FeMS Virtual Happy Hour
Please welcome guest speaker, psychotherapist Nirmala Gratton, for a discussion on the important topics of self care and mental health.

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

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

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

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

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.

Download Schedule

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



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.

Buy the Hardcopy of the slides online at: https://www.amazon.com/dp/1950526054/

There will be no e-copy of the slides provided.

E-copies of the slides as handouts are NOT being provided.

If you desire to secure a hard copy of the slides for your records (or to follow along during the course), you will need to purchase a copy online.
 
TITLE : MSACL Connect - Short Course - LC-MSMS 101 - Jan 2021 
ISBN-10 : 1950526054
ISBN-13 : 978-1950526055

The title is available on Amazon in many countries (non-exhaustive list). 
United States https://www.amazon.com/dp/1950526054/
France https://www.amazon.fr/dp/1950526054/
Germany https://www.amazon.de/dp/1950526054/
UK https://www.amazon.co.uk/dp/1950526054/

It may also be available on Barnes & Noble and other online book-selling retailers.
 
ALERT : While the lead time in the US is currently about 1 week, it could be longer in other countries. 
ALERT : If you desire to have a copy on-hand during the course, it is advised that you order it online As Soon As Possible.

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

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

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 advanced level course 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!

Course material (copies of slides) will be provided as a PDF.

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).

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.

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

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

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.

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.

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.

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.