Translating Pre-Clinical Research to Clinical Patient Care™
MSACL 2018 USPalm Springs: Jan 21-25 |
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Short Courses
MSACL hosts a diverse offering of Short Courses.
Short Courses will occur over the first three days of MSACL (Sunday, Monday, Tuesday of January 21 - 23).
Courses are NOT replicated on different days. They are single courses that span multiple days.
| Course Contact Hours | ||||||
| Sunday PM | Monday AM | Lunch | Monday PM | Tuesday AM | ||
| Clinical MS Review | ||||||
| Clinical MS 301 (Group A) A Comprehensive Review of Clinical Mass Spectrometry Technology & Techniques, including Miniaturization Jack Henion, PhD Mesquite D | Sunday 14:00-18:00 | Monday 8:00-12:00 | Lunch Monday 12:00-13:00 | Monday 13:00-17:00 | Tuesday 8:00-12:00 | |
| Data Science | ||||||
| Data Science 101 (Group A) Breaking up with Excel: A Newbie's Introduction to the R Statistical Programming Language Daniel Holmes, MD & Stephen Master, MD, PhD Room 2 (Catalina) | Sunday 14:00-18:00 | Monday 8:00-12:00 | Lunch Monday 12:00-13:00 | Monday 13:00-17:00 | Tuesday 8:00-12:00 | |
| Data Science 201 (Group B) Going Further With R: Tackling Clinical Laboratory Data Manipulation and Modeling Patrick Mathias, MD, PhD & Randall Julian, PhD Room 1 (Mojave Learning Center) | Sunday 14:00-18:00 | Monday 8:30-12:30 | Lunch Monday 12:30-13:30 | Monday 13:30-17:30 | Tuesday 8:30-12:30 | |
| General Interest | ||||||
| Presentations 101 (Group B) How to Maximize Your Influence Through Creating Compelling Presentations Karen Mahooti, MBA Chino A | Sunday 14:00-18:00 | Monday 8:30-12:30 | Lunch Monday 12:30-13:30 | Monday 13:30-17:30 | Tuesday 8:30-12:30 | |
| Laboratory Medicine | ||||||
| Lab Medicine 101 (Group B) Basics of Laboratory Medicine Prof. Dr. med. Michael Vogeser Agua Caliente |
Not in Session |
Not in Session | Lunch Monday 12:30-13:30 | Monday 13:30-17:30 | Tuesday 8:30-12:30 | |
| LC-MS | ||||||
| LC-MSMS 101 (Group A) Getting Started with Quantitative LC-MS/MS in the Diagnostic Laboratory Judy Stone, PhD, Lorin Bachmann, PhD & Grace van der Gugten Room 3 (Madera) | Sunday 14:00-18:00 | Monday 8:00-12:00 | Lunch Monday 12:00-13:00 | Monday 13:00-17:00 | Tuesday 8:00-12:00 | |
| LC-MSMS 201 (Group C) Understanding and Optimization of LC-MS/MS to Develop Successful Methods for Identification and Quantitation in Complex Matrices Robert D. Voyksner, PhD Andreas | Sunday 14:00-18:00 | Monday 9:00-13:00 | Lunch Monday 13:00-14:00 | Monday 14:00-18:00 | Tuesday 9:00-13:00 | |
| LC-MSMS 202 (Group C) Practical LC-MS Maintenance and Troubleshooting J. Will Thompson, PhD, Erik J. Soderblom, PhD & Chris Shuford, PhD Mesquite H | Sunday 14:00-18:00 | Monday 9:00-13:00 | Lunch Monday 13:00-14:00 | Monday 14:00-18:00 | Tuesday 9:00-13:00 | |
| LC-MSMS 301 (Group A) Development and Validation of Quantitative LC-MS/MS Assays for Use in Clinical Diagnostics Russell Grant, PhD & Matthew Crawford Room 4 (Pasadena) | Sunday 14:00-18:00 | Monday 8:00-12:00 | Lunch Monday 12:00-13:00 | Monday 13:00-17:00 | Tuesday 8:00-12:00 | |
| MALDI | ||||||
| MALDI 102 (Group C) Practical Considerations for MALDI Imaging Mass Spectrometry Michelle Reyzer, PhD Snowcreek | Sunday 14:00-18:00 | Monday 9:00-13:00 | Lunch Monday 13:00-14:00 | Monday 14:00-18:00 | Tuesday 9:00-13:00 | |
| MALDI 103 (Group B) MALDI-MS Fundamentals and its Emerging Role in Pathology and Laboratory Medicine Mark W. Duncan, PhD & Mari L. DeMarco, PhD with Guest lecturers: Zhen Zhao, Weill Cornell Medical School, Fang Wu, University of Saskatchewan, Dobrin Nedelkov, Isoformix Inc, Jeff Spraggins, Vanderbilt, and Clifton Fagerquist, USDA Mesquite G | Sunday 14:00-18:00 | Monday 8:30-12:30 | Lunch Monday 12:30-13:30 | Monday 13:30-17:30 | Tuesday 8:30-12:30 | |
| Metabolomics | ||||||
| Metabolomics 201 (Group B) Application of High Resolution Mass Spectrometry and Metabolomics in Clinical Analysis Timothy Garrett, PhD & Erin Baker, PhD Mesquite F | Sunday 14:00-18:00 | Monday 8:30-12:30 | Lunch Monday 12:30-13:30 | Monday 13:30-17:30 | Tuesday 8:30-12:30 | |
| Microbiology | ||||||
| Microbiology 201 (Group B) Mass Spectrometric Methods of Microbial identification John Lapek, PhD & Chris Cox, PhD Pueblo B |
Not in Session |
Not in Session | Lunch Monday 12:30-13:30 | Monday 13:30-17:30 | Tuesday 8:30-12:30 | |
| Proteomics | ||||||
| Proteomics 201 (Group B) Clinical Proteomics Andy Hoofnagle, MD, PhD, Cory Bystrom, PhD & Chris Shuford, PhD Room 5 (Sierra/Ventura) | Sunday 14:00-18:00 | Monday 8:30-12:30 | Lunch Monday 12:30-13:30 | Monday 13:30-17:30 | Tuesday 8:30-12:30 | |
| Proteomics 202 (Group A) Practical Proteomics Using the Skyline Software Ecosystem Mike MacCoss, PhD, Brendan MacLean, Lindsay Pino, and Sandi Spencer, PhD Chino B | Sunday 14:00-18:00 | Monday 8:00-12:00 | Lunch Monday 12:00-13:00 | Monday 13:00-17:00 | Tuesday 8:00-12:00 | |
| Sample Preparation | ||||||
| Sample Prep 201 (Group C) Sample Preparation and Alternative Matrices for LC-MS Assays William Clarke, PhD & Mark Marzinke, PhD Mesquite E | Sunday 14:00-18:00 | Monday 9:00-13:00 | Lunch Monday 13:00-14:00 | Monday 14:00-18:00 | Tuesday 9:00-13:00 | |
| Toxicology | ||||||
| Forensic Toxicology 101 (Group B) Basic Forensic Toxicology Jarrad Wagner, Ph.D., F-ABFT, Allison Veitenheimer, Ph.D., Russell Lewis, Ph.D., F-ABFT Pueblo A |
Not in Session |
Not in Session | Lunch Monday 12:30-13:30 | Monday 13:30-17:30 | Tuesday 8:30-12:30 | |
Group A
Clinical MS 301 :: A Comprehensive Review of Clinical Mass Spectrometry Technology & Techniques, including Miniaturization
| Instructor(s): | Jack Henion, PhD | ||||||||||||||||||||
| Level: | 2-3 (Intermediate - Advanced) | ||||||||||||||||||||
| Location: | Mesquite D | ||||||||||||||||||||
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Prerequisites: Students who sign up for this advanced course should either have five years or more of personal LC/MS/MS experience and familiarity with the scientific literature or have taken one or more introductory courses which cover atmospheric pressure ionization (API) techniques as well as the basics involved in routine LC/MS and LC/MS/MS analyses.
