MSACL 2024 Program

MSACL 2024 : Conference Program

Monterey, CA • March 17-22, 2024

Abstract Clinical Use Status Key
= Discovery stage. (16.60%, 2024)
= Translation stage. (37.02%, 2024)
= Clinically available. (46.38%, 2024)


Sunday
Sunday
1300
1900
Reg Desk Open for Badge Pick-Up
@ Serra Foyer (Conference Ctr > Ground Floor)
2128
Sunday
1430
1830
Short Course : LC-MSMS 101 : Getting Started with Quantitative LC-MSMS in the Diagnostic Laboratory
@ De Anza 2 (Portola Hotel > Ground Floor)

Grace van der Gugten, B.Sc. Chemistry
Provincial Health Services Authority, BCCDC Toxicology Lab

Deborah French, PhD, DABCC (CC, TC), FADLM
UCSF

Jacqueline Hubbard, PhD, DABCC
Beth Israel Deaconess Medical Center, Harvard Medical School

Lorin Bachmann, PhD, DABCC
VCU Health System


Course Schedule

Segment 1 : Sunday 14:30 - 18:30 (3.50 contact hrs)
Segment 2 : Monday 08:00 - 12:00 (3.50 contact hrs)
Segment 3 : Monday 14:00 - 18:00 (3.50 contact hrs)
Segment 4 : Tuesday 08:00 - 12:00 (3.50 contact hrs)

Total Contact Hours: 14.00
(Ten-minute breaks occur after each full instructional hour when another hour follows. Breaks are excluded from contact hour calculations.)

---------------

Pre-requisites

Interested in a detailed, practical introduction to clinical quantitative LCMS

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:

  1. LC-MS/MS system purchasing, site preparation and installation
  2. Choosing internal standards, solvents, and water, making reagents and calibrators
  3. Selecting and optimizing LC parameters
  4. Selecting and optimizing MS/MS parameters
  5. Selecting and optimizing sample preparation
  6. Adjusting sample preparation, LC and MSMS parameters to achieve the desired assay performance
  7. Establishing data analysis & review criteria
  8. Pre-validation stress testing and method validation
  9. Maintaining quality in production
  10. Preventative maintenance and troubleshooting

Objectives

At the conclusion of this short course, the participant will be able to:

  1. Describe the components of a triple quadrupole mass spectrometer and describe how they work.
  2. Evaluate sample preparation options for LC-MS/MS and explore matrix effect validation experiments.
  3. Explain the importance of developing an LC gradient method that is compatible with their analyte(s) of interest.
  4. Outline MS parameters that need optimization, including source and compound specific parameters.
  5. List quantitation and review criteria options for LC-MS/MS data.
  6. Formulate a validation plan and describe how to execute those experiments for an LC-MS/MS assay.
  7. Appraise equipment options and justify the purchase cost.
2267
Sunday
1430
1830
Short Course : LC-MSMS 201 : Practical LC-MS/MS Method Development and Bioanalytical Method Validation for Clinical and Non-Clinical Samples
@ Ironwood 2 (Portola Hotel > 3rd Floor)

Perry Wang, PhD
LC-MS Technical Expert


Course Schedule

Segment 1 : Sunday 14:30 - 18:30 (3.50 contact hrs)
Segment 2 : Monday 08:00 - 12:00 (3.50 contact hrs)
Segment 3 : Monday 14:00 - 18:00 (3.50 contact hrs)
Segment 4 : Tuesday 08:00 - 12:00 (3.50 contact hrs)

Total Contact Hours: 14.00
(Ten-minute breaks occur after each full instructional hour when another hour follows. Breaks are excluded from contact hour calculations.)

---------------

Pre-requisites

LC-MSMS 101

Overview

Both LC-MS method development and bioanalytical method validation play a crucial role for successfully conducting regulatory studies including nonclinical, biopharmaceutics, and clinical pharmacology studies. The objective of this course is to offer practical training for practitioners, physicians, laboratory scientists, industrial scientists, and health care professionals in the clinical laboratory. It focuses on practical LC-MS method development and bioanalytical method validation for clinical and non-clinical samples. It takes participants step-by-step through the concepts and techniques to develop and validate bioanalytical methods. After this course, participants will be able to independently develop and validate their own LC-MS methods and apply the validated methods for their routine clinical and non-clinical studies.

Objectives:

At the conclusion of this short course, the participant will be able to:

  1. Describe the role of high-performance liquid chromatography (HPLC)
  2. Discuss the principle of HPLC
  3. Apply the resolution equation for chromatographic separation
  4. Develop and optimize HPLC methods
  5. Discuss HPLC troubleshooting cases
  6. Illustrate the principles of mass spectrometry (MS)
  7. Describe Atmospheric pressure ionization (API) in mass spectrometry
  8. Distinguish common ionization modes for MS: ESI, APCI, APPI and MALDI
  9. Develop MS methods
  10. Discuss preparation of clinical samples for LC-MS analysis
  11. Apply the FDA’s Bioanalytical Method Validation Guidance
  12. Describe how clinical sample collection, handling, and storage affect the reliability of the data
  13. Prepare for the challenges of assaying clinical samples by LC-MS
  14. Apply validated methods for clinical and pre-clinical studies
2256
Sunday
1430
1830
Short Course : LC-MSMS 302 : Advanced LC-MS/MS Method Development, Method Troubleshooting and Instrument Operation Needed in Developing Successful Methods for Molecular identification and Quantitation in the Clinical Lab
@ Steinbeck 2 (Conference Ctr > 2nd Floor)

Robert Voyksner, PhD
LCMS Limited


Course Schedule

Segment 1 : Sunday 14:30 - 18:30 (3.50 contact hrs)
Segment 2 : Monday 08:00 - 12:00 (3.50 contact hrs)
Segment 3 : Monday 14:00 - 18:00 (3.50 contact hrs)
Segment 4 : Tuesday 08:00 - 12:00 (3.50 contact hrs)

Total Contact Hours: 14.00
(Ten-minute breaks occur after each full instructional hour when another hour follows. Breaks are excluded from contact hour calculations.)

---------------

Pre-requisites

Working knowledge analytical chemistry, including experience with LC separations and/or mass spectrometry. Attending level 100 or 200 LC/MS courses at MSACL would be beneficial. This is a course for those who want to increase their understanding of LC-MS/MS, who want to learn how to develop a successful quantitative and qualitative LC-MS/MS assay and a deeper understanding the technique to achieve better sensitivity, specificity or throughput in their laboratory.

Overview

This course is designed for the scientist who uses LC-MS/MS in the clinical lab, who wants a deeper understanding in steps towards developing successful methods, optimizing methods, trouble shoot methods and solving problems employing LC-MS/MS.

The course covers important aspects in understanding and optimization ionization with electrospray on multiple instrument platforms including triple quadrupole, time-of-flight, quadrupole time of flight and orbit trap mass analyzers.

The course will discuss sample preparation, modes of chromatography and MS/MS considerations with respect to method development and optimization for the analysis of “real-world” samples by LC-MS/MS, to achieve the best sensitivity, specificity, and sample throughput.

This course focuses on method development method troubleshooting and application for the analysis of both small and large molecules that are clinically relevant. All examples are taken from real world analyses, performed by Dr. Voyksner at LCMS Limited. The concepts presented in the course are reinforced through numerous problem sets the attendees will work on throughout the 16 hour course.

The last part of the course is an open forum where each attendee is invited to share a current LC-MS/MS issue they face. As a class we work through potential solutions and experiments to be performed to find a solution to the student problem, applying the concepts taught in the class and Dr. Voyksner’s 40 plus years of experience in LC-MS/MS. From past classes this has been the attendee’s favorite part of the class.

Topics Covered

  1. Understanding API ionization processes for electrospray, APCI and APPI, what affects the ionization process and how to maximize the ionization for compounds of interest.
  2. Understanding the effects of LC columns (dimensions and particles size), flow rate, and mobile phases have upon the separation and LC/MS analysis.
  3. Determining the type of ions that can form by electrospray and APCI, how to interpret the MS and MS/MS spectra and approaches on how to perform qualitative analysis in LC-MS/MS and high-resolution MS/MS.
  4. Understanding important issues that affect quantitative analytical results and how to optimize the method to achieve the best performance, reduce matrix suppression, reduce background and generate the best accuracy and precision.
  5. Exploring what new techniques are available (e.g. direct analysis MS, chip method and MS instrumentation) that can improve the results one can obtain.
  6. Discuss aspects of method development and method trouble shooting from example problems of real world problem in quantitative LC-MS/MS.
  7. Open forum discussing attendees’ specific problems they face in method development or analysis using LC-MS/MS.

Objectives

At the conclusion of this short course, the participant will be able to:

  1. Improve sensitivity and specificity for LC-MSMS analysis.
  2. Develop methods to analyze the target compounds.
  3. Select correct electrospray or APCI conditions to analyze the target compound.
  4. Reduce matrix suppression.
  5. Troubleshoot a method to improve accuracy, precision, sensitivity and specificity.
  6. Reduce background in LC-MSMS analysis.
2278
Sunday
1430
1830
Short Course : Data Science 101 : Breaking up with Excel: An Introduction to the R Statistical Programming Language
@ Colton 1/2 (Conference Ctr > 2nd Floor)

Dustin Bunch, PhD, DABCC
Nationwide Children's Hospital

Nicholas Spies, MD
University of Utah, ARUP Laboratories


Course Schedule

Segment 1 : Sunday 14:30 - 18:30 (3.50 contact hrs)
Segment 2 : Monday 08:00 - 12:00 (3.50 contact hrs)
Segment 3 : Monday 14:00 - 18:00 (3.50 contact hrs)
Segment 4 : Tuesday 08:00 - 12:00 (3.50 contact hrs)

Total Contact Hours: 14.00
(Ten-minute breaks occur after each full instructional hour when another hour follows. Breaks are excluded from contact hour calculations.)

---------------

Pre-requisites

There will be some handouts and software installation before the meeting but no pre-req classes.

Overview

Does Excel lag on you when you open a file bigger than 1000 rows? Has it ever changed your data to a date against your will? Are you ready to jump right past Tableau and into the world of Data Science using a real programming language?

Well, your wait is over because at MSACL we again 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.

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 Bunch & Spies 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 RStudio interface installed. Students may use Windows, Mac OSX or Linux environments. Both R and RStudio 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

!!! DOWNLOAD PROGRAM PACKAGES PRIOR TO ARRIVAL ONSITE !!! THERE WILL NOT BE OPEN INTERNET WIFI IN THE CONFERENCE CENTER.

!!! POWER : Make sure your computer is charged to hold power for 4-8 hrs, as power outlets may not be available.

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

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

Topics Covered

  1. Brief overview of RStudio, R variables: vectors (numerical, character, logical), matrices, data frames and lists and classes: numeric, character, list and changing between them
  2. Importing data from CVS and Excel
  3. Dealing with non-numeric instrument data & manipulating and cleansing your data
  4. Exporting data in Excel-like format or to share
  5. Basics of tidyverse: dplyr, filter, mutate, join
  6. Regression: ordinary least squares, Passing Bablok, Deming, weighted regression
  7. Non-linear regressions
  8. Looping: Doing things repeatedly
  9. group_by and summarize
  10. Making highly customized figures with base plot or ggplot
  11. Putting it all together projects:
    -- Preparing method comparison regression and Bland Altman plots
    -- Preparing mass spectrometry data for upload to LIS

Objectives

At the conclusion of this short course, the participant will be able to:

  1. Manage and analyze data in the R programming language using RStudio.
  2. Identify resources to continue learning the R programming language.
  3. Develop computational scripts in the R programming Language.
  4. Use both base R and tidyverse tools for data cleansing and data manipulation.
  5. Develop an algorithmic approach to common laboratory data processing needs.
  6. Prepare publication quality figures using ggplot.
2282
Sunday
1430
1830
Short Course : Data Science 203 : Machine Learning : A Gentle Introduction
@ Bonsai (Portola Hotel > Ground Floor)

Randall Julian, PhD
Indigo BioAutomation

Stephen Master, MD, PhD, FADLM
Children's Hospital of Philadelphia


Course Schedule

Segment 1 : Sunday 14:30 - 18:30 (3.50 contact hrs)
Segment 2 : Monday 08:00 - 12:00 (3.50 contact hrs)
Segment 3 : Monday 14:00 - 18:00 (3.50 contact hrs)
Segment 4 : Tuesday 08:00 - 12:00 (3.50 contact hrs)

Total Contact Hours: 14.00
(Ten-minute breaks occur after each full instructional hour when another hour follows. Breaks are excluded from contact hour calculations.)

