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

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

Stuck @Home without a conference in sight? An on-line symposium on mass spectrometry based science in southern California is planned for December 1-2. The program will consist of short talks with keynote presentations by John McLean of Vanderbilt University and Lisa Jones of University of Maryland. We are soliciting abstracts for talks over a broad range of mass spectrometry topics including but not limited to proteomics (bottom up, top-down, native), metabolomics, MS computation, lipidomics, pharma, therapeudics, and clinical MS. We encourage and will select speakers from abstracts submitted by graduate students, post-doctoral fellows and assistant professors located in Southern California for speaking slots. We hope this will be a diverse program covering the many uses to mass spectrometry and bring together the local MS community.

Submit your abstract at www.socalms.org.

Abstract Topics:
Genomics
Proteomics
Lipidomics
Metabolomics
Imaging
Exposome
Environmental
Precision Medicine and clinical chemistry
Pharma and therapeutics
Other (Don't see your topic above? Submit anyway - all Mass Spec research is welcome!)

Keynotes:
John McLean, PhD
December 1, 8:30 - 9:15am Pacific
High Dimensional Molecular Phenomics in Systems, Synthetic, and Chemical Biology
One of the predominant challenges in systems-wide analyses and molecular phenomics is the broad-scale characterization of the molecular inventory in cells, tissues, and biological fluids. Advances in computational systems biology rely heavily on the experimental capacity to make omics measurements, i.e. integrated metabolomics, proteomics, lipidomics, glycomics, etc., accompanied with fast minimal sample preparation, fast measurements, high concentration dynamic range, low limits of detection, and high selectivity. This confluence of figures-of-merit place demanding challenges on analytical platforms for such analyses. Ion mobility-mass spectrometry (IM-MS) provides rapid (ms) gas-phase electrophoretic separations on the basis of molecular structure and is well suited for integration with rapid (us) mass spectrometry detection techniques. This report will describe recent advances in IM-MS integrated omics measurement strategies in the analyses of complex biological samples of interest in systems, synthetic, and chemical biology in clinical chemistry applications. New advances in bioinformatics and biostatistics will also be described to approach biological queries from an unbiased and untargeted perspective and to quickly mine the massive datasets gathered to provide targeted and actionable information.

Lisa Jones, PhD
December 2, 11:04 - 11:50am Pacific
In-Cell Footprinting Coupled with Mass Spectrometry for Proteome-Wide Structural Biology
In recent years, protein footprinting coupled with mass spectrometry has been used to identify protein-protein interaction sites and regions of conformational change through modification of solvent accessible sites in proteins. The footprinting method, fast photochemical oxidation of proteins (FPOP), utilizes hydroxyl radicals to modify these solvent accessible sites. We have further extended the FPOP method for both in-cell and in vivo analysis of proteins which allows for the study of proteins in their native cellular environment. A major application of the in-cell method is for proteome-wide structural biology. In one such application, we used in-cell FPOP (IC-FPOP) to identify on and off targets of the anti-cancer drug Gleevec in triple negative breast cancer cells. We have further extended the FPOP method for analysis in C. elegans, a member of the nematode family. This allows us to study protein structure directly in animal model for human disease.

Jen leads the Global Discovery & Bioanalytical Sciences group at Novartis, where she directs the scientific and operational strategy for the bioanalysis of small and large molecule therapeutics. Jen is also responsible for identifying new bioanalytical technologies and solutions to support the Novartis portfolio. Jen received her BSc in Chemistry from the University of Alberta in Edmonton, AB Canada, then completed her graduate studies receiving a MS and a PhD in Chemistry from the University of Michigan. Jen then completed her postdoctoral fellowship in the analytical chemistry department at Pfizer in Ann Arbor, MI. Jen has worked for numerous pharmaceutical companies over the past 2 decades in the bioanalytical field, spanning the pipeline from discovery through the clinic. She also developed expertise in large molecule mass spectrometry analysis while working at the Proteomics Core facility at Oregon Health and Science University in Portland, OR.