Overview: 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.
- 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).
- 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).
- 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.
- 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.
- 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.
- 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.
- 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.
- 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!
EarlyBird Deadline |
Regular Deadline |
After |
|
| Student / Post-Doc (Trainee) | $80 | $96 | $120 |
| Academic / Non-Profit | $240 | $288 | $360 |
| Commercial / Industry | $400 | $480 | $600 |
Instructor: Jack Henion, PhD
Jack Henion is Professor Emeritus of Toxicology at Cornell University in the Analytical Toxicology Section of the Diagnostic Laboratory within the College of Veterinary Medicine. He is also a co-founder, Chairman and CSO of Advion BioSciences (ABS), Inc., located in Ithaca, New York. Dr. Henion's work in LC/MS relates to the analysis of real-world samples common to pharmaceutical, environmental, and biochemical problems. The instructor has published extensively in the areas of conventional capillary GC/MS as well as LC/MS, SFC/MS, IC/MS, and CE/MS using atmospheric pressure ionization (API) technologies with quadrupole, ion trap, and time-of-flight mass spectrometers.
Group A
Data Science 101 :: Breaking up with Excel: A Newbie's Introduction to the R Statistical Programming Language
| Instructor(s): | Daniel Holmes, MD & Stephen Master, MD, PhD | ||||||||||||||||||||
| Level: | 1-2 (Beginner - Intermediate) | ||||||||||||||||||||
| Location: | Room 2 (Catalina) | ||||||||||||||||||||
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Prerequisites:
- knowledge of Excel
- able to bring a laptop
- able to pre-install software on their laptop...Namely: R and R-studio
- willingness to break up with Excel
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 year at MSACL we will be offering a course for complete programming newbies that 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 two days and time will be evenly split between didactic sessions and hands on problem solving with real data sets. Drs Holmes and Master 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 to bring a laptop with the R language installed 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:
- The major types of R variables: vectors (numerical, character, logical), matrices, data frames and lists.
- The important classes: numeric, character, list and changing between them
- Importing data from Excel
- Dealing with non-numeric instrument data: the “<10”s and “>1000”s.
- Manipulating your data: sub-setting, which, match, sort, unique, cut
- Simple statistical tests: mean, median, quantiles (normal ranges), t-tests, ANOVA, Wilcoxon.
- Data merges: matching rows between sets
- Exporting data to Excel-like format.
- Regressions: Ordinary Least Squares,Passing Bablok, Deming, weighted regressions.
- Non-linear regressions
- Looping: Doing things repeatedly
- Writing your own functions
- Making highly customized graphs: scatter plots, regression lines, histograms, box plots, qq-plots
- Putting it all together projects:
- Preparing method comparison regression and Bland Altman plots
- Preparing mass spectrometry data for upload to LIS.
EarlyBird Deadline |
Regular Deadline |
After |
|
| Student / Post-Doc (Trainee) | $80 | $96 | $120 |
| Academic / Non-Profit | $240 | $288 | $360 |
| Commercial / Industry | $400 | $480 | $600 |
Co-Instructor: Daniel Holmes, MD
Clinical Associate Professor, Department of Pathology and Laboratory Medicine, University of British Columbia
Daniel Holmes did his undergraduate degree in Chemical Physics from the University of Toronto with a focus on Quantum Mechanics. He went to medical school at the University of British Columbia (UBC) where he also did his residency in Medical Biochemistry. He is a Clinical Associate Professor of Pathology and Laboratory Medicine at UBC and Division Head of Clinical Chemistry at St. Paul's Hospital in Vancouver. Interests include laboratory medicine statistics, clinical endocrinology, clinical lipidology and clinical mass spectrometry. Assay development efforts in the last two years have focused on assays specialized endocrine testing.
Co-Instructor: Stephen Master, MD PhD
Associate Professor of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia
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. He is currently Associate Professor of Pathology and Laboratory Medicine at Children’s Hospital of Philadelphia. 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.
Group B
Data Science 201 :: Going Further With R: Tackling Clinical Laboratory Data Manipulation and Modeling
| Instructor(s): | Patrick Mathias, MD, PhD & Randall Julian, PhD | ||||||||||||||||||||
| Level: | 2 (Intermediate) | ||||||||||||||||||||
| Location: | Room 1 (Mojave Learning Center) | ||||||||||||||||||||
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Prerequisites:
- Completed “Breaking Up With Excel” and/or familiar with basic R concepts
- Able to bring a laptop
- Able to pre-install software on their laptop...Namely: R and R-studio
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 course will be run over two days and time will be split between lecture sessions, individual problem solving, and a highly interactive group-level data mining of real data sets (there may even be prizes). 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 to bring a laptop with 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 (as in “Free Beer”) and open-source.
Students should be prepared continue to expand their skill in programming – which, as you learned in the introductory course 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:
- Using the “Tidyverse”: a powerful collection of tools for working with R
- Conceptual basis for keeping data “tidy”
- Using the Import -> Tidy -> Transform -> Visualize -> Model -> Communicate pipeline
- Parsing non-tabular data formats such as XML and JSON
- Importing data from various sources including databases and web scraping
- Data wrangling and tools for cleaning up data before attempting anything
- Data visualization with the ggplot2 library
- Functional programming concepts for efficient iteration (purrr’s map functions)
- Fitting models which contain numeric and non-numeric data
- Introduction to R-Markdown for report generation
- Looping: Doing things repeatedly
- Writing your own functions
- Making highly customized graphs: scatter plots, regression lines, histograms, box plots, qq-plots
- Putting it all together projects:
- Preparing method comparison regression and Bland Altman plots
- Preparing mass spectrometry data for upload to LIS.
