Accelerating the Implementation of Mass Spectrometry in the Clinical Lab

CMS Logo MSACL

MSACL 2019 EU

Salzburg Sept 22-26

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 September 22 - 26).

Courses are NOT replicated on different days. They are single courses that span 1 or 2 days.

Course Contact Hours
Sunday PM Monday AM Lunch Monday PM Tuesday AM
Data Science
Data Science 201 (Intermediate)
Going Further With R: Tackling Clinical Laboratory Data Manipulation and Modeling
Patrick Mathias, MD, PhD & Randall Julian, PhD
Location: TBA
STARTS <
Sunday
14:00-18:00
Monday
9:00-13:00
Lunch
Monday
13:00-14:00
Monday
14:00-18:00
> ENDS
Tuesday
9:00-12:30
Glyco-Proteomics
Glyco-Proteomics 101 (Beginner to Intermediate)
Unravelling The Sweetness Of Life: Clinical Glyco(Proteo)Mics By Mass Spectrometry
Noortje de Haan, PhD & Guinevere Lageveen-Kammeijer, PhD
Location: TBA
STARTS <
Sunday
14:00-18:00
Monday
9:00-13:00
Lunch
Monday
13:00-14:00
Monday
14:00-18:00
> ENDS
Tuesday
9:00-12:30
LC-MS
LC-MSMS 101 (Beginner)
Getting Started with Quantitative LC-MS/MS in the Diagnostic Laboratory
Laura Owen, PhD & Michael Wright
Location: TBA
STARTS <
Sunday
14:00-18:00
Monday
9:00-13:00
Lunch
Monday
13:00-14:00
Monday
14:00-18:00
> ENDS
Tuesday
9:00-12:30
LC-MSMS 301 (Advanced)
Development and Validation of Quantitative LC-MS/MS Assays for Use in Clinical Diagnostics
Brian Rappold & Chris Shuford
Location: TBA
STARTS <
Sunday
14:00-18:00
Monday
9:00-13:00
Lunch
Monday
13:00-14:00
Monday
14:00-18:00
> ENDS
Tuesday
9:00-12:30
Metabolomics
Metabolomics 202 (Beginner to Intermediate)
Metabolomics: Approaches, Applications and Challenges
Julijana Ivanisevic, PhD & Elizabeth Want, PhD
Location: TBA
STARTS <
Sunday
14:00-18:00
Monday
9:00-13:00
Lunch
Monday
13:00-14:00
Monday
14:00-18:00
> ENDS
Tuesday
9:00-12:30
Microbiology
Proteomic Microbiology 201 (Beginner - Intermediate)
Bottom-Up and Top-Down Proteomic Approaches for Bacterial Identification and Characterization, a Focus on MALDI-TOF and Advanced Technologies
Jean Armengaud, PhD,
Location: TBA
Not
in
Session
Not
in
Session
Lunch
Monday
13:00-14:00
STARTS <
Monday
14:00-18:00
> ENDS
Tuesday
9:00-12:30


Data Science 201 :: Going Further With R: Tackling Clinical Laboratory Data Manipulation and Modeling

Level:Intermediate
Prereqs: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
Location:TBA
Instructor(s):Patrick Mathias, MD, PhD & Randall Julian, PhD

Patrick Mathias, MD, PhD, 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.

Randy Julian, PhD, 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.


Course Contact Hours
Sunday PM Monday AM Lunch Monday PM Tuesday AM
STARTS <
Sunday
14:00-18:00
Monday
9:00-13:00
Lunch
Monday
13:00-14:00
Monday
14:00-18:00
> ENDS
Tuesday
9:00-12:30

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
Jul 17, 2019
Regular
Deadline
Aug 15, 2019
After
Aug 15, 2019
Student / Post-Doc (Trainee)€84€100€135
Academic / Non-Profit€250$300€405
Commercial / Industry€420€505€670
*Short Course Registration is separate from Conference Registration.