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

Candice is an Assistant Chemist at the Pacific Environmental Science Centre, working under the supervision of Dr. Dayue Shang. She is also currently a 4th year Honours Chemistry undergraduate student at the University of British Columbia.

Josh is a Laboratory Scientist in the Newborn Screening and Biochemical Genetics Laboratories at BC Children's Hospital in Vancouver, Canada. He has a BSc in Chemistry from Simon Fraser University and a MSc in Chemistry from the University of Toronto. After working in the clinical and pharmaceutical industry for 4 years Josh returned to academia and completed a PhD in Experimental Medicine from the University of British Columbia with a focus on cardiovascular disease. Josh is passionate about developing and implementing innovative analytical strategies in the clinical laboratory with a focus on mass spectrometry!

You are invited to join the British Columbia Mass Spectrometry User's Group meeting.
The virtual session will include:

Speaker: Jennifer Cunliffe, PhD
Title: Application of High Resolution Mass Spectrometry for Proteomics

Speaker: Grace van der Gugten
Title: When Mass Spec gives the wrong answer: Investigating where and why an assay went wrong.
Summary: Routinely unacceptable EQA results for our LC-MS/MS assay for 1,25-dihydroxyvitamin D prompted an investigation into our assay. This presentation will share the investigation steps taken, the possible causes and the resulting solution.

Speaker: Candice Chua
Title: Enhanced weathered crude oil analysis by GC/FID, GC/MS diagnostic ratios, and multivariate statistics
Summary: In a simulated case study, artificially weathered crude oil “spill” samples were matched to unweathered suspect “source” oils through a three-tiered approach as follows: Tier 1 gas chromatography-flame ionization detection (GC/FID), Tier 2 gas chromatography-mass spectrometry (GC/MS) diagnostic ratios, and Tier 3 multivariate statistics of GC/MS data. This study served as proof of concept for a promising and new method of crude oil forensics that applies principal component analysis (PCA) and partial least squares discriminant analysis (PLSDA) in tandem with traditional forensic oil fingerprinting tools to confer additional confidence in challenging oil spill cases.

Speaker: Joshua Dubland, PhD
Title: Making a sour analysis sweet again: Case studies
Summary: Case 1 - Post-validation, an LC-MS/MS assay shows dramatically reduced signal intensity for one analyte following a laboratory reorganization. Case 2 – Differentiating between two co-eluting isomers by GC-MS when changing the column isn’t an option.

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

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

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

This is a 2-Day Course with 7 total contact hours.

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

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

Thursday

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

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

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

Friday

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

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

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

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

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

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

Devin J. Swiner currently is a 5th year, PhD candidate working under Dr. Abraham Badu-Tawiah at The Ohio State University. Since graduating from The University of Pittsburgh in 2016 with her B.S. in Chemistry, her current research is focused on developing a new ionization source for mass spectrometry using cellulose materials for applications in clinical diagnostics. At OSU, she serves as Chapter President of the National Organization for the Professional Advancement of Black Chemists and Chemical Engineers (NOBCChE) and as Vice President for the Black Graduate and Professional Student Caucus. In these capacities, she is able to mentor students as they grow and develop during their programs, an effort that awarded her The Susan M. Hartmann Mentoring and Leadership Award in 2018. In her free time, she also co-runs a blog, #MacScientist, whose goal is to increase representation of black women in STEM fields, and more recently co-founded a #BlackInChem Twitter campaign, to amplify and celebrate Black chemists. Her advocacy work is documented on her professional website, Devinthechemist.com.

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.

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

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.

Needs Assessment: Using mass spectrometry profiling of patient biofluids to reveal unknown biology, guide patient management, and ultimately deploy actionable clinical assays remains just around the corner. An ongoing approach is to build statistical power through collection of large patient plasma and urine metabolomic datasets. Fundamental limitations of liquid-biopsy sample collection, difficulties in separation of similar analytes, and the need to integrate data across multiple disciplines have delayed the clinical deployment of metabolomic analysis.

Mass spectrometry in both research and clinical labs is driven, in part, by the development and use of new technologies. This session will inform the audience as to current limitations of metabolomic mass spectrometry, introduce new approaches that have been developed to circumvent these limitations, and challenge attendees to examine the potential gains from integration of multiple data sources in patient management decisions.