EarlyBird Deadline |
Regular Deadline |
After |
|
| Student / Post-Doc (Trainee) | $80 | $96 | $120 |
| Academic / Non-Profit | $240 | $288 | $360 |
| Commercial / Industry | $400 | $480 | $600 |
Co-Instructor: Patrick Mathias, PhD
Assistant Professor, Department of Laboratory Medicine, University of Washington
Patrick Mathias completed his undergraduate degree in Electrical Engineering at Duke University, followed by a master’s degree in Electrical and Computer Engineering from the University of Illinois at Urbana-Champaign. He then completed a MD degree and a PhD in Bioengineering from the University of Illinois, with a focus on nanophotonics and label-free biosensors. He completed residency training in Clinical Pathology as well as a Clinical Informatics fellowship at the University of Washington. He is currently the Associate Director of the Informatics division in the Department of Laboratory Medicine at the University of Washington. His clinical and research interests lie in improving electronic health record systems to improve ordering and interpretation of laboratory tests, developing infrastructure for novel analytical technologies in the clinical laboratory, and applying analytics to improve laboratory operations and clinical care at a population level.
Co-Instructor: Randy Julian, PhD
CEO, Indigo BioAutomation
Randy Julian is Founder and CEO of Indigo BioAutomation located in Indianapolis, 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. At Lilly Dr. Julian worked on natural product discovery, high throughput screening for RNA anti-viral compounds and researched methods for using proteomics to optimize drug candidates in animal models. Randy founded Indigo based on informatics technology developed during his time with Lilly. Indigo now provides laboratory data analysis software which uses machine intelligence to automatically analyze over 100 million sample results per month for every major clinical laboratory in the US.
Dr. Julian is an active member of the clinical mass spectrometry community, teaches short courses in statistics, informatics and analytics. Randy is the past Chairman of the Human Proteome Organization’s Standards Initiative. He is the coauthor of two international standards for analytical data. He was also the chairman of the ASTM committee on mass spectrometry data standards. Dr. Julian maintains an active research relationship with the faculty at Purdue University where he is an Adjunct Professor of Chemistry.
Group B
Presentations 101 :: How to Maximize Your Influence Through Creating Compelling Presentations
| Instructor(s): | Karen Mahooti, MBA | ||||||||||||||||||||
| Level: | 1-2 (Beginner - Intermediate) | ||||||||||||||||||||
| Location: | Chino A | ||||||||||||||||||||
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Prerequisites: Working knowledge of presentation software. While this course uses PowerPoint, the methods taught can be used with almost any presentation software.
Overview:
You have brilliant ideas with great potential. But it doesn't matter what you know; it matters what you communicate! Knowing how to create and deliver clear and compelling presentation documents can expand your influence and accelerate your career. And the good news is that because there are so many bad presentations out there, armed with the skills in this course, it will be easy for you to stand out in a good way.
This course teaches how to develop compelling presentations using storyboarding - a method used by professionals in major management consulting firms and some of the largest companies in the world. This versatile method will work for you whether you are in academics, business, or a non-profit and whether your audience is colleagues, executives, students, or investors.
While the course has a LOT of very practical information and tips, it is not simply a collection of sound bites and "top 10 tricks." It is a complete, proven process for creating persuasive presentations and shows you step by step exactly how to:
- Structure your content to flow smoothly and logically from start to finish in a way that is highly influential
- Design professional quality slides that make your key points jump off the page. Visual polish goes a long way in establishing credibility. And yes, YOU can do this, even if you are not a graphic designer!
- Orally deliver your presentation in a way that fully engages your audience with your ideas.
Many presentation courses are designed for the person giving a keynote address in front of a large auditorium. But most presentations are created for everyday settings: meetings, lectures, and client discussions. And these presentations have very different challenges. They must organize and communicate large amounts of information in a way that is still engaging. In addition, while they may be used in an oral presentation, they must also stand on their own two feet and be clearly understood whether or not you are there to narrate them. This short course focuses on these challenges!
Day 1: Walk through interactive training in the full methodology for storyboarding, visual design, and oral delivery.
Day 2: The best way to learn is by doing! The second day is a hands-on workshop developing an actual presentation document with the benefit of coaching from the instructor using the tools and techniques taught in Day 1.
Comments from previous MSACL course participants:
"Very useful and practical. It can be applied right away."
"It was very well laid out and easy to understand. The audience interaction was great and very engaging."
"The materials we get to take home are so well organized and so clear that I was able to use the method on my own, 4 months after the short course."
"I felt very prepared when I had to make a presentation on a new topic. I spent far less time creating graphics I didn’t use and re-arranging slides with Karen’s method. Ultimately that led to less stress during the process of preparing the slides, and it improved the clarity and strengthened the message of my presentation."
EarlyBird Deadline |
Regular Deadline |
After |
|
| Student / Post-Doc (Trainee) | $80 | $96 | $120 |
| Academic / Non-Profit | $240 | $288 | $360 |
| Commercial / Industry | $400 | $480 | $600 |
Instructor: Karen Mahooti, MBA
Karen holds an MBA from the Yale University School of Management and is founder and principal at Articulate Consulting. Karen has provided training in presentation development skills to professionals around the world from executives and managers to analysts, consultants, and graduate students. In addition, over her career as both a management consultant and a marketing professional for a Fortune 20 company, Karen has created a multitude of clear and compelling presentations to help senior executives and board members of large companies make better strategic decisions. She understands first-hand the challenges of creating presentations when the stakes are high and clients' expectations are even higher. Karen's style is both visionary and practical. She seeks to inspire others to have confidence in what they can accomplish with their presentations, and also to give them the concrete know-how and tools they need to immediately begin creating presentations that give them the influence they desire.
Group B
Lab Medicine 101 :: Basics of Laboratory Medicine
| Instructor(s): | Prof. Dr. med. Michael Vogeser | ||||||||||||||||||||
| Level: | 1 (Beginner) | ||||||||||||||||||||
| Location: | Agua Caliente | ||||||||||||||||||||
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Prerequisites:
Overview: This 1-day course aims to make scientists familiar with the basic concepts of clinical pathology and laboratory medicine. Typical processes and workflows in the various categories of clinical laboratories are described and discussed. Topics that are addressed include in particular:
- Basic technologies (photometry, immunoassays, electrochemical methods, cytometry, immuno-fluorescence, etc.)