Glyco-Proteomics 101 :: Unravelling The Sweetness Of Life: Clinical Glyco(Proteo)Mics By Mass Spectrometry

Level:Beginner to Intermediate
Prereqs:
Location:TBA
Instructor(s):Noortje de Haan, PhD & Guinevere Lageveen-Kammeijer, PhD

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

Guinevere S.M. Lageveen-Kammeijer, PhD, received her PhD on exploring prostate-specific antigen (PSA), the well-known biomarker for prostate cancer, and its glycosylation by capillary electrophoresis and mass spectrometry. Currently, Guinevere performs her post-doctoral research at the Center for Proteomics and Metabolomics at the Leiden University Medical Center, in the group of prof. Manfred Wuhrer. She currently works on further expanding a mass spectrometry-based PSA glycosylation assay which she developed during her PhD. In addition, she explores the possibilities for the in-depth analysis of glycans and intact glycoproteins for biomarker discovery for other diseases as well as for the characterization of biopharmaceuticals. In 2017, Guinevere joined the organization committee of the Netherlands Area Biotech (NLab) Discussion group of CASSS. In 2019, she became a member of the scientific committee of the glycomics session, and a member of the early career committee, of MSACL EU. Her research interests are focused on bringing together researchers from the field of biomarker discovery with clinical laboratory professionals, ensuring a better translation of potential biomarkers to the clinic. Moreover, she is dedicated to convincing her fellow colleagues that glycosylation is an important subject and should not be neglected just because it is rather complicated.


Course Contact Hours
Sunday PM Monday AM Lunch Monday PM Tuesday AM
STARTS <
Sunday
14:00-18:00
Monday
9:00-13:00
Lunch
Monday
13:00-14:00
Monday
14:00-18:00
> ENDS
Tuesday
9:00-12:30

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

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

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

Brief outline of the course:

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

EarlyBird
Deadline
Jul 17, 2019
Regular
Deadline
Aug 15, 2019
After
Aug 15, 2019
Student / Post-Doc (Trainee)€84€100€135
Academic / Non-Profit€250$300€405
Commercial / Industry€420€505€670
*Short Course Registration is separate from Conference Registration.



LC-MSMS 101 :: Getting Started with Quantitative LC-MS/MS in the Diagnostic Laboratory

Level:Beginner
Prereqs:None.
Location:TBA
Instructor(s):Laura Owen, PhD & Michael Wright

Laura Owen is a Consultant Clinical Scientist at Salford Royal Hospital, where mass spectrometry assays for a variety of small molecule and toxicology services are offered nationally. Prior to working at Salford Laura worked at Wythenshawe Hospital where she has experience of quantitative method development on both LC-MS/MS and exact mass equipment. Laura is a honorary senior lecturer at the University of Manchester, where she lectures on chromatography, mass spectrometry and the adrenal cortex on a national clinical science MSc programme. Laura has also acted as chair of the Association for Clinical Biochemistry’s special interest group for mass spectrometry.

Mike Wright is the Scientific Director at the Drug Development Solutions division of LGC, in Fordham, Cambridgeshire, UK. His team work on the development of assays for the monitoring of drugs and biomarkers, as drug development tools, in a wide variety of matrices. Prior to working at LGC, Mike worked in clinical diagnostics developing LC-MS/MS services for health trusts in the UK and Australia. Mike teaches on LC-MS/MS applications, considerations and troubleshooting and has contributed to a number of online training programs including the AACC’s Introductory Liquid Chromatography Mass Spectrometry certificate.


Course Contact Hours
Sunday PM Monday AM Lunch Monday PM Tuesday AM
STARTS <
Sunday
14:00-18:00
Monday
9:00-13:00
Lunch
Monday
13:00-14:00
Monday
14:00-18:00
> ENDS
Tuesday
9:00-12:30

Overview: Is your laboratory under pressure to purchase an LC-tandem MS or have the instruments arrived and your team are beginning on their mass spectrometry journey? 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 - clinical bench analysts, supervisors, R&D scientists, and laboratory directors. After starting out with a basic chemistry refresher, theoretical concepts necessary for a robust implementation of clinical mass spectrometry will be presented, however, the main focus of the course will be on practical recommendations for:

  • Starting with MSMS, LC and sample extraction parameters
  • Choosing internal standards, solvents, and water, making reagents and calibrators
  • How to fine tune sample preparation, LC and MSMS parameters to achieve the desired assay performance
  • Pre-validation stress testing and method validation
  • Preventative maintenance and troubleshooting
  • Maintaining quality once your new LC-MS/MS assay has gone live
Using real-world examples, recommendations will also be given on:
  • LC-MS/MS system purchasing
  • site preparation and installation (dos and don’ts)
  • establishing data analysis & review criteria and an interface to the LIS

The course will be a steady mixture of lectures, tutorials and problem solving sessions with our goal being 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 theoretical 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
Jul 17, 2019
Regular
Deadline
Aug 15, 2019
After
Aug 15, 2019
Student / Post-Doc (Trainee)€84€100€135
Academic / Non-Profit€250$300€405
Commercial / Industry€420€505€670
*Short Course Registration is separate from Conference Registration.



LC-MSMS 301 :: Development and Validation of Quantitative LC-MS/MS Assays for Use in Clinical Diagnostics

Level:Advanced
Prereqs:The target audience should have extensive familiarity with LC-MS/MS systems.
Location:TBA
Instructor(s):Brian Rappold & Chris Shuford

Brian Rappold is the Director of Mass Spectrometry at LabCorp. He is a renowned expert in the field of method development and validation of mass spectrometry assays for clinical diagnostic use, teaching courses on this subject at numerous scientific conferences. His extensive knowledge and clinical perspective has granted him several opportunities to present his research internationally on the topics of hydrophilic interaction liquid chromatography for bio-analysis, multiplexed mass spectrometric detection of amino acidopathies and the origins and solutions of ion suppression in electrospray ionization. He currently serves as the chair of Clinical Chemistry for the American Society for Mass Spectrometry (ASMS) and has served on the Metabolomics and Small Molecule Analysis/Toxicology Scientific Committee for The Association for Mass Spectrometry: Applications to the Clinical Laboratory (MSACL). His research interests include the realization of open-access mass spectrometric systems and antibody-capture/mass spectrometry applications to diagnostic medicine.

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.


Course Contact Hours
Sunday PM Monday AM Lunch Monday PM Tuesday AM
STARTS <
Sunday
14:00-18:00
Monday
9:00-13:00
Lunch
Monday
13:00-14:00
Monday
14:00-18:00
> ENDS
Tuesday
9:00-12:30

Overview: This 16-hour 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
Jul 17, 2019
Regular
Deadline
Aug 15, 2019
After
Aug 15, 2019
Student / Post-Doc (Trainee)€84€100€135
Academic / Non-Profit€250$300€405
Commercial / Industry€420€505€670
*Short Course Registration is separate from Conference Registration.



Metabolomics 202 :: Metabolomics: Approaches, Applications and Challenges

Level:Beginner to Intermediate
Prereqs:LC/MS hands on experience.
Location:TBA
Instructor(s):Julijana Ivanisevic, PhD & Elizabeth Want, PhD

Julijana Ivanisevic, PhD is the head of the Metabolomics Research Platform (Senior Lecturer) at the Faculty of Biology and Medicine, University of Lausanne. Her research expertise is in mass spec­trometry-based metabolomics applications to biomedical research (brain metabolism, ageing, cancer metabolism), evolutionary biology and ecology. Her postdoctoral research was at the Center for Metabolomics at The Scripps Research Institute in La Jolla, California, USA.

Elizabeth Want, PhD is a Senior Lecturer in Molecular Spectroscopy in the Department of Surgery and Cancer at Imperial College, London and the Director of the Imperial International Phenome Training Centre. She joined Imperial College in 2006 after working as a postdoctoral researcher at the Scripps Research Institute in La Jolla, CA. Her research at Imperial College involves the development, optimisation and application of LC-MS methodologies for the analysis of biological samples, largely in the context of metabolic phenotyping. She applies these methods to biomedical research areas including toxicology, cardiovascular disease, neonatal disease and development, and neurological diseases.