Intended Audience: This session is intended for clinical and anatomic pathologists, physicians, clinical chemists and laboratory directors, and bench and data scientists.

Learning Objectives:
After this session, participants will be able to:
1) Define metabolomic mass spectrometry.
2) Explain the benefits of integrating measurements of endogenous metabolites with proteomic and metagenomic data.
3) Identify contexts where time- or spatially resolved mass spectrometric analyses are of particular value.
4) Differentiate multi-analyte mass spectral profiling from targeted quantitation.
5) Appreciate the expanding role of mass spectrometry in the clinical and anatomic pathology laboratory.

Expected Outcome:
After this session, participants will be able to:
1) Define metabolomic mass spectrometry.
2) Explain the benefits of integrating measurements of endogenous metabolites with proteomic and metagenomic data.
3) Identify contexts where time- or spatially resolved mass spectrometric analyses are of particular value.
4) Differentiate multi-analyte mass spectral profiling from targeted quantitation.
5) Appreciate the expanding role of mass spectrometry in the clinical and anatomic pathology laboratory.

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

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

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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.

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.

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.

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.

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

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

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

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

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

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

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

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

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

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

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

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

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

Notice:
Scholarships are available thanks to a generous grant from SCIEX.
Open to all applicants, no restriction on region or demographics.
Apply Here.

Online Format

This is a virtual version of the short course that has been presented at MSACL. This online course includes 2.5-5 hours of live lecture each day for four days. Using Zoom (live online lectures, breakout rooms for interactive sessions) and Google Classroom (forms and job aids for download, on demand short lecture videos) provides additional opportunities for interactive and self-paced learning, both during the four-day course and beyond.

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

Course Content Description

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

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

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

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

Dr. Kara Lynch is an Associate Professor of Laboratory Medicine at the University of California San Francisco, Co-Director of the Core Laboratory at Zuckerberg San Francisco General Hospital, and Chemistry Director at UCSF Benioff Children’s Hospital Oakland. She received her PhD in Biochemistry from the University of Wisconsin and did a post-doctoral fellowship in Clinical Chemistry at UCSF. Her laboratory conducts studies aimed at identifying and quantifying endogenous and exogenous small molecules using novel diagnostic technologies, such as high resolution mass spectrometry, direct to mass spec technologies, and thin-film interferometry label-free immunoassays, and correlating findings with clinical pathologies.

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.

This course presents presents a comprehensive overview of technology and techniques of analytical mass spectrometry and from that foundation extends into exciting, disruptive recent developments.

1. Sample preparation




• Topics: New types of extraction, Issues to consider, Isolation of proteins from biological samples Ultrafiltration, Affinity techniques, Molecularly Imprinted Polymers (MIP?s), Aptamers, Thermo's MSIA pipette tips, Electro Extraction, Quechers, SISCAPA, Micro extractions: Dried blood spots (DBS), Dried Plasma Spots (DPS).
  


2. Advanced separation techniques for large molecules




• Topics: UHPLC, Hydrophobic Interaction Chromatography (HIC), Nano-UHPLC, Micro LC/MS, Size Exclusion Chromatography (SEC), ion exchange chromatography, Capillary Electrophoresis (CE), Differential Mobility Spectrometry (DMS).
  




3. Ionization techniques for MS




• Topics: Electrospray ionization (ESI), Nano ESI, Micro ESI, Atmospheric pressure chemical ionization (APCI), Atmospheric pressure photoionization (APPI), Matrix assisted laser desorption ionization (MALDI), LAESI, Electron Ionization (EI) and its potential for LC/MS.
  


• 
  To Discuss: New ionization techniques which may be used without on-line separation science technology. This area has evolved into a variety of ambient ionization techniques such as DESI, DART, ASAP, etc.
  





4. Mass Analyzers




• Quadrupoles, Ion traps, linear and quadrupole, Time-of-Flight (TOF), Orbitraps, Hybrid mass analyzer systems, Ion mobility spectrometers, and Differential Mobility Spectrometry (DMS).
  