- Automation and working characteristics of analyzer configurations including total laboratory automation
-Concept of total testing process including pre- and post-analytical processes
- Performance characteristics
- Quality management
- Regulatory background
- Sample materials
- Clinical decision making, reference ranges, decision levels, diagnostic and clinical algorithms
- Logistics, sample transport
- Economic considerations
- Characteristics of IVD industry
EarlyBird Deadline |
Regular Deadline |
After |
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| Student / Post-Doc (Trainee) | $60 | $72 | $90 |
| Academic / Non-Profit | $180 | $216 | $270 |
| Commercial / Industry | $300 | $360 | $450 |
Dr. Michael Vogeser, MD, is specialist in Laboratory Medicine and senior physician at the Hospital of the University of the Ludwig-Maximilians-University Munich, Germany (Institute of Laboratory Medicine). As an Associate Professor he is teaching Clinical Chemistry and Laboratory Medicine.The main scope of his scientific work isthe application of mass spectrometric technologies in routine clinical laboratory testing as translational diagnostics. Besides method development in therapeutic drug monitoring and endocrinology a further particular field of his work isquality and risk management in mass spectrometry and in clinical testing in general.Michael has published >150 articles in peer reviewed medical journals and is secretary of the German Association of Clinical Chemistry and Laboratory Medicine (DGKL) (2016 – 2019).
Group A
LC-MSMS 101 :: Getting Started with Quantitative LC-MS/MS in the Diagnostic Laboratory
| Instructor(s): | Judy Stone, PhD, Lorin Bachmann, PhD & Grace van der Gugten | ||||||||||||||||||||
| Level: | 1-2 (Beginner - Intermediate) | ||||||||||||||||||||
| Location: | Room 3 (Madera) | ||||||||||||||||||||
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Prerequisites:
Overview: 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:
- LC-MS/MS system purchasing
- site preparation and installation
- defining preliminary MSMS and LC parameters for your first method
- selecting and optimizing sample preparation for your first method
- choosing internal standards, solvents, and water, making reagents and calibrators
- adjusting sample preparation, LC and MSMS parameters to achieve the desired assay performance
- establishing data analysis & review criteria and an interface to the LIS
- pre-validation stress testing and method validation
- preventative maintenance and troubleshooting
- 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.
Previous exposure to the principles of clinical method validation, either didactic or practical, is assumed. A glossary of common LC-MSMS terms/acronyms, and diagrams delineating basic LC and MSMS instrument components and functions will be emailed to attendees a week prior to the beginning of the course. This material will also be addressed at the beginning of the course, but the initial learning curve can be steep and review prior to the course will be beneficial if you have absolutely no previous exposure with LC-MSMS.
EarlyBird Deadline |
Regular Deadline |
After |
|
| Student / Post-Doc (Trainee) | $80 | $96 | $120 |
| Academic / Non-Profit | $240 | $288 | $360 |
| Commercial / Industry | $400 | $480 | $600 |
Co-Instructor: Judy Stone, MT (ASCP), PhD, DABCC
Judy is Sr. Technical Specialist in the Mass Spectrometry Laboratory at the University of California, San Diego Health Center for Advanced Laboratory Medicine. Her research is focused on small molecule method development, interfacing and automation for clinical LC-MSMS. She was faculty chair for the 2009 AACC certificate program “Using Mass Spectrometry in the Clinical Laboratory” and she teaches a workshop at the annual AACC meeting on “Troubleshooting for LC-MSMS”.
Co-Instructor: Lorin Bachmann, PhD, DABCC
Lorin is Associate Professor of Pathology and Co-Director of Chemistry at Virginia Commonwealth University Medical Center. Dr. Bachmann’s areas of interest include implementation of LCMS in the clinical laboratory and laboratory test standardization. She routinely contributes to development of laboratory practice guidelines and has provided many lectures on practical implementation of clinical mass spectrometry.
Co-Instructor: Grace Van Der Gugten
Grace is 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!
Group C
LC-MSMS 201 :: Understanding and Optimization of LC-MS/MS to Develop Successful Methods for Identification and Quantitation in Complex Matrices
| Instructor(s): | Robert D. Voyksner, PhD | ||||||||||||||||||||
| Level: | 2 (Intermediate) | ||||||||||||||||||||
| Location: | Andreas | ||||||||||||||||||||
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Prerequisites: General knowledge of laboratory techniques associated with HPLC and mass spectrometry and some hands-on experience with running an LC/MS system.
Overview: This course is designed for the chromatographer / mass spectrometrist who want 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:
- Optimization ionization in API techniques,
- understanding and minimizing matrix suppression,
- relative merits of various LC column lengths, particle sizes and column diameters for LC/MS/MS analysis,
- introduction into the interpretation of MS/MS spectra,
- important issues in LC/MS/MS quantitation, and
- 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.
EarlyBird Deadline |
Regular Deadline |
After |
|
| Student / Post-Doc (Trainee) | $80 | $96 | $120 |
| Academic / Non-Profit | $240 | $288 | $360 |
| Commercial / Industry | $400 | $480 | $600 |
Instructor: Robert D. Voyksner, PhD
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. He was employed at Research Triangle Institute (RTI) from 1983-2001 as the director of the mass spectrometry facility and has been responsible for developing extraction, separation and mass spectrometric methods for biologically and environmentally significant compounds. His work earned him the Presidents Award, the highest award within RTI. In 2001 he co-founded LCMS Limited in Raleigh, NC and has been the President of the company to date. Under his direction LCMS Limited is working on technological advancements in LC/MS, offering services to pharmaceutical, clinical and agrochemical industry for solving unique problems by LC/MS/MS and offering training in LC/MS/MS and MS/MS interpretation and on LC/MS/MS instrumentation. Dr Voyksner is also an Adjunct professor at the North Carolina a School of Vetinary Medicine and at The University of North Carolina School of Pharmacy.
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 Directors for 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, 2003 and 2007 Montreux LC/MS Symposia. Dr. Voyksner has taught over 100 courses on LC/MS, CE/MS and CID interpretation during the past 10 years for ASMS, pharmaceutical companies; ISSX, PBA, HPCE and HPLC focused meetings.
Group C
LC-MSMS 202 :: Practical LC-MS Maintenance and Troubleshooting
| Instructor(s): | J. Will Thompson, PhD, Erik J. Soderblom, PhD & Chris Shuford, PhD | ||||||||||||||||||||
| Level: | 2 (Intermediate) | ||||||||||||||||||||
| Location: | Mesquite H | ||||||||||||||||||||
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Prerequisites: Experience with LC-MS systems.
Overview: The general goal of the course is to enable practitioners of LC-MS/MS in the clinical laboratory to quickly recognize and diagnose specific problems with instrumentation, in order to decrease downtime and cost of repairs. The course includes ‘best practices’ for instrumentation installation, upkeep and maintenance, practical troubleshooting workflows for LC and MS, and will use problem sessions to reinforce skillsets. Although the course uses examples from specific instrumentation for demonstration, the content is geared to be vendor-neutral and applicable to all LC-MS systems. Additionally, we will provide an opportunity to have instrumentation troubleshooting questions from your laboratory addressed by the facilitators.
Brief outline of course content:
- General “Best Practices” for Successful LC/MS Operation
- Best Practices; Getting Started on the Right Foot
- Breaking the System Down
- System Suitability! What is it, and how do I properly implement?
- Focus on Liquid Chromatography
- Diagnostics using the “heartbeat” of your Chromatographic system
- Key System components and where things go wrong
- LC troubleshooting workflow
- Maintenance Intervals; service contract or do-it-yourself?