---------------

Pre-requisites

Data Science 101 or 201 (or equivalent experience)

Overview

Machine learning techniques have been highly successful in driving the growth of companies like Amazon, Google, Netflix, and other companies that rely on identifying patterns in big data. More importantly, these algorithms are beginning to revolutionize clinical diagnosis and mass spectrometry, from FDA-approved retinal image analysis to robust detection of mass spec chromatographic peaks.

But ... what exactly is machine learning? How does it work? How can you apply it to your own data?

In this course, we will help you sort through the hype and provide an introduction to machine learning, including an overview of common approaches, known pitfalls, and other important concepts.

We will include practical instruction on applying machine learning algorithms using the R statistical language, so familiarity with R at the level of the material taught in Data Science 101 and/or 201 is desirable.

Topics Covered

  1. What is machine learning?
  2. Basic practices
  3. Exploring your data
  4. Preparing your data for ML algorithms
  5. Features: Selection and Engineering
  6. Decision trees
  7. Model evaluation
  8. Solutions to overfitting: Ensembles
  9. Random Forests
  10. Explaining complex models
  11. Gradient Boosting with XGBoost

Objectives

At the conclusion of this short course, the participant will be able to:

  1. Explain principles of machine learning
  2. Describe machine learning processes
  3. Perform classification using multiple machine learning models
  4. Evaluate and test the performance of machine learning models
2288
Sunday
1430
1830
Short Course : Metabolomics 102 : Microsampling and Mass Spectrometry – Fit for Purpose in the Clinical Screening and Monitoring Space
@ Cottonwood 1 (Portola Hotel > 3rd Floor)

Donald Chace, PhD, MSFS, FACB
Capitainer

Tim Garrett, PhD
University of Florida College of Medicine


Course Schedule

Segment 1 : Sunday 14:30 - 18:30 (3.50 contact hrs)
Segment 2 : Monday 08:00 - 12:00 (3.50 contact hrs)

Total Contact Hours: 7.00
(Ten-minute breaks occur after each full instructional hour when another hour follows. Breaks are excluded from contact hour calculations.)

---------------

Pre-requisites

None.

Overview

The classic dried blood spot (Guthrie Spot, NBS spot) has been used routinely for 60 years in inborn errors of metabolism (rare disease screening of newborns) space in addition to health monitoring of the detected disorders. Mass spectrometry advanced this space 30 years ago to take advantage of its multianalyte profiles (the early days of metabolomics) to detect rare diseases. It was the introduction of multiple biomarkers in clinical assessment. As mass spec evolved in this space, new workflows and pre-analytical methods, sample preparation chemistry was altered by taking advantage of the dried microsample format and extraction chemistry. DBS offered a replacement to liquid microsamples, and the risks and costs associated with infectious disease exposure, cost of shipping using the cold chain, storage and most recently patient centered sampling where remote, or home sampling is made possible.

Most chemistry workflows are still dominated by liquid blood or plasma and immunoassay platforms, they are not necessarily suitable for microsample collection as demonstrated in the choice for newborn screening (200-300 µL) versus 1-10 mL for a venous blood draw. Furthermore, a dried microsample offers better improved stability for some molecules due to degradation of active enzyme, light or heat. Beyond newborn screening standard, the pace of adoption of dried blood versus liquid plasma is slowed because of the lack of bridging studies. Therefore, an understanding of DBS versus liquid is critical in designing these experiments. This course will describe the advantages of filter paper for mass spec workflows in areas of sample cleanup, extraction, manipulation as well as examples of successful analysis. We will provide examples of existing methods in use in clinical analysis and will expand upon last year’s MSACL course.

As important are its advantages, we will discuss limitations from the lack of precision of classic Guthrie cards because of volume uncertainties to the problems of some mass spectrometry analysis of molecules like proteins. Finally, we will correlate these issues with the ever-expanding area of metabolomics, lipidomic and more important how a DBS can be integrated with other technique like molecular and immunoassays to provide a better clinical result from which the clinician can make earlier accurate diagnosis. Ultimate DBS can improve health care services as well as access with remote collection.

Objectives

At the conclusion of this short course, the participant will be able to:

  1. Describe the best fit for DBS utilization in clinical mass spectrometry and bioanalytical research including “omics” applications.
  2. Discuss bridge strategies for adopting existing MS methods that utilize venous blood, plasma or other liquids to the dried microsample format.
  3. Compare the advances in the quantitative micro sampling space and discuss issues with volume and solid matrix additives.
  4. Interpretate approaches for multiplexed analysis and multi-omics.
2301
Sunday
1830
2200
Welcome Dinner Buffet
@ Ferrantes (Marriott > 10th Floor)
2130
Sunday
2100
Monterey Conference Center Closes
@ Serra Foyer (Conference Ctr > Ground Floor)
2348

Monday
Monday
645
800
Short Course Breakfast
@ Club Room (Portola Hotel > Ground Floor)
2132
Monday
700
1900
Registration Desk Open
@ Serra Foyer (Conference Ctr > Ground Floor)
2133
Monday
800
1200
Short Course : LC-MSMS 101 : Getting Started with Quantitative LC-MSMS in the Diagnostic Laboratory
@ De Anza 2 (Portola Hotel > Ground Floor)
2268
Monday
800
1200
Short Course : LC-MSMS 201 : Practical LC-MS/MS Method Development and Bioanalytical Method Validation for Clinical and Non-Clinical Samples
@ Ironwood 2 (Portola Hotel > 3rd Floor)
2271
Monday
800
1200
Short Course : LC-MSMS 203 : Validation of Quantitative LC-MS/MS Assays for Clinical and Academic Use
@ De Anza 3 (Portola Hotel > Ground Floor)

Claire Knezevic, PhD
Lurie Childrens Hospital

Joshua Hayden, PhD, DABCC, FACB
Cleveland Clinic


Course Schedule

Segment 1 : Monday 08:00 - 12:00 (3.50 contact hrs)
Segment 2 : Monday 14:00 - 18:00 (3.50 contact hrs)
Segment 3 : Tuesday 08:00 - 12:00 (3.50 contact hrs)

Total Contact Hours: 10.50
(Ten-minute breaks occur after each full instructional hour when another hour follows. Breaks are excluded from contact hour calculations.)

---------------

Pre-requisites

Individuals with previous mass spectrometry experience (clinical or academic) or those who have taken the LC-MSMS 101 and/or 201 course and are looking to expand their knowledge.

Overview

This course is intended for those with previous mass spectrometry experience who are looking to expand their knowledge and skills with regards to assay validation for both clinical and academic purposes. The course will heavily focus on quantitative small molecule assays.

The course will provide a short overview of development followed by an in-depth discussion of how to validate liquid chromatography tandem mass spectrometry assays. The course will conclude with a discussion of the measures and metrics to use for monitoring assay performance once testing is live.

Throughout each section, applicable and practical guides for validation experiments and acceptance criteria will be provided, as well as processes for ensuring assay performance post-go-live. For each step of assay development, we will highlight experiments to perform along the way to identify issues pre-validation. Validation studies will include an overview of the studies necessary for both clinical and academic purposes. The clinical validation requirements for CLIA, CAP, NY State, and FDA regulated environments will be presented. The academic validation requirements for submitting such assays (or studies using them) to high-impact, peer-reviewed journals (Clinical Chemistry, Molecular & Cellular Proteomics, Journal of Clinical Endocrinology and Metabolism, etc) will be presented. Post-go live monitoring will include discussion of essential performance metrics, performing staff competency, minimizing manual data entry and how to facilitate interfacing with LIS, and finally a discussion of post-go-live issues.

Topic Covered

This short course will include 12 approximately 1 hour modules with 15 min for exercises and Q&A at the end of each module.

  1. Optimizing signal/tuning
  2. Chromatography
  3. Internal standard
  4. Reportable range
  5. Calibration and calibrators
  6. Matrix effect studies
  7. Stability studies
  8. Precision studies
  9. Accuracy and correlation studies
  10. Going live
  11. Performance metrics for post-go-live monitoring
  12. Discussion of post-go-live issues

Objectives:

At the conclusion of this short course, the participant will be able to:

  1. Design a validation plan for a target assay.
  2. Define performance characteristics for the intended use of the assay.
  3. Identify and address potential pitfalls in the developed assay.
2275
Monday
800
1200
Short Course : LC-MSMS 302 : Advanced LC-MS/MS Method Development, Method Troubleshooting and Instrument Operation Needed in Developing Successful Methods for Molecular identification and Quantitation in the Clinical Lab
@ Steinbeck 2 (Conference Ctr > 2nd Floor)
2279
Monday
800
1200
Short Course : Data Science 101 : Breaking up with Excel: An Introduction to the R Statistical Programming Language
@ Colton 1/2 (Conference Ctr > 2nd Floor)
2283
Monday
800
1200
Short Course : Data Science 203 : Machine Learning : A Gentle Introduction
@ Bonsai (Portola Hotel > Ground Floor)
2292
Monday
800
1200
Short Course : Sample Preparation 201 : Sample Preparation and Alternative Matrices for LC-MS Assays
@ Redwood 2 (Portola Hotel > 3rd Floor)

William Clarke, PhD, MBA, DABCC
Johns Hopkins University School of Medicine

Mark Marzinke, PhD, DABCC, FAACC
Johns Hopkins University School of Medicine


Course Schedule

Segment 1 : Monday 08:00 - 12:00 (3.50 contact hrs)
Segment 2 : Monday 14:00 - 18:00 (3.50 contact hrs)
Segment 3 : Tuesday 08:00 - 12:00 (3.50 contact hrs)

Total Contact Hours: 10.50
(Ten-minute breaks occur after each full instructional hour when another hour follows. Breaks are excluded from contact hour calculations.)

---------------

Pre-requisites

Individuals with previous mass spectrometry experience looking to expand their knowledge.

Summary:

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 section of the course 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 section of the course will elaborate on the foundations established in the first half, and expand into newer technologies and automated alternatives for sample processing. Topics will be covered through lecture, Q&A, Case Studies, and small group exercises.

Topics covered include

  • Pain points in clinical LC-MS
  • Overview of specimen processing in laboratory medicine
  • Off-line and On-line sample processing
  • Analysis of blood and urine
  • Alternate body fluid specimens (e.g. CSF, breast milk, tissue, etc.)
  • Dried specimens as matrices
  • Automation of sample processing
Learning Objectives

After attending this short course, participants will be able to:

  1. Describe various pain points and challenges in clinical LC-MS;
  2. Discuss the impact of various specimen preparation approaches on LC-MS assay performance;
  3. Implement a fit-for-purpose approach to selection of a specimen preparation approach in their laboratory practice;
  4. Describe alternative specimen types and their potential utility in clinical practice or research.
2296
Monday
800
1200
Short Course : Metabolomics 102 : Microsampling and Mass Spectrometry – Fit for Purpose in the Clinical Screening and Monitoring Space
@ Cottonwood 1 (Portola Hotel > 3rd Floor)

Course Schedule

Segment 1 : Sunday 14:30 - 18:30 (3.50 contact hrs)
Segment 2 : Monday 08:00 - 12:00 (3.50 contact hrs)

Total Contact Hours: 7.00
(Ten-minute breaks occur after each full instructional hour when another hour follows. Breaks are excluded from contact hour calculations.)

---------------

Pre-requisites

None.

Overview

The classic dried blood spot (Guthrie Spot, NBS spot) has been used routinely for 60 years in inborn errors of metabolism (rare disease screening of newborns) space in addition to health monitoring of the detected disorders. Mass spectrometry advanced this space 30 years ago to take advantage of its multianalyte profiles (the early days of metabolomics) to detect rare diseases. It was the introduction of multiple biomarkers in clinical assessment. As mass spec evolved in this space, new workflows and pre-analytical methods, sample preparation chemistry was altered by taking advantage of the dried microsample format and extraction chemistry. DBS offered a replacement to liquid microsamples, and the risks and costs associated with infectious disease exposure, cost of shipping using the cold chain, storage and most recently patient centered sampling where remote, or home sampling is made possible.

