Daniel Holmes did his undergraduate training in Chemistry and Physics at the University of Toronto before deciding to pursue medicine as a career. He attended medical school at the University of British Columbia where pathology became his area of major interest. The strong influence of his academic mentors led him to enter the Medical Biochemistry residency training program at UBC. This allowed him to use his background knowledge of chemistry in application to medicine. Areas of clinical interest are diagnostic lipidology/endocrinology and research interests are in the utilization of mathematics and computer diagnostics to laboratory medicine.

I did my undergraduate training in Medical Laboratory Science, and post-graduate training in Pathology and Laboratory Medicine, as well as Clinical Chemistry. Currently, I work with the clinical mass spectrometry laboratory at Lurie Children’s, and use data analytics and data science principles and tools on a day-to-day basis. I’ve used R for assay development, test utilization, quality assurance, clinical reporting, and process improvement projects. I also use Excel but don’t tell Dan that.

EDUCATION:
Graduate School: University of Virginia (Chemistry), Charlottesville, VA
Clinical Chemistry and Laboratory Medicine Fellowship: University of Virginia, Charlottesville, VA

CLINICAL:
Laboratory testing in Clinical Chemistry, Toxicology, Hemostasis, and Endocrinology.

RESEARCH:
Liquid chromatography mass spectrometry assay methods.

William Slade, PhD did his undergraduate degree in Biology from Concord University with a focus on Recombinant Gene Technology. He completed a PhD in Biological Sciences at Virginia Tech with a focus on Biological Mass Spectrometry before postdoctoral work at the University of North Carolina at Chapel Hill in the Analytical Chemistry department. He is currently a Researcher in the Mass Spectrometry Research and Development group at Laboratory Corporation of America Holdings in Burlington, North Carolina. His interests include clinical mass spectrometry and informatics.

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

Have you ever tried to do Deming regression in Excel only to discover that it is not available? Have you had your figure rejected by a journal because the resolution was not good enough? Have you wished that you could figure out a way to stop manually transcribing your LC-MS/MS results into the LIS?

Well, your wait is over because this 4-day ONLINE ONLY course (via Zoom) for complete programming newbies will help you get going analyzing real data related to LC-MS/MS assay development, validation, implementation and publication. The only background expected is the ability to use a spreadsheet program. The skills that you will acquire will allow you to take advantage of the many tools already available in the R language and thereafter, when you see that your spreadsheet program does not have the capabilities to do what you need, you will no longer have to burst into tears. You will be empowe-R-ed.

The course will be run over four days (4 contact hours per day) and time will be evenly split between didactic sessions and hands on problem solving with real data sets. The instructors will adopt a “no student left behind policy”. Students will be given ample time to solve mini problems taken from real life laboratory work and focused on common laboratory tasks. All attendees will need a laptop or desktop computer with both the R language installed and R Studio interface installed. Students may use Windows, Mac OSX or Linux environments. Both R and R studio are free and open-source. No cash required.

Students should be prepared for learning what computer programming is really like. This may involve some personal frustration but it will be worth it.

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. The major types of R variables: vectors (numerical, character, logical), matrices, data frames and lists.
2. The important classes: numeric, character, list and changing between them
3. Importing data from Excel
4. Dealing with non-numeric instrument data: the “<10”s and “>1000”s.
5. Manipulating your data: sub-setting, which, match, sort, unique, cut
6. Simple statistical tests: mean, median, quantiles (normal ranges), t-tests, ANOVA, Wilcoxon.
7. Data merges: matching rows between sets
8. Exporting data to Excel-like format.
9. Regressions: Ordinary Least Squares,Passing Bablok, Deming, weighted regressions.
10. Non-linear regressions
11. Looping: Doing things repeatedly
12. Writing your own functions
13. Making highly customized graphs: scatter plots, regression lines, histograms, box plots, qq-plots
14. Putting it all together projects:
--> Preparing method comparison regression and Bland Altman plots
--> Preparing mass spectrometry data for upload to LIS.

Dr. Robert D. Voyksner received his B.S. in Chemistry at Canisius College in 1978 and his Ph.D. at the University of North Carolina at Chapel Hill in 1982.

As a member of the Research Triangle Institute staff since 1983, Robert has been responsible for developing extraction, separation and mass spectrometric methods for biologically and environmentally significant compounds. He has primarily employed HPLC/MS on quadrupoles, sectors and ion trap mass spectrometers for positive and negative ion detection for specific compounds. His pioneering work in HPLC/MS and HPLC/ion trap MS has demonstrated the capability to perform analysis of compounds not amenable to analysis by GC/MS. Specifically, he has worked on the development and evaluation of electrospray HPLC/MS methods for the analysis of high molecular weight opioid peptides, antimalarials, anticancer drugs, nucleotides, antibiotics, proteins and cyclodextrins. He has been working with FDA for the past nine years to develop new methodology using electrospray HPLC/MS and capillary electrophoresis-MS to detect and measure antibiotics (-lactams and aminoglycosides) in food and milk to insure human food safety.
In addition, he is has developed methods and evaluated the use of electrospray HPLC/MS and ion trap MS/MS for environmental monitoring, particularly for the detection of azo dyes and pesticides (including carbamate, methyl urea, triazine, organophosphorous and phenolic acid ). He has developed CE/MS and CE/Ion trap MS methods for the identification of DNA adducts from exposure to nitrocompounds and pesticides.

Dr. Voyksner's research in mass spectrometry has resulted in over 230 publications and presentations, primarily in the area of HPLC/MS. He has served on the Board of The American Society For Mass Spectrometry (ASMS), is on the organization committee for The Montreux LC/MS Symposium, and was the organizer for the 1995, 1999 and 2003 Montreux LC/MS Symposium. He is the organizer for the 2007 Montreux LC/MS Symposium (location yet to be determined). Dr. Voyksner has taught LC/MS short courses for the past 15 years for ASMS, every major pharmaceutical company, ISSX, PBA, HPCE and other HPLC focused meetings.

Now, as president of LCMS Limited, Robert has brought his expertise in mass spectrometry along with years of experience in training and problem solving together into focus and guides LCMS Limited to strive for excellence in its mission of "...chasing tomorrow through research, innovation and education today....."

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

This course is designed for the chromatographer / mass spectrometrist who wants to be successful in developing methods, method optimization and solving problems using LC-MS/MS. The course covers the atmospheric pressure ionization (API) techniques of electrospray, pneumatically assisted electrospray and atmospheric pressure chemical ionization (APCI) and atmospheric pressure photo ionization (APPI) using single quadrupole, triple quadrupole, time-of-flight and ion trap mass analyzers.

Discussions of sample preparation and chromatography will target method development and optimization for the analysis of "real-world" samples by LC-MS/MS.

The course highlights the following topics with respect to optimization a method to achieve the best sensitivity, specificity and sample throughput:

1. Optimization ionization in API techniques,
2. Understanding and minimizing matrix suppression,
3. Relative merits of various LC column lengths, particle sizes and column diameters for LC-MS/MS analysis,
4. Introduction into the interpretation of MS/MS spectra,
5. Important issues in LC/MS/MS quantitation, and
6. Optimization of an quantitative analysis.

Applications of LC-MS/MS to analyze compounds of clinical interest in biological matrices will be discussed throughout the course to emphasize the topics covered.

Course material will be provided electronically.

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 VIRTUAL 2-Day Course with 8 total contact hours. CE to be provided.

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.

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.

Online Format

This is a virtual version of the short course that has been presented at MSACL. This online course includes 4 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.

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.