- Problem sets
- Focus on Mass Spectrometry
- Discussion of Source, Transfer Optics, Vacuum and how each is critical to your system
- MS Troubleshooting workflow
- Ion optics cleaning and upkeep; what is ‘charging’?
- Problem sets
- Integrated System
- Ionization
- System Communications
- Multi-vendor configurations
- Strategies to simplify
- Integrated real-lab problem scenarios and team exercises
While some basics of instrument component operation will be covered, it will be most beneficial to scientists with experience actively using LC-MS/MS as an analysis tool. While an in-depth discussion of how to operate each individual instrument is surely outside the scope of any short course, specific system setups will be used as examples and attendees will be encouraged to ask questions about specific systems in their own laboratories.
EarlyBird Deadline |
Regular Deadline |
After |
|
| Student / Post-Doc (Trainee) | $80 | $96 | $120 |
| Academic / Non-Profit | $240 | $288 | $360 |
| Commercial / Industry | $400 | $480 | $600 |
Co-Instructor: Will Thompson, PhD
Dr. Thompson received his Ph.D. in Analytical Chemistry from the University of North Carolina at Chapel Hill under Professor James Jorgenson in 2006. Following his Ph.D. he pursued a career in the application of UHPLC with high resolution mass spectrometry in the Disease and Biomarker Proteomics group of Dr. Arthur Moseley at GlaxoSmithKline, leaving GSK in 2008 to join Dr. Moseley in establishing the Duke Proteomics Core Facility. Dr. Thompson is currently the Assistant Director of the Duke Proteomics and Metabolomics Shared Resource, and a Research Assistant Professor in Department of Pharmacology and Cancer Biology. His research interests involve improving the throughput and sensitivity of unbiased and targeted proteomics and metabolomics approaches, with an eye towards generating assays which are easily translatable to the diagnostic laboratory.
Co-Instructor: Erik J. Soderblom, PhD
Dr. Erik Soderblom currently holds a joint appointment as a Research Scientist at Duke University’s Proteomics and Metabolomics Core Facility and as an Assistant Research Professor in Duke University’s Department of Cell Biology. He received a PhD in Molecular and Structural Biochemistry from North Carolina State University in 2008, prior to joining the Core Facility. His expertise lies in the utilization of various liquid chromatography-mass spectrometry (LC-MS) platforms to support a wide variety of research efforts from small scale basic science studies to larger scale clinical proteomics studies. Dr. Soderblom has over 10 years’ experience in differential expression proteomics using single and multi-dimensional nanoscale capillary chromatography coupled to high-resolution mass spectrometers, targeted proteomic analysis using triple quadrupole mass spectrometers (MRM) or high-resolution mass spectrometers (PRM), and comprehensive analysis of post-translational modifications such as phosphorylation and acetylation. As part of his normal responsibilities, Dr. Soderblom is involved in routine maintenance and troubleshooting of both LC and MS components across various instrument platforms, including design and execution of system suitability analysis to assess platform performance over time.
Co-Instructor: Christopher Shuford, PhD
Chris Shuford, Ph.D., is Technical Director for research and development at LabCorp’s Center for Esoteric Testing in Burlington, North Carolina. Chris received his B.S. in Chemistry & Physics at Longwood University and obtained his Ph.D. in Bioanalytical Chemistry from North Carolina State University under the tutelage of Professor David Muddiman, where his research focused on applications of nano-flow chromatography (<500 nL/min) for multiplexed peptide quantification using protein cleavage coupled with isotope dilution mass spectrometry (PC-IDMS). In 2012, Chris joined LabCorp’s research and development team where his efforts have focused on development of high-flow chromatographic methods (>1 mL/min) for multiplexed and single protein assays for clinical application.
Group A
LC-MSMS 301 :: Development and Validation of Quantitative LC-MS/MS Assays for Use in Clinical Diagnostics
| Instructor(s): | Russell Grant, PhD & Matthew Crawford | ||||||||||||||||||||
| Level: | 3 (Advanced) | ||||||||||||||||||||
| Location: | Room 4 (Pasadena) | ||||||||||||||||||||
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Prerequisites: The target audience should have extensive familiarity with LC-MS/MS systems.
Overview: This course will briefly introduce the key aspects of the LC-MS/MS experimental workflow and then focus on processes and experimental designs for assay development and analytical validation of assays to be employed within clinical diagnostics.
The first day will describe method development in detail, including how-to guides for initial optimization of mass spectrometry systems, chromatographic development and sample preparation schemes. Techniques and technologies for streamlining analytical performance will also be described. Transitional experiments from development to validation will be discussed in detail to stress test methodologies prior to analytical validation.
Day two will cover all details pertinent in validation of LC-MS/MS analytical workflows. Experimental designs for all aspects of validation, putative acceptance criteria and analytical solutions will be shown. Key validation criteria of selectivity, carry-over, matrix effect, accuracy, precision, linearity, stability and inter-assay correlation will be described using multiple case studies.
EarlyBird Deadline |
Regular Deadline |
After |
|
| Student / Post-Doc (Trainee) | $100 | $120 | $150 |
| Academic / Non-Profit | $300 | $360 | $450 |
| Commercial / Industry | $500 | $600 | $750 |
Co-Instructor: Russell Grant, PhD
Dr. Grant received his PhD in chromatographic and mass spectrometric technologies from Swansea University in 1995. He continued his scientific training in various industrial settings which have included: senior scientist at GSK, principal scientist at Cohesive Technologies, Technical Director at Eli Lilly and Director of Mass Spectrometry at Esoterix Endocrinology.
Dr. Grant has pioneered the use of direct injection technologies, chromatographic systems multiplexing, utility of automation and new analytical platforms for application in bioanalytical applications. His research goals are focused upon improvements in speed, sensitivity and quality of LC-MS/MS analytical systems and assays.
Co-Instructor: Matthew Crawford
Matthew Crawford is a Researcher at LabCorp for the Mass Spectrometry Research and Development department. He received his Bachelors of Science in Biochemistry from California State University, Northridge in 2005. He entered the clinical lab space as a technician at LabCorp’s Esoterix Endocrinology and then moved to be a part of the corporate R&D team. His efforts are focused high-throughput small molecule method development, laboratory automation, and method validation (CAP, CLIA, and FDA Bioanalytical).
Group C
MALDI 102 :: Practical Considerations for MALDI Imaging Mass Spectrometry
| Instructor(s): | Michelle Reyzer, PhD | ||||||||||||||||||||
| Level: | 1-2 (Beginner - Intermediate) | ||||||||||||||||||||
| Location: | Snowcreek | ||||||||||||||||||||
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Prerequisites: Attendees should have a general knowledge of mass spectrometry, but knowledge of imaging and/or MALDI is not required.