Most chemistry workflows are still dominated by liquid blood or plasma and immunoassay platforms, they are not necessarily suitable for microsample collection as demonstrated in the choice for newborn screening (200-300 µL) versus 1-10 mL for a venous blood draw. Furthermore, a dried microsample offers better improved stability for some molecules due to degradation of active enzyme, light or heat. Beyond newborn screening standard, the pace of adoption of dried blood versus liquid plasma is slowed because of the lack of bridging studies. Therefore, an understanding of DBS versus liquid is critical in designing these experiments. This course will describe the advantages of filter paper for mass spec workflows in areas of sample cleanup, extraction, manipulation as well as examples of successful analysis. We will provide examples of existing methods in use in clinical analysis and will expand upon last year’s MSACL course.

As important are its advantages, we will discuss limitations from the lack of precision of classic Guthrie cards because of volume uncertainties to the problems of some mass spectrometry analysis of molecules like proteins. Finally, we will correlate these issues with the ever-expanding area of metabolomics, lipidomic and more important how a DBS can be integrated with other technique like molecular and immunoassays to provide a better clinical result from which the clinician can make earlier accurate diagnosis. Ultimate DBS can improve health care services as well as access with remote collection.

Objectives

At the conclusion of this short course, the participant will be able to:

  1. Describe the best fit for DBS utilization in clinical mass spectrometry and bioanalytical research including “omics” applications.
  2. Discuss bridge strategies for adopting existing MS methods that utilize venous blood, plasma or other liquids to the dried microsample format.
  3. Compare the advances in the quantitative micro sampling space and discuss issues with volume and solid matrix additives.
  4. Interpretate approaches for multiplexed analysis and multi-omics.
2302
Monday
800
1200
Short Course : Clinical Proteomics 201 : Clinical Proteomics
@ Steinbeck 3 (Conference Ctr > 2nd Floor)

Andy Hoofnagle, MD, PhD
University of Washington

Cory Bystrom, PhD
Ultragenyx

Christopher Shuford, PhD
Labcorp


Course Schedule

Segment 1 : Monday 08:00 - 12:00 (3.50 contact hrs)
Segment 2 : Monday 14:00 - 18:00 (3.50 contact hrs)
Segment 3 : Tuesday 08:00 - 12:00 (3.50 contact hrs)

Total Contact Hours: 10.50
(Ten-minute breaks occur after each full instructional hour when another hour follows. Breaks are excluded from contact hour calculations.)

---------------

Pre-requisites

None.

Overview

The main goal of this course is to provide an interactive forum in which attendees will be introduced to critical aspects of clinical protein measurements.

The topics of this course will be templated on the framework of CLIS guidance document, C64: Quantitative Measurement of Proteins and Peptides by Mass Spectrometry.

The motivation for using mass spectrometry to quantify proteins in clinical research and in clinical care will be discussed as part of this interactive workshop. Technical topics uniquely affecting quantitative protein and peptides measurements by mass spectrometry will be a point of emphasis. Case studies from assay inception through validation will be presented and participants will work interactively to critique various aspects of clinical proteomic measurements.

Topics Covered

  1. Protein vs Peptide Measurands
  2. Workflows
  3. Sample Preparation (Digestion & Enrichment)
  4. Internal standards
  5. Calibration
  6. Validation
  7. Quality control

Objectives

At the conclusion of this short course, the participant will be able to:

  1. Describe the holistic process of delivering a clinically relevant mass spectrometry based protein/peptide assay from inception to validation.
  2. Recognize the factors in assay development that are unique to proteins and peptides in comparison to traditional small molecule assays.
  3. Use guidance documents in conjunction with rigorous experimental design to support fit-for-purpose method development strategies.
2305
Monday
800
1200
Short Course : Clinical Proteomics 202 : MS-based Precision Diagnostics by Molecular Protein Analysis
@ Ironwood 1 (Portola Hotel > 3rd Floor)

Renee Ruhaak, PhD
LUMC

Mirjam Kruijt, PhD
Amsterdam UMC

Esther Reijnders, MSc.
LUMC


Course Schedule

Segment 1 : Monday 08:00 - 12:00 (3.50 contact hrs)
Segment 2 : Monday 14:00 - 18:00 (3.50 contact hrs)
Segment 3 : Tuesday 08:00 - 12:00 (3.50 contact hrs)

Total Contact Hours: 10.50
(Ten-minute breaks occur after each full instructional hour when another hour follows. Breaks are excluded from contact hour calculations.)

---------------

Pre-requisites

A background in quantitative proteomics is helpful but not required. You will need to know the principles of LC and QQQ analysis through multiple reaction monitoring.

Overview

Download Full Syllabus Here

Did you know proteins may exist in hundreds of molecular proteoforms? And that each specific proteoform may have different functionality, potentially leading to a pathophysiological clinical phenotype ? How could we measure such proteoforms using mass spectrometry? And how could measurement of proteoforms aid in precision diagnostics?

In this course, we will explain what proteoforms are, and why they may be relevant to measure in a medical laboratory. We will use real-lab examples of proteoforms known to affect the patients’ health status and guide you through the potential methods on identifying and characterizing proteoforms with multiple-reaction-monitoring MS. We will start the course with the rationale on when and how to develop new diagnostic tests. We will explain the diversity in proteoforms, with a focus on proteoforms caused by mutations, but we will also touch upon PTM-induced proteoforms. Lastly, we will discuss several quality related aspects of these tests. In the end, our aim is to provide the knowledge necessary to apply proteoform analysis by MS in your own (clinical) laboratory.

The course will consist of theoretical background, examples of applications and interactive sessions. A background in quantitative proteomics is helpful but not required. You will need to know the principles of LC and QQQ analysis through multiple reaction monitoring. At the end of the course, you will know why molecular protein analysis could be beneficial and how you can apply it in your laboratory.

Objectives

At the conclusion of this short course, the participant will be able to:

  1. Discuss what proteoforms are and why they may be relevant to quantify.
  2. Discuss how the analysis of proteoforms will contribute to precision diagnostics and how clinical care pathways may be altered based on molecular protein measurements.
  3. Discriminate proteoforms using multiple-reaction-monitoring mass spectrometry.
  4. Evaluate molecular MS data and provide answers for laboratory specialists
  5. Ensure performance and quality of proteoform-based tests.
2308
Monday
800
1200
Short Course : GlycoProteomics 101 : Clinical Glyco(proteo)mics by Mass Spectrometry
@ Cottonwood 2 (Portola Hotel > 3rd Floor)

Tamás Pongrácz, PhD
Karolinska Institute

Guinevere Lageveen-Kammeijer, PhD
University of Groningen


Course Schedule

Segment 1 : Monday 08:00 - 12:00 (3.50 contact hrs)
Segment 2 : Monday 14:00 - 18:00 (3.50 contact hrs)
Segment 3 : Tuesday 08:00 - 12:00 (3.50 contact hrs)

Total Contact Hours: 10.50
(Ten-minute breaks occur after each full instructional hour when another hour follows. Breaks are excluded from contact hour calculations.)

---------------

Pre-requisites

Knowledge on basic mass spectrometry and spectral interpretation.

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? 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 and data analysis approaches will be covered. We will close-up with a session about glycomic biomarker discovery.

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.

Objectives:

At the conclusion of this short course, the participant will be able to:

  1. Discuss glycan nomenclature and biosynthesis
  2. Select an appropriate analytical method for a specific glycomics research question.
  3. Interpret mass spectrometry data using the biological background of a sample and the biosynthetic restrictions of the system.
  4. Define the identity of released glycan and glycopeptide molecules using MS1 and MS2 data.
  5. Select the appropriate software tools to aid glyco(proteo)mics MS data processing knowing the used analytical platforms.
2313
Monday
1200
1400
Lunch On Own
@ Off-site

Recommended Places to Eat
2142
Monday
1400
1800
Short Course : LC-MSMS 101 : Getting Started with Quantitative LC-MSMS in the Diagnostic Laboratory
@ De Anza 2 (Portola Hotel > Ground Floor)
2269
Monday
1400
1800
Short Course : LC-MSMS 201 : Practical LC-MS/MS Method Development and Bioanalytical Method Validation for Clinical and Non-Clinical Samples
@ Ironwood 2 (Portola Hotel > 3rd Floor)
2272
Monday
1400
1800
Short Course : LC-MSMS 203 : Validation of Quantitative LC-MS/MS Assays for Clinical and Academic Use
@ De Anza 3 (Portola Hotel > Ground Floor)

Course Schedule

Segment 1 : Monday 08:00 - 12:00 (3.50 contact hrs)
Segment 2 : Monday 14:00 - 18:00 (3.50 contact hrs)
Segment 3 : Tuesday 08:00 - 12:00 (3.50 contact hrs)

Total Contact Hours: 10.50
(Ten-minute breaks occur after each full instructional hour when another hour follows. Breaks are excluded from contact hour calculations.)

---------------

Pre-requisites

Individuals with previous mass spectrometry experience (clinical or academic) or those who have taken the LC-MSMS 101 and/or 201 course and are looking to expand their knowledge.

Overview

This course is intended for those with previous mass spectrometry experience who are looking to expand their knowledge and skills with regards to assay validation for both clinical and academic purposes. The course will heavily focus on quantitative small molecule assays.

The course will provide a short overview of development followed by an in-depth discussion of how to validate liquid chromatography tandem mass spectrometry assays. The course will conclude with a discussion of the measures and metrics to use for monitoring assay performance once testing is live.

Throughout each section, applicable and practical guides for validation experiments and acceptance criteria will be provided, as well as processes for ensuring assay performance post-go-live. For each step of assay development, we will highlight experiments to perform along the way to identify issues pre-validation. Validation studies will include an overview of the studies necessary for both clinical and academic purposes. The clinical validation requirements for CLIA, CAP, NY State, and FDA regulated environments will be presented. The academic validation requirements for submitting such assays (or studies using them) to high-impact, peer-reviewed journals (Clinical Chemistry, Molecular & Cellular Proteomics, Journal of Clinical Endocrinology and Metabolism, etc) will be presented. Post-go live monitoring will include discussion of essential performance metrics, performing staff competency, minimizing manual data entry and how to facilitate interfacing with LIS, and finally a discussion of post-go-live issues.

Syllabus

Format – This short course will include 12 approximately 1 hour modules with 15 min for exercises and Q&A at the end of each module.

Topics:

  1. Optimizing signal/tuning
  2. Chromatography
  3. Internal standard
  4. Reportable range
  5. Calibration and calibrators
  6. Matrix effect studies
  7. Stability studies
  8. Precision studies
  9. Accuracy and correlation studies
  10. Going live
  11. Performance metrics for post-go-live monitoring
  12. Discussion of post-go-live issues

Objectives:

At the conclusion of this short course, the participant will be able to:

  1. Design a validation plan for a target assay.
  2. Define performance characteristics for the intended use of the assay.
  3. Identify and address potential pitfalls in the developed assay.
2276
Monday
1400
1800
Short Course : LC-MSMS 302 : Advanced LC-MS/MS Method Development, Method Troubleshooting and Instrument Operation Needed in Developing Successful Methods for Molecular identification and Quantitation in the Clinical Lab
@ Steinbeck 2 (Conference Ctr > 2nd Floor)
2280
Monday
1400
1800
Short Course : Data Science 101 : Breaking up with Excel: An Introduction to the R Statistical Programming Language
@ Colton 1/2 (Conference Ctr > 2nd Floor)
2284
Monday
1400
1800
Short Course : Data Science 201 : Flexing with R : Databases to Dashboards
@ Colton 3 (Conference Ctr > 2nd Floor)

Shannon Haymond, PhD
Northwestern University Feinberg School of Medicine

Patrick Mathias, MD, PhD
University of Washington


Course Schedule

Segment 1 : Monday 14:00 - 18:00 (3.50 contact hrs)
Segment 2 : Tuesday 08:00 - 12:00 (3.50 contact hrs)

Total Contact Hours: 7.00
(Ten-minute breaks occur after each full instructional hour when another hour follows. Breaks are excluded from contact hour calculations.)

---------------

Pre-requisites

An introductory R course (including MSACL Data Science 101) and/or experience using R for data analysis.

Overview

Do you have data files that you would like to accumulate over time into an organized, accessible format and then visualize different aspects of the combined data in an interactive, web-based dashboard?

