quality of LC-MS methods in production and staff training for clinical LC-MSMS. She served as faculty chair for the 2009 AACC online certificate program “Using Mass Spectrometry in the Clinical Laboratory”, as a scientific committee member for the MSACL Practical Training track, and is editor-in-chief for the AACC Clinical Laboratory News quarterly feature series on Clinical LC-MS. She enjoys documenting and presenting esoteric as well as absurdly common LC-MS problems in creative ways in order to help trainees learn troubleshooting (and avoid repeating her mistakes).

Learn the tools and strategies of LC-MSMS troubleshooting and work through cases found all too often during routine operation. Selected best practices for robust instrument operation, preventative maintenance and basic repairs are presented.

1. list 3 troubleshooting tools for LC-MSMS,

2.create a calendar for LC-MSMS preventative maintenance,

3.describe checks to distinguish an LC problem from a Sample Preparation mistake from an MSMS loss of sensitivity.