Overview: This course will provide an introduction to the basic concepts involved in running a MALDI Imaging Mass Spectrometry experiment, including key parameters of sample preparation, matrix application, imaging acquisition, instrumental parameters, data analysis, and imaging processing. The course will focus on MALDI mass spectrometry, but other mass spectrometry sources currently used for imaging will be touched on. This course will be presented at the beginner to intermediate level, and will be appropriate for clinicians/pathologists looking to learn more about IMS as well as for mass spectrometrists looking to apply this technology to more clinical samples.
EarlyBird Deadline |
Regular Deadline |
After |
|
| Student / Post-Doc (Trainee) | $80 | $96 | $120 |
| Academic / Non-Profit | $240 | $288 | $360 |
| Commercial / Industry | $400 | $480 | $600 |
Instructor: Michelle Reyzer, PhD
Michelle 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.
Group B
MALDI 103 :: MALDI-MS Fundamentals and its Emerging Role in Pathology and Laboratory Medicine
| Instructor(s): | Mark W. Duncan, PhD & Mari L. DeMarco, PhD
with Guest lecturers: Zhen Zhao, Weill Cornell Medical School, Fang Wu, University of Saskatchewan, Dobrin Nedelkov, Isoformix Inc, Jeff Spraggins, Vanderbilt, and Clifton Fagerquist, USDA | ||||||||||||||||||||
| Level: | 1-2 (Beginner - Intermediate) | ||||||||||||||||||||
| Location: | Mesquite G | ||||||||||||||||||||
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Prerequisites: Attendees should have some background in mass spectrometry and the basics of clinical and/or analytical chemistry, but this is not essential.
Overview: This 2-day course introduces the key aspects of MALDI-MS, and current and emerging applications in medicine. This course is designed for those interested in developing, implementing and/or refining clinical applications of MALDI-MS.
In the first half of the course we will review MALDI-MS instrument fundamentals, sample requirements, workflows, and MALDI-MS data. We will highlight both the strengths and weaknesses of MALDI-MS. Thereafter, we will illustrate potential MALDI-MS applications to patient care from the perspective of pathology and laboratory medicine. In each section we will discuss relevant experimental design/operation, assay development, analytical validation and utility. Basic “how-to guides” will be presented.
The second half of the course is dedicated to a series of lectures from acknowledged experts in the application of MALDI-MS to relevant areas (e.g., clinical microbiology, clinical chemistry, genomics, and anatomic pathology). Each expert will give a targeted “real-world” lecture followed by a question-and-answer period. The course will conclude with an informal round-table discussion centered on topics of specific interest to the participants.
Specific topics covered in this course include the following:
- Introduction to MALDI-MS: how a MALDI-MS instrument works; advantages and disadvantages of MALDI-MS; variations on the MALDI theme – MALDI, SELDI, DIOS, DESI, LAESI, etc; different instrument configurations and analyzer types; advances in instrumentation; the basics of how to generate a spectrum and critical practical considerations (e.g., selection of matrix, laser power, shot number and other experimental variables).
- Applications in Clinical Microbiology: basic principles; strengths & weaknesses; the laboratory process; development and application of databases for automatic interpretation of MALDI spectra (concepts); data analysis; systems available for FDA approved pathogen identification and their features.
- Applications in Clinical Chemistry: clinical applications/potential of MALDI-TOF – qualitative applications; quantification by MALDI-MS; TOF-TOF quantification; related quantitative strategies; loss mass analyte analysis; approach to developing new assays by MALDI-TOF; sample processing (dilution, concentration, purification, etc.; transfer to MALDI plate; matrix choice and deposition; instrument parameters).
- Mass Spectrometry Imaging: Fundamentals; strengths & weaknesses; sample considerations; tissue processing and matrix application; clinical applications of MALDI imaging and profiling by MS.
- Future potential and prospects: The second half of the course will focus on advanced “real-world” applications of MALDI-MS presented by experts in their respective fields.
EarlyBird Deadline |
Regular Deadline |
After |
|
| Student / Post-Doc (Trainee) | $80 | $96 | $120 |
| Academic / Non-Profit | $240 | $288 | $360 |
| Commercial / Industry | $400 | $480 | $600 |
Co-Instructor: Mark W. Duncan, PhD
Biodesix Inc, Boulder, CO, USA
Mark Duncan’s research interests include clinical mass spectrometry, biomarker development and MALDI-MS. He is senior director of proteomic technology development at Biodesix Inc., and a visiting professor of medicine at the University of Colorado. He has extensive experience in the application of MALDI-MS, both as a qualitative and a quantitative tool.
Co-Instructor: Mari L. DeMarco, PhD DABCC FACB FCACB
Clinical Associate Professor, Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada; Michael Smith Foundation for Health Research Scholar
Mari DeMarco’s 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.
Group B
Metabolomics 201 :: Application of High Resolution Mass Spectrometry and Metabolomics in Clinical Analysis
| Instructor(s): | Timothy Garrett, PhD & Erin Baker, PhD | ||||||||||||||||||||
| Level: | 2 (Intermediate) | ||||||||||||||||||||
| Location: | Mesquite F | ||||||||||||||||||||
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Prerequisites: LC/MS hands on experience.
Overview: Metabolomics describes the analysis of the small molecules present in our body and ingested from the surrounding environment (i.e. drugs, pesticides, etc.). The analysis of these metabolites has recently been utilized to discover new markers of disease and perturbed metabolic pathways. Metabolomic analyses can be performed with either targeted or untargeted measurements. In targeted studies, only a small subset of metabolites is analyzed and this prevalent in clinical analyses for measurements such as those for newborn screening. Untargeted measurements, however, study all possible small molecules in a single injection and heavily rely on the use of high resolution mass spectrometry to precisely measure the m/z values across many samples. Untargeted measurements are almost always coupled to either gas or liquid chromatography or ion mobility as the retention time or mobility provides an important secondary distinguishing characteristic of each specific metabolite. It is expected that both targeted and untargeted metabolomic measurements will have an important place in future clinical studies.
Given the growth of metabolomics over the past several years, the use of high resolution mass spectrometry has rapidly progressed. High resolution approaches to measure small molecules offer several advantages for clinical analyses such as confirmation via accurate mass of the precursor and product ions and an evaluation of the isotopic abundance. This short course will cover the application of high resolution mass spectrometry to both quantitative and semi-quantitative analyses with a focus on metabolomics.
Topics in this short course include: mass accuracy for identification, tandem mass spectrometry, quantitative aspects of high resolution mass spectrometry, identifying and measuring the metabolome, statistical analysis, ion mobility spectrometry, and liquid and gas chromatography coupled to high resolution MS.