If so, this course is for you!

Reproducibility is an important principle for making data analysis trustworthy and reliable. Automation enables users to scale their data analysis steps. The R programming language is one of many tools that can help users automate data analysis workflows while adopting best practices in reproducibility, but there are several packages to choose from when developing these skills.

In this short course we will introduce a combination of workflows, packages, and tools that help learners set up data analysis projects, develop pipelines for extracting and storing data, and then develop interactive visualizations to gain understanding from the data.

First, we will orient learners to reproducible document formats such as R Markdown and Quarto, emphasizing how data analyses can be communicated effectively.

Next, we will do a crash course on relational databases such as SQLite, which can be powerful tools for storing and accessing data at scale.

We will then tie together concepts in iteration and automation to develop the basics needed to set up a data ingestion pipeline.

In the last portion of the course, we align these concepts with interactive visualization tools to develop an automated dashboard.

This short course will be interactive, with frequent short exercises to reinforce new concepts. Familiarity with the R programming language, either from an introductory course or self-learning, is required to participate in the exercises.

Finally, concepts in this short course overlap material taught in previous intermediate R courses at MSACL, but here we will focus putting together the tools to develop reproducible, automated dashboards for visualization of laboratory data and provide updates to include some of the latest developments in the R ecosystem.

Obtaining the Software

!!! DOWNLOAD PROGRAM PACKAGES PRIOR TO ARRIVAL ONSITE !!! THERE WILL NOT BE OPEN INTERNET WIFI IN THE CONFERENCE CENTER.

!!! POWER : Make sure your computer is charged to hold power for 4-8 hrs, as power outlets may not be available.

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

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

Topics Covered

  1. Reproducible workflows using computational notebooks
  2. Organizing data in relational databases
  3. Reading files and iterating
  4. Tools to automate routine tasks
  5. Flexing with some sweet dashboards

Objectives

At the conclusion of this short course, the participant will be able to:

  1. Utilize best practices for reproducible data analyses.
  2. Configure a database within R and load data into it.
  3. Automate tasks such as file reading.
  4. Create web-based dashboards.
  5. Implement packages available in R to organize data into relational databases, automate routine tasks, and create web-based dashboards.
  6. Apply learned skills to organize data analysis projects reproducibly using tools such as Quarto, dashboards, and databases.
2286
Monday
1400
1800
Short Course : Data Science 203 : Machine Learning : A Gentle Introduction
@ Bonsai (Portola Hotel > Ground Floor)
2293
Monday
1400
1800
Short Course : Sample Preparation 201 : Sample Preparation and Alternative Matrices for LC-MS Assays
@ Redwood 2 (Portola Hotel > 3rd Floor)
2297
Monday
1400
1800
Short Course : Metabolomics 203 : Practical Bioinformatics and Statistics in Metabolomics
@ Cottonwood 1 (Portola Hotel > 3rd Floor)

Tim Garrett, PhD
University of Florida College of Medicine


Course Schedule

Segment 1 : Monday 14:00 - 18:00 (3.50 contact hrs)
Segment 2 : Tuesday 08:00 - 12:00 (3.50 contact hrs)

Total Contact Hours: 7.00
(Ten-minute breaks occur after each full instructional hour when another hour follows. Breaks are excluded from contact hour calculations.)

---------------

Pre-requisites

Basic understanding of the field of metabolomics and LC-MS.

Overview

Metabolomics refers to the comprehensive measurement of small molecules in biofluids by either mass spectrometry (MS) or nuclear magnetic resonance (NMR) with the aim of covering multiple KEGG pathways, exposome products, and chemical reactions to provide new insights into disease etiologies. MS based metabolomics generally requires the use of liquid chromatography to separate metabolites based on polarity and high-resolution MS to accurately measure the mass-to-charge (m/z). The combination of retention time and m/z accuracy provides a reliable method to identify metabolites, which is critical for making disease marker discoveries. Understanding how data is generated is key to understand how to process data. This short course will instruct attendees on bioinformatics components to data processing in metabolomics with hands on instruction using an open source software package. This short course will also discuss basic principles of statistical analysis with hands experiences provided.

Topics Covered

  1. Introduction to metabolomics science
  2. Experimental design for success in metabolomics
  3. Measuring quality in Metabolomics
  4. Data processing in metabolomics using MZmine 2.53 (open source and platform independent)
    -- This is an older version of MZmine, but useful to first use in a data processing work flow. Works with Mac and Windows.
    -- A laptop with MZmine 2.53 preloaded is not a requirement, but you can follow along with the instruction using your own laptop if available
    -- Data to work with will be provided
  5. Statistical analysis using Metaboanalyst, online statistical analysis package for metabolomics
    -- Step by step tutorial
    -- Data will be provided for students to go through the steps on their own followed by a discussion and additional walkthroughs
  6. Open session at the end for discussion and additional help to students in data processing and statistical analysis

Objectives

At the conclusion of this short course, the participant will be able to:

  1. Describe experimental design in metabolomics.
  2. Manipulate data from LC-HRMS metabolomics analysis including software to process data (bioinformatics).
  3. Describe statistical analysis in relation to metabolomics data.
  4. Perform metabolomic data processing using MZmine 2.53
  5. Perform statistical analysis using Metaboanalyst.
2303
Monday
1400
1800
Short Course : Clinical Proteomics 201 : Clinical Proteomics
@ Steinbeck 3 (Conference Ctr > 2nd Floor)
2306
Monday
1400
1800
Short Course : Clinical Proteomics 202 : MS-based Precision Diagnostics by Molecular Protein Analysis
@ Ironwood 1 (Portola Hotel > 3rd Floor)
2309
Monday
1400
1800
Short Course : Lipidomics 101 : Mass Spectrometry-based Lipidomics and Clinical Applications
@ Redwood 1 (Portola Hotel > 3rd Floor)

Anne K. Bendt, PhD
Singapore Lipidomics Incubator (SLING), National University of Singapore

Amaury Cazenave Gassiot, PhD
Singapore Lipidomics Incubator (SLING) and Department of Biochemistry, National University of Singapore

Michael Chen, MD MSc
The University of British Columbia


Course Schedule

Segment 1 : Monday 14:00 - 18:00 (3.50 contact hrs)
Segment 2 : Tuesday 08:00 - 12:00 (3.50 contact hrs)

Total Contact Hours: 7.00
(Ten-minute breaks occur after each full instructional hour when another hour follows. Breaks are excluded from contact hour calculations.)

---------------

Pre-requisites

LC-MS/MS, clinical translation, lipidomic applications, method harmonization AND an interest in lab medicine and clinical lipidology.

Overview

This one-day course is meant to (1) create awareness for the importance and therefore potential value of lipid testing beyond cholesterol and triglycerides for future clinical applications. We will (2) then outline currently available technologies and their respective opportunities and challenges, and (3) discuss candidate molecules in the context of current case studies.

Topics Covered

  1. Looking beyond cholesterol and TAG:
    - Potential of blood-based lipid testing
    - Gain an understanding of the universe of lipids, how they are intricately linked to biology and their implications in health and diseases (e.g., inherited genetic disorders, cardiovascular disease, clinical nutrition, etc.)
    - Identify physiologically relevant candidate lipids for adoption by the clinical community, for future studies towards establishing clinical utility
  2. Current lipidomics R&D workflows:
    - Path of translation from R&D laboratory-style methods towards robust and quantitative assays with appropriate turnaround times
    - Pre-analytics (sampling requirements, plasma vs serum, storage, etc.)
    - Analytics (i.e., batches, internal standards, lipid extractions, direct infusion vs LC-MS and LC-MS/MS, quality assurance)
    - Post-analytics (raw data processing, lipid annotations, quality control, quantification)
    - Ongoing harmonization efforts
  3. Case studies of markers that have advanced to clinical settings
  4. Outreach and Engagement between the analytical scientist specialized in mass spectrometry of lipids, the clinician researcher and laboratory medicine as the end user are key to the development of impactful/ useful lipidomics in clinical applications

Objectives

At the conclusion of this short course, the participant will be able to:

  1. Discuss the lipid universe beyond cholesterol and triglycerides,
  2. Explain what lipid molecular species are.
  3. Describe the process of biomarker validation and implementation in clinical labs and how the analysis of lipid metabolites will contribute to precision diagnostics.
  4. Describe how to measure lipid metabolites using multiple-reaction-monitoring mass spectrometry.
  5. Evaluate the performance and quality of lipid metabolite-based tests.
  6. Review molecular MS data and provide answers for laboratory specialists.
2311
Monday
1400
1800
Short Course : GlycoProteomics 101 : Clinical Glyco(proteo)mics by Mass Spectrometry
@ Cottonwood 2 (Portola Hotel > 3rd Floor)
2314
Monday
1800
1830
Happy Half-Hour
@ Steinbeck Foyer (Conference Ctr > 2nd Floor)
2258
Monday
1830
2000
Dinner On Own
@ Off-site

Recommended Places to Eat
2151
Monday
2000
2330
MSACL Hospitality Lounge
@ Club Room (Portola Hotel > Ground Floor)

Drinks provided.
2152
Monday
2100
Monterey Conference Center Closes
@ Serra Foyer (Conference Ctr > Ground Floor)
2349

Tuesday
Tuesday
645
800
Short Course Breakfast
@ Club Room (Portola Hotel > Ground Floor)
2154
Tuesday
700
2130
Registration Desk Open
@ Serra Foyer (Conference Ctr > Ground Floor)
2155
Tuesday
800
1200
Short Course : LC-MSMS 101 : Getting Started with Quantitative LC-MSMS in the Diagnostic Laboratory
@ De Anza 2 (Portola Hotel > Ground Floor)
2270
Tuesday
800
1200
Short Course : LC-MSMS 201 : Practical LC-MS/MS Method Development and Bioanalytical Method Validation for Clinical and Non-Clinical Samples
@ Ironwood 2 (Portola Hotel > 3rd Floor)
2273
Tuesday
800
1200
Short Course : LC-MSMS 203 : Validation of Quantitative LC-MS/MS Assays for Clinical and Academic Use
@ De Anza 3 (Portola Hotel > Ground Floor)

Course Schedule

Segment 1 : Monday 08:00 - 12:00 (3.50 contact hrs)
Segment 2 : Monday 14:00 - 18:00 (3.50 contact hrs)
Segment 3 : Tuesday 08:00 - 12:00 (3.50 contact hrs)

Total Contact Hours: 10.50
(Ten-minute breaks occur after each full instructional hour when another hour follows. Breaks are excluded from contact hour calculations.)

---------------

Pre-requisites

Individuals with previous mass spectrometry experience (clinical or academic) or those who have taken the LC-MSMS 101 and/or 201 course and are looking to expand their knowledge.

Overview

This course is intended for those with previous mass spectrometry experience who are looking to expand their knowledge and skills with regards to assay validation for both clinical and academic purposes. The course will heavily focus on quantitative small molecule assays.

The course will provide a short overview of development followed by an in-depth discussion of how to validate liquid chromatography tandem mass spectrometry assays. The course will conclude with a discussion of the measures and metrics to use for monitoring assay performance once testing is live.

Throughout each section, applicable and practical guides for validation experiments and acceptance criteria will be provided, as well as processes for ensuring assay performance post-go-live. For each step of assay development, we will highlight experiments to perform along the way to identify issues pre-validation. Validation studies will include an overview of the studies necessary for both clinical and academic purposes. The clinical validation requirements for CLIA, CAP, NY State, and FDA regulated environments will be presented. The academic validation requirements for submitting such assays (or studies using them) to high-impact, peer-reviewed journals (Clinical Chemistry, Molecular & Cellular Proteomics, Journal of Clinical Endocrinology and Metabolism, etc) will be presented. Post-go live monitoring will include discussion of essential performance metrics, performing staff competency, minimizing manual data entry and how to facilitate interfacing with LIS, and finally a discussion of post-go-live issues.

Syllabus

Format – This short course will include 12 approximately 1 hour modules with 15 min for exercises and Q&A at the end of each module.