Course Contact Hours
Sunday PM Monday AM Lunch Monday PM Tuesday AM
STARTS <
Sunday
14:00-18:00
Monday
9:00-13:00
Lunch
Monday
13:00-14:00
Monday
14:00-18:00
> ENDS
Tuesday
9:00-12:30

Overview:

Metabolome: Downstream of Genome

  • Central Dogma of Molecular Biology – From Genotype to Metabotype
  • Historical Perspective of Metabolomics
  • Technological platforms (NMR, GC/MS, LC/MS) and Applications
  • OmicChallenge – Metabolite Diversity

Approaches in Metabolomics

  • Targeted versus Untargeted (work on the front end vs. work on the back end, instrumentation, etc.)
  • Experimental Design and Sample Preparation (depending on the approach)
  • Choice of Analytical Platform (depending on the approach and metabolites of interest)
  • OmicChallenge – « Big » Data Reduction

Data (Pre)Processing in Untargeted Experiments

  • Step by step from peak picking to peak grouping and annotation
  • Open-access platforms
  • Hands-on XCMS Online
  • Omic Challenge – Metabolite Identification

Statistical Analysis, Metabolite Identification and Mapping onto Pathways

  • Univariateversus Multivariate Statistics (SIMCA, MetaboAnalyst)
  • Metabolite Matching against Metabolite Databases (METLIN, HMDB, LIPIDMAPS, MassBank)
  • Metabolite Set Enrichement Analysis and Network Modeling (MetaboAnalyst, KEGG, BioCyc, Mummichog, Ingenuity)
  • Omic Challenge – Integration with other Omic Technologies in a Biologically Relevant Context

EarlyBird
Deadline
Jul 17, 2019
Regular
Deadline
Aug 15, 2019
After
Aug 15, 2019
Student / Post-Doc (Trainee)€84€100€126
Academic / Non-Profit€250$300€380
Commercial / Industry€420€505€630
*Short Course Registration is separate from Conference Registration.



Proteomic Microbiology 201 :: Bottom-Up and Top-Down Proteomic Approaches for Bacterial Identification and Characterization, a Focus on MALDI-TOF and Advanced Technologies

Level:Beginner - Intermediate
Prereqs:None.
Location:TBA
Instructor(s):Jean Armengaud, PhD,

Jean Armengaud, PhD is best known for his work on proteogenomics of bacteria and the characterization of pathogens and radiotolerant organisms. He directs a mass spectrometry research unit located near Avignon in France that is dedicated to proteomics-based identification and quantitation of pathogens and environmentally relevant bacteria.


Course Contact Hours
Sunday PM Monday AM Lunch Monday PM Tuesday AM
Not in Session Not in SessionLunch
Monday
13:00-14:00
STARTS <
Monday
14:00-18:00
> ENDS
Tuesday
9:00-12:30

Overview: This course will present an overview of bottom-up and top-down techniques for microbial identification using mass spectrometry-based technologies as well as their use in determination of microbial characteristics such as antibiotic resistance profiles. Topics to be discussed include:

  • Comparison of bottom-up versus top-down proteomic approaches,
  • Why top down proteomics is well-suited for microbial identification and characterization,
  • Discrimination of closely related strains by top-down proteomics approaches.,
  • Collection and interpretation of MALDI-TOF data,
  • Proteogenomics as a means for improving annotations based on genomic sequence analysis and its use in identification of key protein markers in MALDI-TOF spectra.
  • The concept of proteoforms as a means of categorizing the PTM states of proteins.
  • The application of these techniques and technologies to antibiotic resistance determination,
  • Novel methodologies that are currently emerging for the analysis of difficult samples, such as mixtures of pathogens and spores present within complex matrices.
  • Recent advances for pathogen quantitation by tandem mass spectrometry.
  • Use of MALDI-TOF for identification of viruses, molds and parasites.

EarlyBird
Deadline
Jul 17, 2019
Regular
Deadline
Aug 15, 2019
After
Aug 15, 2019
Student / Post-Doc (Trainee)€60€72€90
Academic / Non-Profit€180$216€270
Commercial / Industry€300€360€450
*Short Course Registration is separate from Conference Registration.