EarlyBird Deadline |
Regular Deadline |
After |
|
| Student / Post-Doc (Trainee) | $80 | $96 | $120 |
| Academic / Non-Profit | $240 | $288 | $360 |
| Commercial / Industry | $400 | $480 | $600 |
Co-Instructor: Timothy Garrett, PhD
TBA
Co-Instructor: Erin Baker, PhD
Dr. Erin Baker is a bioanalytical chemist with more than 16 years' experience utilizing ion mobility spectrometry in conjunction with mass spectrometry (IMS-MS) to study environmental and biological systems. In the last 10 years she has worked primarily on IMS-MS applications in the field of proteomics and more recently she has worked to optimize IMS-MS metabolomic, glycomic and lipidomic separations. Her research involves the development and evaluation of high-throughput IMS-MS, SPE-IMS-MS and LC-IMS-MS analyses to quickly study numerous samples in a short time period without losing valuable biological information, as well as assessing the number and quality of features detected with IMS-MS for comparison with existing MS platforms. Dr. Baker is also presently working with the PNNL Informatics team to design and implement software tools that automatically analyze the complex multidimensional SPE-IMS-MS and LC-IMS-MS data.
Group B
Microbiology 201 :: Mass Spectrometric Methods of Microbial identification
| Instructor(s): | John Lapek, PhD & Chris Cox, PhD | ||||||||||||||||||||
| Level: | 2 (Intermediate) | ||||||||||||||||||||
| Location: | Pueblo B | ||||||||||||||||||||
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Prerequisites:
Overview: This course will present an overview of bottom-up and top-down mass spectrometry-based proteomics techniques for identification of microbes, the use of imaging mass spectrometry in microbiology, and screening for antibiotic resistance. Specific topics to be covered include:
- Comparison of Bottom-up and Top-down techniques
- Clinical applications using MALDI-TOF
- Small molecule (non-protein-based methods) microbial IDs
- Informatics
- Metaproteomics of microbial communities
- Proteogenomics
- Biomarker Identification
EarlyBird Deadline |
Regular Deadline |
After |
|
| Student / Post-Doc (Trainee) | $60 | $72 | $90 |
| Academic / Non-Profit | $180 | $216 | $270 |
| Commercial / Industry | $300 | $360 | $450 |
Co-Instructor: Chris Cox, PhD
Assistant Research Professor Department of Chemistry, Colorado School of Mines, Golden, CO
Dr. Cox’s research interests center on microbial identification, diagnostics development and MALDI-TOF MS with an emphasis on novel fatty acid and bacteriophage-based mass spectrometric methods of microbial analysis and antibiotic resistance profiling. He serves as Director of the Mass Spectrometry Research Laboratory at the Colorado School of Mines. Dr. Cox has over a decade of experience in the fields of pathogen ID, phage biology and modeling of bacterial GI tract colonization and virulence.
Co-Instructor: John Lapek, PhD
IRACDA Post-Doctoral Scholar
Department of Pharmacology, University of California, San Diego, La Jolla, CA
Dr. Lapek’s research interests focus on utilization of quantitative proteomics approaches to better understand the complexity of host-pathogen interactions. Dr. Lapek has been involved in the development of methods to detect under-appreciated phosphorylation events and integrated computational tools to construct networks of functional and physical protein interactions. He has over a decade of experience in the fields of proteomics and quantitative proteomics.
Group B
Proteomics 201 :: Clinical Proteomics
| Instructor(s): | Andy Hoofnagle, MD, PhD, Cory Bystrom, PhD & Chris Shuford, PhD | ||||||||||||||||||||
| Level: | 2-3 (Intermediate - Advanced) | ||||||||||||||||||||
| Location: | Room 5 (Sierra/Ventura) | ||||||||||||||||||||
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Prerequisites: Practical knowledge of quantitative mass spectrometry.
Overview: This course will explore the background of clinical proteomics and approaches to method development and validation. We will provide the motivation for using mass spectrometry to quantify proteins in clinical research and in clinical care. The promise of mass spectrometry to improve the accuracy and precision of results is only realized with robust methods. In order to prepare participants to begin to develop their own robust methods for quantification we will focus on the following topics:
- Why mass spec for peptides and proteins
- Optimization of digestion and other aspects of the method
- Internal standards
- Calibration
- Immunoaffinity enrichment
- Validation
- Quality control
- Case studies
EarlyBird Deadline |
Regular Deadline |
After |
|
| Student / Post-Doc (Trainee) | $80 | $96 | $120 |
| Academic / Non-Profit | $240 | $288 | $360 |
| Commercial / Industry | $400 | $480 | $600 |
Co-Instructor: Andy Hoofnagle, MD, PhD
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.
Co-Instructor: Cory Bystrom, PhD
Dr. Cory Bystrom serves as Director of Research and Development at Cleveland HeartLab where he is responsible for novel biomarker identification, validation and commercialization with an emphasis on quantitative biological mass spectrometry. Dr. Bystrom has over a decade of experience as a laboratory leader and chemist. Prior to joining CHL, he was at Quest Diagnostics Nichols Institute as associate director of research and development with responsibilities for development of tests and identification of analytical strategies for commercialization of new biomarkers. He also has held research and development roles at Oregon Health Science University, Fonterra, and Pharmacia and Upjohn.
Co-Instructor: Christopher Shuford, PhD
Chris Shuford, Ph.D., is Technical Director for research and development at LabCorp’s Center for Esoteric Testing in Burlington, North Carolina. Chris received his B.S. in Chemistry & Physics at Longwood University and obtained his Ph.D. in Bioanalytical Chemistry from North Carolina State University under the tutelage of Professor David Muddiman, where his research focused on applications of nano-flow chromatography (<500 nL/min) for multiplexed peptide quantification using protein cleavage coupled with isotope dilution mass spectrometry (PC-IDMS). In 2012, Chris joined LabCorp’s research and development team where his efforts have focused on development of high-flow chromatographic methods (>1 mL/min) for multiplexed and single protein assays for clinical application.
Group A
Proteomics 202 :: Practical Proteomics Using the Skyline Software Ecosystem
| Instructor(s): | Mike MacCoss, PhD, Brendan MacLean, Lindsay Pino, and Sandi Spencer, PhD | ||||||||||||||||||||
| Level: | 1-3 (Beginner -Advanced) | ||||||||||||||||||||
| Location: | Chino B | ||||||||||||||||||||
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Prerequisites: A basic understanding of quantitative analysis using liquid chromatography-mass spectrometry. We won't cover the basics of electrospray, chromatography, or CID, but otherwise people who have done any LC-MS should be ok in the course.
Overview: This course will explore practical aspects of setting up and performing a quantitative proteomics experiment. The course will focus on how to develop methods and perform the analysis using the Skyline Software Ecosystem (http://skyline.ms). Specifically, we will cover practical issues we have faced in performing data collection and in the interpretation of data. At the end of the course each participant will be familiar with:
- Introduction to quantitation of proteins by mass spectrometry.
- Strategies for peptide selection as a proxy for a protein.
- Using Skyline for method refinement and data analysis.
- Automated strategies for LC-MS system suitability monitoring.
- Visualization and assessment of multiplex peptide LC-MS/MS data.
- Sharing data using Panorama.