Topics:

  1. Optimizing signal/tuning
  2. Chromatography
  3. Internal standard
  4. Reportable range
  5. Calibration and calibrators
  6. Matrix effect studies
  7. Stability studies
  8. Precision studies
  9. Accuracy and correlation studies
  10. Going live
  11. Performance metrics for post-go-live monitoring
  12. Discussion of post-go-live issues

Objectives:

At the conclusion of this short course, the participant will be able to:

  1. Design a validation plan for a target assay.
  2. Define performance characteristics for the intended use of the assay.
  3. Identify and address potential pitfalls in the developed assay.
2277
Tuesday
800
1200
Short Course : LC-MSMS 302 : Advanced LC-MS/MS Method Development, Method Troubleshooting and Instrument Operation Needed in Developing Successful Methods for Molecular identification and Quantitation in the Clinical Lab
@ Steinbeck 2 (Conference Ctr > 2nd Floor)
2281
Tuesday
800
1200
Short Course : Data Science 101 : Breaking up with Excel: An Introduction to the R Statistical Programming Language
@ Colton 1/2 (Conference Ctr > 2nd Floor)
2285
Tuesday
800
1200
Short Course : Data Science 201 : Flexing with R : Databases to Dashboards
@ Colton 3 (Conference Ctr > 2nd Floor)
2287
Tuesday
800
1200
Short Course : Data Science 203 : Machine Learning : A Gentle Introduction
@ Bonsai (Portola Hotel > Ground Floor)
2294
Tuesday
800
1200
Short Course : Sample Preparation 201 : Sample Preparation and Alternative Matrices for LC-MS Assays
@ Redwood 2 (Portola Hotel > 3rd Floor)
2298
Tuesday
800
1200
Short Course : Metabolomics 203 : Practical Bioinformatics and Statistics in Metabolomics
@ Cottonwood 1 (Portola Hotel > 3rd Floor)
2304
Tuesday
800
1200
Short Course : Clinical Proteomics 201 : Clinical Proteomics
@ Steinbeck 3 (Conference Ctr > 2nd Floor)
2307
Tuesday
800
1200
Short Course : Clinical Proteomics 202 : MS-based Precision Diagnostics by Molecular Protein Analysis
@ Ironwood 1 (Portola Hotel > 3rd Floor)
2310
Tuesday
800
1200
Short Course : Lipidomics 101 : Mass Spectrometry-based Lipidomics and Clinical Applications
@ Redwood 1 (Portola Hotel > 3rd Floor)
2312
Tuesday
800
1200
Short Course : GlycoProteomics 101 : Clinical Glyco(proteo)mics by Mass Spectrometry
@ Cottonwood 2 (Portola Hotel > 3rd Floor)
2315
Tuesday
945
1045
Workshop : Concepts in Histology and Histopathologic Diagnosis for Researchers
@ De Anza 1 (Portola Hotel > Ground Floor)

Albert Tsai, MD, PhD
Stanford


How pathologists diagnose human tissue samples differs markedly from how many researchers study them. Research approaches often seek to reduce two-dimensional tissue imaging to single cell data, i.e. cytometry-on-a-slide. However, these methods are complicated by technical aspects of tissue processing, and they may miss the overarching histologic patterns which underlie pathologic diagnosis. Thus, early engagement with pathologists is useful not only for obtaining tissue samples, but also for understanding structure-function relationships and relevance to disease. Furthermore, pathologists regularly integrate multiple data modalities to classify diseases, e.g. histology with antibody-based protein detection and DNA sequencing. Their understanding of the utilities of each modality within the larger diagnostic context is helpful for identifying potential roles for new technologies.
2323
Tuesday
1100
1200
Get-the-Basics : MALDI Mass Spectrometry Imaging – A New Method in Pathology?
@ De Anza 1 (Portola Hotel > Ground Floor)

Kristina Schwamborn, MD, PhD
Technical University of Munich


Matrix assisted laser desorption ionization (MALDI) mass spectrometry imaging (MSI) combines the excellence in molecular characterization of mass spectrometry with microscopic imaging capabilities of stained tissue samples, enabling the precise location of different analyte classes (e.g., proteins, peptides, lipids, glycans) directly within intact tissue. In particular in the field of pathology, that can aid in tumor diagnosis, tumor subtyping, biomarker identification, prognostic prediction, and characterization of tumor margins during tumor resection procedures. Since MALDI MSI goes far beyond microscopy, it is ideal for these endeavors. It can generate molecular maps of tissue sections that can elucidate the underlying biochemistry or provide information on how therapeutics or toxins influence the function or misfunction of an organ. Thus, it has the potential to overcome limitations of other approaches in the identification and routine diagnostic measurement of new marker molecules/profiles.

Different applications in the field of pathology/ oncology will be presented that highlight possible applications of MALDI MSI in Pathology. Combining MALDI MSI, histology, and statistical analysis allows for reliable and fast subtyping in a number of different tumor types while also conserving material that could be used for additional testing.

2332
Tuesday
1200
1400
Lunch On Own or at Industry Workshop
@ Off-site

Recommended Places to Eat

Alternatively attend an lunch industry workshop.

2167
Tuesday
1215
1345

Industry Lunch Workshop(s)

Lunch provided for the first 150 workshop attendees.
Agilent Technologies
@ San Carlos 3 (Marriott > Mezzanine | Stairs from Lobby or SkyBridge from Conference Ctr)

Pre-Register

A Novel Strategy utilizing SIL mouse reference material from different tissues and body fluids enabling Absolute Quantitation Of Proteins in human tissues
Christoph Borchers, PhD
Jewish General Hospital, McGill University Montreal, QC, Canada
Intact Protein Quantitation – using iFAMS Quant+: Gabor-Transform Software for Automated Biomolecular Mass Spectrometry Signal Deconvolution and Quantitation
James Prell, PhD
University of Oregon
An efficient and fully automated end-to-end sample preparation strategy using the AssayMAP Bravo for Evosep-MRM
Nicolai Bache, PhD
Evosep

Ionpath
@ San Carlos 4 (Marriott > Mezzanine | Stairs from Lobby or SkyBridge from Conference Ctr)

Pre-Register

Unveiling Cellular Interactions: A Mass Spectrometry Approach to Spatial Proteomics
Mate Nagy, PhD
Ionpath
Jay Tarolli, PhD
Ionpath

Tuesday
1400
1600
Workshop : Design of Experiments for Optimization of LC-MS Clinical Assays
@ Steinbeck 1 (Conference Ctr > 2nd Floor)

Margret Thorsteinsdottir, PhD
University of Iceland

Finnur Freyr Eiriksson, PhD
University of Iceland / ArcticMass


Objectives

The objective of the workshop is to provide an introduction into design of experiments (DoE) for clinical application with special focus on optimization of MS-based clinical assays. The workshop is focused on practical implementation of DoE and will demonstrate how method development of sample preparation and UPLC-MS/MS method for quantification of clinical biomarkers can become much more efficient by utilizing DoE.

Summary

Design of experiments (DoE) is an efficient tool for development and optimization of UPLC-MS/MS platform for quantification of biomarkers in complex biological matrices. The UPLC-MS/MS platform is composed of several processes which involve many experimental factors that need to be simultaneously optimized to obtain a true maximum sensitivity with adequate resolution at minimum retention time. DoE offers a practical approach for performing experiments in accordance with a predefined plan, modelling by empirical functions, and graphical visualization. Basic concept of DoE will be presented with emphasis on practical implementation of DoE which includes the three main stages, screening, optimization, and robustness testing. To demonstrate the benefit of DoE, two case studies will be presented. The first case is DoE optimization of sample preparation in bottom-up targeted protein workflow. The second case is DoE optimization of UPLC-MS/MS assay for clinical diagnostic and therapeutic drug monitoring of patients with adenine phosphoribosyltransferase (APRT) deficiency. A polynomial model which corresponds to the objective of the case study is specified and an experimental design that supports the selected model is generated. Significant factors were studied via central composite design and related to responses utilizing partial least square regression. Both cases showed that DoE is an excellent tool for optimization of sample preparation for biological samples and UPLC- MS/MS quantification method for clinical biomarkers. A significant reduction of sample preparation time was achieved with increased yields for selected peptides and a reliable UPLC-MS/MS assay for simultaneous quantification of urinary 2,8-dihydroxyadenine (DHA) and adenine was optimized efficiently with DoE.

Syllabus

• Design of Experiments (DoE) – Get it right from the beginning
• Basic concept and assessment of DoE
• Optimization of sample preparation and UPLC-MS/MS clinical assay by DoE

2174
Tuesday
1400
1600
Workshop : Study Design for Metabolomics
@ Steinbeck 2 (Conference Ctr > 2nd Floor)

Jerzy Adamski, PhD
Metaron Diagnostics i.G., Technical University of Munich


CANCELLED : Due to the presenter being unable to attend (March 2, 2024).

Objective

This workshop will address study design challenges for metabolomics that must be performed prior to metabolomics measurement and data processing.

Summary

The workflow of a metabolomics experiment follows several interdependent phases. The scientific question determines the study model and the type of metabolite detection. Pilot studies are often performed to validate the research question and the analytical approach chosen. Sample identity, preanalytics, sample matrix, confounders, timing, randomization, budgeting and resources, contingency plan, legal issues, governance, and replication are important considerations in the study design phase. Metabolomics requires special quality control and quality assurance procedures because of the many variables involved in sample preparation and analysis. Analytical procedures include quality assurance, matrix-matched reference samples, and analytical quality control. Data validation is performed to verify technical parameters, evaluate sample quality, and identify outliers. In the initial phase of a project, it is critical to define the dataset to be released, which must include metabolomics data, SOPs, assays used, randomization type, normalization structure, and data imputation protocols.

Specific Topics

• understanding cohort structure
• essential clinical phenotyping
• procedures for sample selection
• sample quality assessment
• analytical assay selection
• randomization for measurements
• requirements for preparation for metadata and data depositories
• GOFAIR initiative for sustainable research

2168
Tuesday
1400
1600
Workshop : Ion Mobility in the Clinical Lab: What's Next?
@ Steinbeck 3 (Conference Ctr > 2nd Floor)

Christopher Chouinard, PhD
Clemson University

Robin Kemperman, PhD
Children’s Hospital of Philadelphia


Objectives

Attendees will learn the basic principles of ion mobility, benefits and challenges to routine implementation in the clinical lab, method development, and current applications.

Objective 1: Understand the basic operating principles of IMS and the differences between the different techniques (e.g., drift tube, traveling wave, FAIMS/DMS, etc.)

Objective 2: Recognize the benefits and limitations to incorporating IMS into conventional LC-MS/MS workflows in the clinic.

Objective 3: Become familiar with method design and development and current/future applications.

Summary

Ion mobility-mass spectrometry (IM-MS) has become a cornerstone of biomedical analysis, with applications ranging from isomeric small molecule differentiation to the study of protein structure. Despite its advantages, IM-MS has yet to see routine implementation in the clinical lab due to challenges in quantitation, limited universal standards, data processing software, and reproducibility across different IM techniques/vendor platforms. This workshop will introduce common IM techniques and their operating principles, expanding upon the benefits of incorporating IM into conventional LC-MS/MS workflows and discussing its challenges. More importantly, recent advances in hardware, software, and data processing approaches will be highlighted. Finally, an overview of current applications (including metabolomics, lipidomics, and proteomics examples) will be provided.

Syllabus

1. Basic Operating Conditions of IMS: Electric field application, experimental conditions (temperature, pressure, gas composition)
2. Different IMS techniques: Drift tube/traveling wave, field asymmetric/differential mobility, emerging techniques (i.e., TIMS, SLIM, cIMS, etc.)
3. Applications: Current examples from metabolomics, lipidomics, and proteomics

2172
Tuesday
1400
1600
Workshop : Isotope Ratio Mass Spectrometry: The Dark Horse of Clinical MS?
@ Colton (Conference Ctr > 2nd Floor)

Cajetan Neubauer
University of Colorado, Boulder

Alan Rockwood, PhD, DABCC
University of Utah, School of Medicine


Objectives

Participants will 1) learn the basic principles of isotopic effects and be able to explain how they can be used to study human metabolism, including drug metabolism, and 2) be able to explain how emerging measurements on bioanalytical mass spectrometers such as ESI-Orbitrap systems can perform accurate isotope ratios on molecular species.