• 
  To Discuss: Developments and improvements in mass analyzers including linear ion traps, FTMS, time-of-flight (TOF), orbitraps, and accelerator mass spectrometry (AMS), the latter currently being applied to micro-dosing experiments by the pharmaceutical industry. Issues such as full-scan acquisition rates, high-resolution mass spectrometry (HRMS), the importance and usefulness of exact mass measurements for qualitative and quantitative analysis, and the analytical merits compared with modern SRM LC/MS experiments will be discussed with many practical examples and applications. The latter will include clinical chemistry issues as well as pharmaceutical, food safety, environmental and industrial examples.
  




5. Imaging and profiling by MS




• Applications of recently reported ionization techniques for imaging the location of chemicals in various matrices employing MALDI, DESI, LAESI, LESA and other techniques.


• 
  Topics: The technique of MALDI and its applications to tissue imaging as well as DESI, LAESI and also liquid extraction surface analysis (LESA) employing nano-electrospray. A comparison of the various classes of compounds where MALDI and nano ESI provide complimentary coverage of certain compounds found in biological and other matrices.
  




6. High resolution MS




• Topics: Fundamentals, Mass Defects, Isotopic patterns, Mass axis calibration, Types of HRMS systems, Qual/Quan Analysis, Data mining processes, Future directions
  


• To Discuss: The analytical merits of HRAMS from QTOF as well as orbitraps and FTMS systems will be presented. Instances where either SRM LC/MS or LC HRAMS may be preferred for optimal selectivity due to chemical background or other interference issues.
  




7. Miniaturization in MS




• Topics: Purdue University "Mini 11", Torion, Microsaic, Advion expression CMS, Waters QDa
  


• 
  To Discuss: The benefits and limitations of smaller analytical instrumentation systems will be compared. This includes miniaturization of HPLC systems as well as the mass spectrometers themselves. The commercial introduction of chip-based HPLC systems closely integrated with mass spectrometers offers a glimpse of future directions in analytical chemistry.
  




8. Synergistic Integration




• A systematic overview via specific examples with applications highlighting noted examples of innovative novel and non-standard technologies which demonstrate the analytical potential of new analytical technologies.
  


• 
  Developing instrumentation and technologies will be important aspects of future mass spectrometry techniques and its expansion to important new applications. An extremely important example is the need for LC/MS bioanalysis (quantitation) of biologics (ADC?s, large molecules, RNA, etc.) in biological samples employing both bottom up and top down methods. HRAMS coupled with „protein friendly? chromatography will significantly expand our present analytical capabilities. Ion mobility spectrometry (IMS) and transportable mass spectrometers could lead to point-of-care applications and other far reaching applications of mass spectrometry beyond what we are doing today. The future is very exciting!
  

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

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

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

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

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

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

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

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

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

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


Overview:

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

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

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

Obtaining the Software

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

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

Course Description

The course will cover:

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

Course material will be provided electronically.

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.

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. Currently, Guinevere performs her post-doctoral research at the Center for Proteomics and Metabolomics at the Leiden University Medical Center, in the group of prof. Manfred Wuhrer. 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.

Noortje is conducting her post-doctoral research at the Center for Proteomics and Metabolomics at the Leiden University Medical Center, The Netherlands. She obtained her MSc degree in Pharmaceutical Sciences at the VU University Amsterdam, The Netherlands, with a focus on biomarker research and clinical chemical analysis. She received her PhD at the Leiden University Medical Center, under the supervision of prof. Manfred Wuhrer, on the development and application of various mass spectrometry-based methods for the analysis of (antibody) glycosylation. Noortje’s enthusiasm for glycoproteomic-related research started early in her scientific career and this remains a key drive in her current work. She is interested in the development of mass spectrometric methods and data analysis protocols for addressing clinical research questions.

Did you ever encounter glycans, but you -kind of- neglected them as they seemed too complicated to characterize? Or did you just perform a glycan release to make the analysis of your protein a lot easier? Do you have no idea how to interpret your data when a glycan is present? Fear no more! We are here to provide you with the basics in the field of mass spectrometric glycomics and glycoproteomics.