- Assessing assay figures of merit.
- Different mass spectrometry data acquisition strategies used in proteomics.
EarlyBird Deadline |
Regular Deadline |
After |
|
| Student / Post-Doc (Trainee) | $80 | $96 | $120 |
| Academic / Non-Profit | $240 | $288 | $360 |
| Commercial / Industry | $400 | $480 | $600 |
Co-Instructor: Michael J. MacCoss, Ph.D.
Mike became interested in biomedical applications of mass spectrometry while working in Dr. Patrick Griffin’s protein mass spectrometry lab at Merck Research Laboratories. He obtained a Ph.D. with Professor Dwight Matthews and pursued a postdoc with Professor John R. Yates III. In 2004 he started the MacCoss lab at the University of Washington and it became obvious that while mass spectrometry data could be collected quickly and robustly, the lack of computational tools for the visualization and analysis of these data was a stumbling block. In 2009 he recruited Brendan MacLean with the goal of developing professional quality software tools for quantitative proteomics. Mike has worked closely with the Skyline development team and our outstanding group of laboratory scientists and collaborators to ensure that our software uses analytical approaches that have been thoroughly vetted by the mass spectrometry community.
Co-Instructor: Brendan MacLean
Brendan worked at Microsoft for 8 years in the 1990s where he was a lead developer and development manager for the Visual C++/Developer Studio Project. Since leaving Microsoft, Brendan has been the Vice President of Engineering for Westside Corporation, Director of Engineering for BEA Systems, Inc., Sr. Software Engineer at the Fred Hutchinson Cancer Research Center, and a founding partner of LakKey Software. In this last position he was one of the key programmers responsible for the Computational Proteomics Analysis System (CPAS), made significant contributions to the development of X!Tandem and the Trans Proteomic Pipeline, and created the LabKey Enterprise Pipeline. Since August, 2008 he has worked as a Sr. Software Engineer within the MacCoss lab and been responsible for all aspects of design, development and support in creating the Skyline Targeted Proteomics Environment and its growing worldwide user community.
Co-Instructor: Lindsay K. Pino
Lindsay is a Ph.D. candidate at the University of Washington’s Department of Genome Sciences in the MacCoss lab. Her research interests include the development of large-scale proteomics assays using data independent acquisition-MS to investigate complex mixtures and applying computational techniques to mine the resulting high-dimensional data. Prior to joining the MacCoss lab, she worked as a research associate at the Broad Institute of MIT and Harvard in Dr. Steve Carr’s Proteomics Platform, where she worked under Dr. Susan Abbatiello to improve the speed and selectivity of targeted proteomics assays using high-field asymmetric waveform ion mobility spectrometry (FAIMS).
Co-Instructor: Sandi Spencer, Ph.D.
Sandi is currently a postdoctoral researcher in the MacCoss lab at the University of Washington working on method development for targeted proteomics and improvement of nanoLC robustness. She earned her Ph.D. from the University of North Carolina at Chapel Hill working in the Glish lab on real-time analysis of compounds in organic aerosol particles.
Group C
Sample Prep 201 :: Sample Preparation and Alternative Matrices for LC-MS Assays
| Instructor(s): | William Clarke, PhD & Mark Marzinke, PhD | ||||||||||||||||||||
| Level: | Beginner / Intermediate | ||||||||||||||||||||
| Location: | Mesquite E | ||||||||||||||||||||
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Prerequisites: Familiarity with LC-MS/MS.
Overview: This course will encompass various sample preparation approaches used for LC-MS assays. The course will highlight not only the importance of sample processing in the clinical laboratory environment, but also illustrate the “fit for purpose” application of processing techniques in clinical mass spectrometry. This course will also discuss the theory behind different specimen preparation methods, strengths and weaknesses of each approach, as well as opportunities for automation. The first 8 hours will serve as a primer of the role of upfront sample management, utilizing examples in blood and urine specimen sources. There will also be an introduction to the application of LC-MS approaches in alternative matrices. The second 8 hours will elaborate on the foundations established in the first half, and expand into newer technologies and automated alternatives for sample processing.
Specific topics to be covered include:
- Pain points in clinical LC-MS
- Overview of specimen processing in laboratory medicine
- Off-line sample processing
- On-line sample processing
- Analysis of blood and urine
- LC-MS of tissue specimens
- Alternate body fluid specimens (e.g. CSF, breast milk, etc.)
- Intracellular and metabolite analysis
- Dried specimens as matrices
- Automation of sample processing
Topics will be covered through lecture, Q&A, Case Studies, and small group exercises.
EarlyBird Deadline |
Regular Deadline |
After |
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| Student / Post-Doc (Trainee) | $80 | $96 | $120 |
| Academic / Non-Profit | $240 | $288 | $360 |
| Commercial / Industry | $400 | $480 | $600 |
Group B
Forensic Toxicology 101 :: Basic Forensic Toxicology
| Instructor(s): | Jarrad Wagner, Ph.D., F-ABFT, Allison Veitenheimer, Ph.D., Russell Lewis, Ph.D., F-ABFT | ||||||||||||||||||||
| Level: | 1 (Beginner) | ||||||||||||||||||||
| Location: | Pueblo A | ||||||||||||||||||||
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Prerequisites: None.
Overview: This 1-day, 8-hour course aims to make scientists familiar with the basic concepts of forensic toxicology. It is presented at the beginner level and is ideal for attendees that wish to learn more about the forensic toxicology landscape. Specific topics that are addressed include:
- History of Forensic Toxicology
- Analytical Techniques in Forensic Toxicology (Colorimetric, Immunoassay, Hyphenated Chromatography-Detection)
- Human Performance Toxicology (Description, Specimen Types, Analytical Techniques, Interpretation Challenges, Case Studies)
- Postmortem Toxicology (Description, Specimen Types, Analytical Techniques, Interpretation Challenges, Case Studies)
- Workplace Drug Testing (Description, Specimen Types, Analytical Techniques, Interpretation Challenges, Case Studies)
- Quality Assurance in Forensic Toxicology (Validation, Accreditation and Certification)
EarlyBird Deadline |
Regular Deadline |
After |
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| Student / Post-Doc (Trainee) | $60 | $72 | $90 |
| Academic / Non-Profit | $180 | $216 | $270 |
| Commercial / Industry | $300 | $360 | $450 |
Dr. Jarrad Wagner is a Professor of Forensic Sciences at Oklahoma State University-Center for Health Sciences (OSU CHS) in Tulsa, OK where he is the forensic chemistry/toxicology track lead in the accredited Master’s of Science in Forensic Sciences degree program. Dr. Allison Veitenheimer is a Research Toxicologist in the Forensic Toxicology and Trace Laboratory at OSU CHS. Dr. Russell (Rusty) Lewis is the Forensic Sciences Supervisor in the Civil Aerospace Medical Institute of the Federal Aviation Administration in Oklahoma City, OK.
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