Summary

Isotope ratio mass spectrometry (IRMS) measures the relative abundance of different isotopes of an element, providing valuable insights into the molecular mechanism of metabolic diseases, drug metabolism, and links between nutrition and health. In classical IRMS complex molecules are converted to low molecular weight gases, thus losing important intramolecular isotopic information. IRMS is now becoming possible on bioanalytical mass spectrometers such as ESI-Orbitrap systems.These recent advances give access to isotopic information in intact biomolecules, drugs, and metabolites. This workshop will introduce the principles that cause isotopic effects in the human body, introduce the technologies used to make highly precise measurements of isotope ratios in metals and biomolecules, and illustrate how recent advanced on doing IRMS using ESI-MS instrument can open new avenues of IRMS for biomedical and clinical research application. Methods and studies we highlight will help stimulate thought on new application areas for IRMS in biomedical research and eventual clinical diagnostics.

Topics Covered

* Principles that cause isotope effects in the human body
* IRMS technologies and current advances
* Applications of IRMS for biomedical and clinical research

2171
Tuesday
1400
1600
Workshop : Surgical Mass Spectrometry – Delivering the Technology to the Operating Room
@ De Anza 1 (Portola Hotel > Ground Floor)

Zoltan Takats, PhD
Imperial College

Lauren Ford, BSc (Hons), PhD
Imperial College London


Objectives

To identify methods to deliver mass spectrometry guided surgery to become routinely used in the clinical interventional world. The workshop will focus on the interpretation of clinical information/data and how this should be fed back to healthcare professionals and ultimately patients. The workshop will highlight the limitations of current technologies and developments enabling clinical adoption.

Summary

The need for in-situ, real time tissue identification has been dramatically increasing with the development and deployment of robotic and other high-precision surgical approaches. While surgical mass spectrometry techniques have been continuously developed, published, and demonstrated in human surgical theatres, none of these approaches have reached regulatory approval and routine application in surgery. We will use this interactive setting to discuss overcoming current roadblocks to delivering technology for patients and healthcare professionals. The workshop will give an overview of the current mass spectrometry technology developed and the strengths and weaknesses in each approach. This will be followed by discussing the embedding of the approach both into existing oncology and clinical diagnostic systems. Using Mass Spectrometry in surgery will change how interventional cancer care is delivered, hence it is important to ensure data tools are developed which can be relied on. Delivery of the obtained clinical information in the operating theatre is also important to explore. As part of this workshop, we will discuss data visualisation strategies such as in the virtual reality space, delivery of feedback to the clinical healthcare professionals and tools developed to advance usability, such as navigation. Data interpretation in the wider context of clinical oncology will also be explored.

Syllabus/Topics

• Surgical mass spectrometry methods – strengths, weaknesses, applications and future perspectives
• Embedding of technology into healthcare systems. How to deliver clinical information, data interpretation, navigation guidance and feedback.
• Regulatory and health economics aspects.

2173
Tuesday
1400
1600
Workshop : A Path from Discovery to Verification and Validation of Biomarkers in Clinical Samples
@ De Anza 2 (Portola Hotel > Ground Floor)

Annie Moradian, PhD
Precision Biomarker Laboratories/Cedars-Sinai Medical Center

Chi Nguyen, PhD
Precision Biomarker Laboratories Cedars-Sinai Medical Center Los Angeles


Objectives

A case study approach will be used to demonstrate the following:
- Introduce tools used for unbiased biomarker identification and discuss recent discovery proteomics techniques
- How to utilize and mine discovery proteomics data to create targeted proteomics methods
- Demonstrate software tools and applications used to develop targeted methods

Summary

In this workshop, we will describe in detail the path from collecting and utilizing comprehensive information from various sources of discovery proteomics analyses to the creation of targeted proteomics methods for the verification of protein biomarkers. This workshop will be divided in two sections. In the first section, a discovery proteomics strategy will be discussed with a focus on the study design, the data acquisition approach, and the data analysis pipeline for biomarker selection. An example case study will be presented and discussed. In the second section, the attendees will be guided through a step-by-step instruction on how to utilize pertinent information acquired from the discovery approach to develop a targeted proteomics method. A brief introduction on Skyline and instructions on working with spectral libraries in Skyline will be included. Furthermore, technical aspects such as the choice of instrument, flowrate and acquisition strategy at every step of the targeted proteomics assay development will be tackled and discussed.

2170
Tuesday
1400
1600
Workshop : Accreditation of Clinical Mass Spectrometry Laboratories
@ De Anza 3 (Portola Hotel > Ground Floor)

Judy Stone, MT (ASCP), PhD, DABCC
Clinical Chemist (retired)

Prof. Dr. med. Michael Vogeser
University Hospital, LMU Munich


Objective

To explain the basic principles, requirements, and processes of laboratory accreditation; with examples and a focus on laboratories that are in transition from research to patient care.

Summary

Many more countries are now requiring clinical laboratory accreditation to ISO 15189 or alternative standards. Accreditation presents a particular challenge for highly complex in-house testing such as mass spectrometry, but can also offer significant potential for improving processes and overall performance. Advantages and disadvantages of accreditation, risks, opportunities, and preparation strategies will be discussed. Extensive experience from both the perspective of the client and the assessor (inspector) will be shared. Our personal experience is with laboratory accreditation in the United States and the EU, but we will attempt to present these concepts from a global perspective.

Some Useful Documents

2319
Tuesday
1600
1630
Coffee Break
@ Steinbeck Foyer (Conference Ctr > 2nd Floor)
2175
Tuesday
1630
1650
Welcome & Scientific Orientation
@ Steinbeck Ballroom (Conference Ctr > 2nd Floor)

Timothy Collier, PhD
Quest Diagnostics

2176
Tuesday
1650
1740
Michael S Bereman Award for Innovative Proteomics : From Research to Routine Clinical Care: The Winding Road of New Protein and Peptide Biomarkers
@ Steinbeck Ballroom (Conference Ctr > 2nd Floor)

Melissa Budelier, PhD
TriCore Reference Laboratories


What does it take for a biomarker to make the leap from research to the clinical laboratory? Through the lens of biomarkers for Alzheimer’s Disease and related neurodegenerative disorders, we’ll discuss the various steps of identifying promising biomarkers, developing and optimizing mass spectrometry assays to measure these biomarkers, and considerations for moving assays from research to the clinic. We’ll cover lessons learned from experience in the early development stages of mass spectrometry assays for neurofilament light (NfL), including the importance of selecting the right target peptides, as well as the role of multiplexing to create biomarker panels. We’ll also discuss perspectives from the clinical lab, such as understanding ROC curves, the role of prevalence, and the importance of having clear intended use criteria. This presentation will highlight the benefits of working collaboratively and how coupling perspectives from both basic research and the clinical laboratory can help advance patient care.

Declaration of Competing Interests

Dr. Budelier receives expenses and/or honoraria from Waters, Roche Diagnostics. She is co-inventor and receives licensing income from patents covering multiplexed assay methods. The presenter will not mention or discuss Specific Products or Services of the company(ies) or technology listed in their Financial Disclosures, or of ANY other commercial entity, except in general, generic terms ensuring balance and impartiality.

Moderated by:

Timothy Collier, PhD
Quest Diagnostics

2177
Tuesday
1740
1830
Distinguished Contribution Award Lecture : Grit and Guinness; Confronting Bias and Imprecision without Compromising Scalability
@ Steinbeck Ballroom (Conference Ctr > 2nd Floor)

Russell Grant, PhD
Labcorp


On the Award.

This lecture will describe the vicissitudes and victories in the presenter's peregrinations to provide analytically and clinically accurate results to patients. Strategies learned on this journey, yielding a symphony of sample preparation, separation science and mass spectrometry technologies at the scale of a clinical reference laboratory, shall be discussed.

Declaration of Competing Interests

Dr. Grant declares that he receives salary from LabCorp and owns stock in LabCorp. He consults for HepQuant. He shall not speak to product offerings for HepQuant but will discuss scientific work and learning derived from my time at Labcorp and its wholly owned subsidiary, Esoterix Endocrinology.

Moderated by:

Gwen McMillin, PhD
NMS Labs

Stephen Master, MD, PhD, FADLM
Children's Hospital of Philadelphia

2178
Tuesday
1830
2130
Opening Exhibits Reception
@ Exhibit Hall - Serra (Conference Ctr > Ground Floor)
2179
Tuesday
2000
2100
Booth Tours
@ Exhibit Hall - Serra (Conference Ctr > Ground Floor)

Sign-up and meet at Tour Rally Point in Booth 8. Recommended for first-time attendees. Open to all.
2189
Tuesday
2130
2330
MSACL Hospitality Lounge
@ Club Room (Portola Hotel > Ground Floor)

Drinks provided.
2181
Tuesday
2230
Monterey Conference Center Closes
@ Serra Foyer (Conference Ctr > Ground Floor)
2350

Wednesday
Wednesday
700
1900
Registration Desk Open
@ Serra Foyer (Conference Ctr > Ground Floor)
2259
Wednesday
730
825

Industry Breakfast Workshop(s)

Breakfast provided for the first 150 workshop attendees.
Thermo Fisher Scientific
@ Steinbeck 1 (Conference Ctr > 2nd Floor)

Pre-Register

Practical Considerations for Standardizing LC-MS assays in Clinical Labs

An optimized, simplified workflow for the targeted proteomic analysis of fibrinogen in 4,200 plasma samples
Stefani Thomas, PhD, DABCC, NRCC
University of Minnesota
FAIMS: The perfect complement to established LC-MS/MS techniques
Anthony Maus, B.S., Ph. D.
Mayo Clinic

Indigo BioAutomation
@ Steinbeck 2 (Conference Ctr > 2nd Floor)

Pre-Register

Elevating Laboratory Analysis

Elevating Laboratory Analysis
Jim Edwards
Indigo BioAutomation

Waters Corporation
@ Steinbeck 3 (Conference Ctr > 2nd Floor)

Pre-Register

Simpler, Smarter Solutions: The Waters Total LC-MS/MS Workflow

Simpler, Smarter Solutions: The Waters Total LC-MS/MS Workflow
Anna Wynn, MS, MBA
Waters
Simpler, Smarter Analysis: Quantification of Serum Thyroglobulin for Clinical Research
Dominic Foley, BSc
Waters Corporation
Simpler, Smarter Services: Waters Professional Services and Customer Education Platform
Julius Aguila, BS Chemistry
Waters Corporation

Wednesday
825
900
Coffee Break
@ Steinbeck Foyer (Conference Ctr > 2nd Floor)
2325
Wednesday
900
950
Plenary : Proteogenomics as a driver for discovery of novel mechanisms and therapeutic targets in lymphoma pathogenesis
@ Steinbeck Ballroom (Conference Ctr > 2nd Floor)

Kojo Elenitoba-Johnson, MD
Memorial Sloan Kettering Cancer Center


Declaration of Competing Interests

Dr. Elenitoba-Johnson declares no conflicts of interest.

Moderated by:

Stephen Master, MD, PhD, FADLM
Children's Hospital of Philadelphia

2190
Wednesday
1000
1050
Plenary : Steroid Metabolomics for Diagnostic and Prognostic Biomarker Development
@ Steinbeck Ballroom (Conference Ctr > 2nd Floor)

Wiebke Arlt, MD DSc FRCP FMedSci
Medical Research Council Laboratory of Medical Sciences


I will discuss steroid metabolomics, the combination of mass spectrometry-based steroid profiling with machine learning-based steroid data analysis. I will provide two clinically relevant examples: (1) the development of a new diagnostic biomarker test for the detection of adrenal cancer, with a timeline covering the last 15 years and including discovery, optimisation and prospective validation - adrenal cancer is rare but regularly discovered upon the investigation of incidentally discovered adrenal nodules, which are detected in 5% of all cross-sectional imaging scans; (2) the exploration of the steroid metabolome in a large comprehensively phenotyped cohort of newly diagnosed and treatment naïve women with polycystic ovary syndrome (PCOS), a condition affecting 10-15% of women worldwide and associated with significantly increased metabolic disease risk. Showing our data from this cohort, I will describe the potential of steroid metabolomics for detailed phenotyping, mechanistic exploration, prognostic prediction and therapeutic stratification in this underserved population.

Declaration of Competing Interests

Dr. Arlt declares no conflicts of interest.