The course will start with a historical overview on glycan research (i.e. how did glycans work their way up to being acknowledged as important study objects) and we will guide you through the maze of different nomenclatures. Moreover, although glycans are well known for their complexity, we will reveal to you the “rules of glycan structures” based on known biosynthetic pathways. This will be followed by an in-depth discussion on glyco(proteo)mic mass spectrometric technologies and workflows. In addition, different sample preparation steps will be covered. We will close-up with a session about glycomic biomarker discovery, as it can hardly be considered a coincidence that, for example, more than 80% of the currently used cancer biomarkers are glycosylated.

The course will run over 4 days and time will be split between lectures and workshops (e.g. how do you recognize a glycan in a mass spectrum and how do you assign it). While not everything can be covered within these 4 days we will ensure that you will know your “glyco-basics” in the end. Moreover, participants are encouraged to submit any specific glyco-questions they have prior to the course and we will try to discuss them during the course.

Brief outline of the course:

1. Historical overview of glycosylation research
2. Glycans from a chemical perspective
3. The biosynthetic pathway of N-glycans, O-glycan and glycosphingolipids
4. Biological function of glycans
5. Historical overview of glycoanalytics
6. How to analyze and interpret your glycan, glycopeptide and/or glycoprotein with mass spectrometry
7. Glycomic biomarker discovery - Finding the sweet spot of the disease

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. Currently, Guinevere performs her post-doctoral research at the Center for Proteomics and Metabolomics at the Leiden University Medical Center, in the group of prof. Manfred Wuhrer. 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.

Noortje is conducting her post-doctoral research at the Center for Proteomics and Metabolomics at the Leiden University Medical Center, The Netherlands. She obtained her MSc degree in Pharmaceutical Sciences at the VU University Amsterdam, The Netherlands, with a focus on biomarker research and clinical chemical analysis. She received her PhD at the Leiden University Medical Center, under the supervision of prof. Manfred Wuhrer, on the development and application of various mass spectrometry-based methods for the analysis of (antibody) glycosylation. Noortje’s enthusiasm for glycoproteomic-related research started early in her scientific career and this remains a key drive in her current work. She is interested in the development of mass spectrometric methods and data analysis protocols for addressing clinical research questions.

This is a continuation of the course from Part 1 and is not intended to be taken separately.

this isn't it

Randy Julian is CEO, President, and Founder of Indigo BioAutomation (originally, Indigo Biosystems) located in Indiana. Randy earned a Ph.D. in Chemistry from Purdue University in 1993 and then worked in Discovery Chemistry at Eli Lilly for 14 years. Randy founded Indigo based on informatics technology developed in his research group. Dr. Julian led Indigo from its founding to profitability, building a world class management, engineering and research team to commercialize laboratory data analysis software.

Dr. Julian is a frequent speaker in the mass spectrometry community and teaches short courses in statistics and data analysis. Randy is the past Chairman of the Human Proteome Organization’s Proteomics Standards Initiative Steering Group where he coauthored two international standards for analytical data. He was also the chairman of the ASTM committee on analytical data standards. Dr. Julian also maintains an active research relationship with the faculty at Purdue University where he is an Adjunct Professor of Chemistry.

Level: Intermediate
Prereqs: Data Science 101 or 201 (or equivalent experience)

Overview: Machine learning techniques have been highly successful in driving the growth of Amazon, Google, Netflix, and other companies that rely on identifying patterns in big data. More importantly, these algorithms are beginning to revolutionize clinical diagnosis and mass spectrometry, from FDA-approved retinal image analysis to robust detection of mass spec chromatographic peaks. But ... what exactly is machine learning? How does it work? How can you apply it to your own data? In this course, we will help you sort through the hype and provide an introduction to machine learning, including an overview of common approaches, known pitfalls, and other important concepts. We will include practical instruction on applying machine learning algorithms using the R statistical language, so familiarity with R at the level of the material taught in Data Science 101 and/or 201 is desirable.