Moderated by:

Prof. Dr. med. Michael Vogeser
University Hospital, LMU Munich

2192
Wednesday
1100
1130
Plenary : Graham Cooks Lifetime Achievement Award & Mini-Lecture : Mass Spectrometry in Diagnostics and Therapeutics: the Long View
@ Steinbeck Ballroom (Conference Ctr > 2nd Floor)

R. Graham Cooks, PhD
Purdue University


R. Graham Cooks1,2, Nicolás Morato1,2, Andrew Mesecar1,3
1Department of Chemistry, 2Department of Biochemistry, and 3Purdue Institute for Cancer Research, Purdue University. West Lafayette, IN 47907

This talk covers an as-yet-unfinished journey. It describes a suite of methods and instrumentation that is the work of many individuals over a long period. Applications to diagnostics, especially intraoperative diagnostics, are ongoing for brain and other cancers. The long view espoused here, describes a series of steps that stretches from half-century old mass spectrometry to new drug candidates, specifically for the case of prostate cancer.

1. MS and MS/MS: because mass spectrometry (MS) is a well suited to characterizing organic compounds, it can be used to characterize complex mixtures, provided sample ionization produces a corresponding mixture of molecular ions. This 1:1 transformation (molecule -> molecular ion) was first achieved by the then-new method of chemical ionization. This allowed two stages of mass analysis, MS/MS, to became an alternative to GC/MS (and later to LC/MS) for mixture analysis.[1]

2. Ambient ionization: the simplest, most direct form of MS, ionizes objects/materials/samples in the open air. Electrospray ionization provided the lead on atmospheric pressure ionization, but ambient ionization [2] goes further and avoids sample manipulation or purification. Desorption electrospray ionization (DESI) effects ionization by localized solvent extraction.[3]

3. MS imaging: any directed ionizing agent (ions in SIMS, neutrals in FAB, photons in LDI, droplets in DESI) is inherently an imaging method.[4]

4. Biomarker discovery: Comparisons of diseased and healthy tissue point to potential biomarkers, e.g. DESI MS/MS analysis of prostate tissue showed preferential localization of cholesterol sulfate in diseased tissue.[5].

5. Target validation: knockdown studies established an association of cholesterol sulfate transferase with prostate cancer.[6]

6. Late stage functionalization: High throughput DESI instrumentation [7] uses accelerated reactions in microdroplets [8,9] to synthesize large numbers of new drug candidates on the millisecond time scale.[10]

7. Enzyme inhibition: Collection of the functionalized products followed by enzyme kinetic measurements [10] validated inhibition for several particular compounds as potential prostate cancer drugs. 8. Animal, safety and efficacy studies lie in the future.

Support from NCATS and Waters, Inc. is gratefully acknowledged.

[1] R. W. Kondrat and R. G. Cooks, Anal. Chem. 50 (1978) 81A
[2] R. Graham Cooks, Zheng Ouyang, Zoltan Takats, Justin M. Wiseman, Science, 311 (2006) 1566-1570
[3] Zoltán Takáts, Justin Wiseman, Bogdan Gologan and R. Graham Cooks, Science, 306 (2004) 471 – 473
[4] Justin M. Wiseman, Demian R. Ifa, Qingyu Song, R. Graham Cooks”, Angew. Chem. Int. Ed. 45 (2006) 7188 – 7192
[5] Livia S. Eberlin; Allison L. Dill; Anthony B. Costa; Demian R. Ifa; Liang Cheng; Timothy Masterson; Michael Koch; Timothy L. Ratliff; R. Graham Cooks, Anal. Chem., 82 (2010) 3430–3434
[6] Renee E Vickman, Scott A. Crist, Kevin Kerian, Livia Eberlin, R. Graham Cooks, Grant N. Burcham, Kimberly K Buhman, Chang-Deng Hu, Andrew D. Mesecar, Laing Cheng and Timothy Ratliff, Mol. Cancer Res. 14 (2016) 776 – 786
[7] Michael Wleklinski, Bradley P. Loren, Christina R. Ferreira, Zinia Jaman, Larisa Avramova, Tiago J. P. Sobreira, David H. Thompson and R. Graham Cooks, Chem. Sci. 9 (2018) 1647 – 1653
[8] Xin Yan, Ryan M. Bain, and R. Graham Cooks Angew. Chem. Int. Ed. 55 (2016) 12960-12972
[9] R. Graham Cooks, Yunfei Feng, Kai-Hung Huang, Nicolás M. Morato, and Lingqi Qiu, Israel J. Chem. 63 (2023) e202300034
[10] Kai-Hung Huang, Nicolás M. Morato, Yunfei Feng, and R. Graham Cooks Angew. Chem. (2023) e202300956

Declaration of Competing Interests

The Cooks lab receives grant support from Waters.

Moderated by:

Hannah Brown, Hennepin Healthcare; University of Minnesota
Hennepin Healthcare; University of Minnesota

2322
Wednesday
1130
1330
Exhibits & Lunch Buffet
@ Exhibit Hall - Serra (Conference Ctr > Ground Floor)
2195
Wednesday
1215
1330
Poster Session 1
@ Exhibit Hall - Serra (Conference Ctr > Ground Floor)
2194

Scientific Session 1

Steinbeck 1

Metabolic Disorders

Chair
Donald Chace
Capitainer
2nd
Yanchun Lin
Washington University School of Medicine in St louis

Steinbeck 2

The Biomarker Pipeline : Omics Discovery and Translation

Chair
Stephen Pennington
University College Dublin, School of Medicine

Steinbeck 3

Advances in Small Molecule Analysis

Chair
Robert Voyksner
LCMS Limited
2nd
Jessica Colón-Franco
Cleveland Clinic Foundation

Colton

Practical Training : Toxicology

Chair
Deborah French
UCSF

De Anza 1

In Honor of R. Graham Cooks : Intraoperative MS : DESI

Chair
Peter Verhaert
ProteoFormiX
2nd
Livia Eberlin
Baylor College of Medicine

Wednesday
1330
1350
LC-MS/MS Method for Porphobilinogen in Urine: What We Learned from High Sensitivity Measurements
Mark Kushnir
ARUP Institute for Clinical & Experimental Pathology
Fibrosis-Specific Blood N-Glycomic Signatures in Metabolic-Dysfunction Associated Steatotic Liver Disease Indicate Low Levels of Global α2,3-Sialylation
Tamás Pongrácz
Karolinska Institute
Alterations in Glutamate to Glutamine Ratios Detected by Direct Mass Spectrometry Techniques Allow Diagnosis and Molecular Subtyping of Breast Cancer
Keziah Liebenberg
Baylor College of Medicine
Is the Fentanyl Result Real? Tackling Interfering Substances Amid the Opioid Epidemic
Hsuan-Chieh (Joyce) Liao, Briana Fitch
Desorption Electrospray Ionisation: 22 Successful Years and Still Counting
Zoltan Takats
Imperial College
Wednesday
1350
1410
Mass Spectrometry Unraveling a ‘Secondary’ AKR1D1 Deficiency and Monitoring the Successful Resolution of Neonatal Acute Liver Failure by Cholic Acid Therapy
Kenneth Setchell
Cincinnati Children’s Hospital Medical Center
Practical Barriers to Developing Diagnostic Serum Protein Biomarkers for High-Grade Serous Ovarian Cancer … With Higher Specificity Than CA-125
Stefani Thomas
University of Minnesota
Catecholamines and metanephrines: A 24-hour microdialysis chronicle analyzed by LC-MS/MS
Martijn van Faassen
University Medical Center Groningen
...
Extended Talk
...
Desorption Ionization Mass Spectrometry for Intraoperative Cancer Diagnostics
Hannah Brown
Hennepin Healthcare; University of Minnesota
Wednesday
1410
1430
Development and Validation of a Liquid Chromatography Tandem Mass Spectrometry Bioanalytical Method for the Lysosphingomyelin in Plasma
Brett Holmquist
Labcorp
The Accredited Medical Laboratory Setting as a Fundament for Robust Quantitative Clinical Chemistry Proteomics in Large Clinical Trials
Esther Reijnders
LUMC
Pilot Study on the Prototype of a Fully Automated Mass-Spectrometry Based Clinical Laboratory Analyzer System
Michael Vogeser
University Hospital, LMU Munich
Addl Info (PDF)

...
Extended Talk
...
Intra-operative Mass Spectrometry in Neurosurgery
Diogo Garcia
Mayo Clinic
Wednesday
1430
1545
Poster Session 2 with Poster Tours
@ Exhibit Hall - Serra (Conference Ctr > Ground Floor)

Sign-up and meet at Tour Rally Point in Booth 8 for Poster Tours.
2197

Scientific Session 2

Steinbeck 1

Ion Mobility

Chair
Carrie Adler
Agilent Technologies
2nd
Robin Kemperman
Children’s Hospital of Philadelphia

Steinbeck 2

Leveraging MS to Improve Proteomic Assay Standardization

Chair
Kwasi Mawuenyega
MilliporeSigma
2nd
Stephen Pennington
University College Dublin, School of Medicine

Steinbeck 3

Omics using Model Systems for Pathobiology

Chair
Tim Garrett
University of Florida College of Medicine
2nd
Angela Kruse
Ohio State University

Colton

Practical Training : Dried Blood Spots

Chair
Grace van der Gugten
Provincial Health Services Authority, BCCDC Toxicology Lab

De Anza 1

Intraoperative MS : MasSpec Pen

Chair
Kristina Schwamborn
Technical University of Munich
2nd
Hannah Brown
Hennepin Healthcare; University of Minnesota

Wednesday
1545
1605
Using Ion Mobility to Help Make Mass Spec Mainstream: A Case Study in Urine Toxicology
Frederick Strathmann
MOBILion Systems
Antibody Light-Chain Quantitation with LC-MS: Advantages of Specificity to Improve Accuracy and Precision
James Prell
University of Oregon
Development of Diagnostic Biomarkers for Determination of Traumatic Brain Injury
Samuel Krug
Dartmouth Hitchcock Medical Center
Applications of Dried Matrix Spots and MS Testing in the Clinical Lab
Jessica Colón-Franco, William Clarke, Dustin Bunch
Providing In Vivo Tissue Sensing Capabilities to Surgeons with the MasSpec Pen: Challenges and Opportunities
Livia Eberlin
Baylor College of Medicine
Wednesday
1605
1625
Ion Mobility and Tandem Mass Spectrometry for Fentanyl Analogs and Other New Psychoactive Substances
Christopher Chouinard
Clemson University
Simultaneous Quantification of Proinsulin, Des Proinsulins, Insulin, C-Peptide, and C-Peptide Cleavage Variants by LC-MS/MS
Ryan Pearce
Mayo Clinic
Understanding the Development of Pain Due to Tissue Injury Through Novel Metabolic Changes
Elizabeth Want
Imperial College London
...
Extended Talk
...
...
Extended Talk
...
Wednesday
1625
1645
Taking LC-MS/MS Steroid Measurements to the Next Level with Differential Mobility Spectrometry
Anthony Maus
Mayo Clinic
High Resolution Liquid Chromatography – Mass Spectrometry (LC-MS) For Rapid, High-Throughput Clinical Testing of β2-Transferrin in Human Nasal Secretions
Morgan Mann
University of Wisconsin - Madison
Development and Validation of a Platform for Volatile Organic Compound Detection From Cancer Organoids Using Selected Ion Flow Tube Mass Spectrometry
Piers Boshier
Imperial College London
...
Extended Talk
...
...
Extended Talk
...
Wednesday
1645
1745
Exhibits & Happy Hour
@ Exhibit Hall - Serra (Conference Ctr > Ground Floor)

Take a moment to catch up with vendors and make plans for dinner with colleagues.
2213
Wednesday
1745
1845
Discussion Group : NIH Funding to Support Technology Development, Translation, and Transfer
@ De Anza 1 (Portola Hotel > Ground Floor)

Kelly Crotty, PhD
National Cancer Institute (NCI)


Technical innovation can improve and transform our ability to understand, prevent, diagnose, and treat human disease. NIH drives early-stage innovative technology development and the translation of emerging tools into laboratory and clinical use through several technology-focused grant programs. Dr. Crotty will discuss several of these programs and the diverse technologies that have been supported through them, as well as resources for tech transfer that are offered through NIH.

Moderated by:

Hannah Brown, Hennepin Healthcare; University of Minnesota
Hennepin Healthcare; University of Minnesota

2316
Wednesday
1745
1915
Discussion Group : Troubleshooting Cases
@ De Anza 2 (Portola Hotel > Ground Floor)

Elizabeth Mast
IU Health

Leslie Farris, B.S.
Cleveland Clinic Foundation

Kathryn Smith, PhD
ARUP Laboratories

Kayla Moehnke, M.S. in MLS; B.S. in MLS
Mayo Clinic

Emily Chegwidden, MPH
Cleveland Clinic

Rene Garay, B.S. Chemistry
Duke University Health System


An evening of 6 Troubleshooting Case Presentations.

The MSACL Troubleshooting Forum provides a setting for discussion between LC-MSMS users working in clinical diagnostics. The interaction is meant to be collegial, not critical, with the goal of attendees learning from the presenter's experience and the presenter learning from any insight attendees can contribute.

17:45
Positive Bias in Fractionated Vitamin D2-D3 Method as Determined via LC-MS/MS
Elizabeth Mast (IU Health)

18:00
Ordeals of Developing a Method to Measure Low-Level Concentrations of Serum Testosterone and my Troubleshooting Journey
Leslie Farris (Cleveland Clinic)

18:15
Troubleshooting the Transformation of Arsenic Species in Urine by HPLC-ICP-MS
Kathryn Smith (ARUP Laboratories)

18:30
Optimized Extraction Protocol for Analysis of 2,3-Dinor 11β-Prostaglandin F2α in Urine
Kayla Moehnke (Mayo Clinic)

18:45
You Don’t Know What You Don’t Know : How Automating Data Review Helped Uncover Chromatography Variations and Issues
Emily Chegwidden (Cleveland Clinic)

19:00
Failed Proficiency Result for 11-Nor-9-Carboxy-THC
Rene Garay (Duke University Health System)

Moderated by:

Grace van der Gugten, B.Sc. Chemistry
Provincial Health Services Authority, BCCDC Toxicology Lab

Deborah French, PhD, DABCC (CC, TC), FADLM
UCSF

Jacqueline Hubbard, PhD, DABCC
Beth Israel Deaconess Medical Center, Harvard Medical School

2317
Wednesday
1745
1915
Career Exploration in Clinical Mass Spectrometry : Networking Event
@ De Anza 3 (Portola Hotel > Ground Floor)

Laura Sanchez, PhD
University of California, Santa Cruz

Lee Williams
Biotage GB Limited

Kara Lynch, PhD, DABCC
University of California San Francisco

Matthew Crawford
Labcorp


This networking event is geared to early career attendees, but open to all. Get insights through informative, concise presentations on various job profiles within clinical mass spectrometry. Experts and seasoned professionals will guide you through diverse roles, making it easier to envision your own journey in this exciting industry.

More info here

Moderated by:

Kara Lynch, PhD, DABCC
University of California San Francisco

Matthew Crawford
Labcorp

2318
Wednesday
1915
2030
Dinner On Own
@ Off-site

Recommended Places to Eat
2214
Wednesday
2000
2330
MSACL Hospitality Lounge
@ Club Room (Portola Hotel > Ground Floor)

Drinks provided.
2215
Wednesday
2030
2130
Discussion Group : FDA Regulation of LDTs
@ Bonsai (Portola Hotel > Ground Floor)

E. Ellen Jones, PhD
National Center for Toxicological Research, FDA


Regulation of LDTs or laboratory developed tests by the FDA has long been a topic of interest and discussion. With the advent of new technologies and approaches there remains a gap between what is analytically possible with newer instrumentation versus what is currently allowed for regulatory use. Clearly, the FDA is aware of new analytical methods and capabilities and knows that new guidance’s are needed. This workshop will discuss some of the historical information on these LDT’s and provide a perspective from a non-regulatory FDA research scientist who is also working on incorporating novel technologies to inform regulatory decision making within the FDA.

Moderated by:

Peggi Angel, PhD
MUSC Proteomics Center

2321
Wednesday
2100
Monterey Conference Center Closes
@ Serra Foyer (Conference Ctr > Ground Floor)
2351

Thursday
Thursday
700
1730
Registration Desk Open
@ Serra Foyer (Conference Ctr > Ground Floor)
2260
Thursday
730
825

Industry Breakfast Workshop(s)

Breakfast provided for the first 50 workshop attendees.
Thermo Fisher Scientific
@ Steinbeck 1 (Conference Ctr > 2nd Floor)

Pre-Register

Unlocking the Potential for Large-Cohort Proteomic Studies with the Orbitrap Astral Mass Platform

Paradigm shift in biomarker translation: an innovative and automated pipeline to generate and select clinical-grade signature peptides during DIA discovery
Jennifer van Eyk, PhD
Cedars-Sinai Heart Institute
Introducing the Orbitrap Astral Mass Spectrometer
Yue Xuan, PhD, MBA
Thermo Fisher Scientific

Thursday
830
915
Spatial Proteomics: Considerations for Clinical and Research Applications
@ De Anza 1 (Portola Hotel > Ground Floor)

Megan Lim, MD, PhD
Memorial Sloan Kettering Cancer Center


20 minute Presentation followed by a Group Discussion.

Moderated by:

Peggi Angel, PhD
MUSC Proteomics Center

Angela Kruse, PhD
Ohio State University

2333
Thursday
830
915
Coffee Roundtables & Exhibits
@ Exhibit Hall - Serra (Conference Ctr > Ground Floor)

Stephen Pennington, PhD
University College Dublin, School of Medicine

Mike Badeau
YYZ Pharmatech Inc.

Robert DeWitte, PhD

Rejwi Dahal, PhD
Indiana University School of Medicine

Carolyn Slade, MsHIM, CMM, HMCC
CASSS – Sharing Science Solutions

Mikaela Sanford
CASSS - Sharing Science Solutions

Timothy Collier, PhD
Quest Diagnostics

Stephen Master, MD, PhD, FADLM
Children's Hospital of Philadelphia

Bruce Wilcox, PhD
PrognomiQ

Johanna Camara, PhD
NIST

Ashley Beasley-Green, PhD
NIST

Sean Pawlowski, PhD
Ionpath

Carrie Adler, MSFS
Agilent Technologies


Table 1: Translational Research: Insights for Today and Tomorrow
Stephen Pennington

In this roundtable we will discuss where we are as a translational research community, the complexities, tools available to researchers, strategies employed, and considerations for the future.

Table 2: YYZ Pharmatech - Is a tsunami coming? The role for LCMS in Alzheimer's Disease diagnostics
Rob DeWitte and Mike Badeau

With the approval of Aducanumab, Lecanemab and Donanemab, treatment options available for care of patients with Alzheimer's Disease have changed dramatically. This has lead to new hope for patients experiencing cognitive impairment, and a renewed focus on identifying disease progression earlier.

Treatment changes have also begun to influence laboratory operations as new invitro tests based on CSF are serving as surrogates for expensive imaging-based diagnostics. Blood based tests are also on the horizon for the most important markers (i.e. Aβ(1-42)/Aβ(1-40), P‐tau181 and P‐tau217), with the important benefits of sampling patients non-invasively, lowering costs and scaling without new infrastructure.

This all leads to the question: Is a tsunami coming?

Please join YYZ Pharmatech as we host a discussion about the impact of these shifts on the clinical laboratory, including:

  • What tests are being offered, and where?
  • How are laboratories adapting their technologies and workflows to support these trends?
  • What are the operational challenges?
  • What technical challenges remain to be solved?
  • What potential benefits do LCMS methods provide?

Table 3: Building a Toxicology Testing Area - Tox Lab
Rejwi Dahal

Even though there is a need for definitive testing in clinical settings, there aren’t many guidelines available on what should be taken into consideration as laboratory directors tackle design and establishment of toxicology laboratory. This session will provide valuable information to early career professionals who may be tasked with starting up a toxicology section. Even though some vendors are available to assist with site design, site preparation responsibilities fall upon the site personnel. Thus, it is important to have a basic understanding of what is needed to start the project. This roundtable session will address many personal ‘lessons-learned’ based on experience working with design and construction team in an Academic Hospital Laboratory, including factors associated with space design (electrical needs, ventilation needs) that should be taken into consideration before unboxing the LC-MS/MS crates. Well-designed space will assist in facilitating seamless transition from instrument validation to method validations.

Objective 1: Understand the requirements for LC-MS/MS installation.

Objective 2: Discuss the journey of building a toxicology testing area from scratch.

Table 4: Don’t Slow Your Role: Moving the Needle on DE&I in a Damaged Workplace Culture
Carolyn Slade, Mikela Sanford

Diversity, equity, and inclusion (DE&I) goals cannot succeed as a standalone strategy in organizations where the culture is damaged. Signs of a damaged culture include favoritism, unconscious bias, and a lack of psychological safety. To be impactful, DEI initiatives require a strategic and intentional approach all year long, reaching all employees, and building equity into external programs and internal processes. What happens when two, black women who have suffered the most inequities, decide to move the needle on DE&I? Join this interactive roundtable discussion to hear how both transformed their experiences in toxic workplaces into achievable DE&I goals.

Attendees of this session will:

  • Discuss the signs of a toxic workplace and discuss coping mechanisms
  • Recognize DE&I does not begin or end with a specific title or place within an organizational chart
  • Identify ways you can foster an inclusive and diverse workplace culture, and uphold principles of psychological safety in everyday practice
  • Discuss tools and strategies for implementing DE&I principles in small group dynamic

Table 5: Do Identical Instruments Produce Comparable Patient Results? A Stumbling Block of Harmonizing LC-MS/MS Assays in Clinical Laboratories
Joyce Liao

Clinical mass spectrometry laboratories usually validate individual assays on more than one instrument for continuous operation. Instrument comparison is a requirement of the College of American Pathologists and should be monitored at least twice a year to ensure comparability of results. Although the same style of liquid chromatography-tandem mass spectrometry system is preferred to minimize the variations between instruments, labs will inevitably encounter bias between two or more identical LC-MS/MS systems. Even in the absence of bias, the same instrument model with two different serial numbers may require different instrument settings to obtain similar sensitivity and specificity. In this roundtable session, we will review several comparison data sets from the same extractions injected and analyzed on two LC-MS/MS systems of the same make and model. We will discuss the potential factors, including mass spectrometer hardware (probe type and cleanness), software settings (gradients, transitions, cone voltages, and collision energies), and matrix effect that could bias patient results and how to establish quality assurance policies to ensure adequate data review and accurate resulting. Examples of challenges we have faced and approaches we have found useful will be presented as a starting point for discussion.

Table 6: Use of Reference Materials for Calibration and Validation in Clinical Mass Spectrometry Applications
Ashley Beasley Green and Johanna Camara

Reference materials (RMs), including certified reference materials (CRMs), are provided by the National Institute of Standards and Technology (NIST) and other RM producers to support global clinical measurement standardization and harmonization. Standardization is when clinical results are uniform across routine clinical methods and traceable to the International System of Units (SI) via higher-order RMs and Reference Measurement Procedures (RMPs). However, harmonization is established to make clinical results more equivalent across clinical methods when no higher-order RMs or RMPs exist. To support both systems, RMs are available in various forms, including neat powders, solutions, and clinical matrices and the intended uses include calibration and validation, depending on the material. The choice of which RM to use and how to incorporate it into a measurement system depends on laboratory goals. Many RMs are ideally suited for mass spectrometry-based measurement procedures. Many matrix matched RMs (blood serum, plasma, urine) are value assigned based on mass spectrometry-based RMPs. These RMPs typically separate and quantify individual peptides, metabolites, epimers, or other chemical variations of clinically relevant measurands that are not necessarily separated and detected by other laboratory techniques, such as immunoassays or microbiological assays. This roundtable is designed to discuss RM production, availability, and options for incorporating RMs into clinical applications. RM users may also need to propagate the measurement uncertainty of RMs or other calibrator values to clinical results. Therefore, the factors that should be accounted for when estimating measurement uncertainty will also be highlighted in the roundtable discussion.

Table 7: Quality Control Strategies for Large, Multiplexed, Omics Panels
Tim Collier, Steve Master, Brian Wilcox

Objective: Discussion of quality control strategies for large, multiplexed LC-MS Omics Panels

Summary: Recent Technological developments in LC-MS/MS instrumentation and bioinformatics approaches have enabled rapid, reproducible, and robust quantitative strategies for the measurement of hundreds, if not thousands of analytes that have the capacity to revolutionize the contribution of mass spectrometry based omics measurements to precision medicine. However, a major hurdle to the translation of large panels into a regulated clinical laboratory environment is how to properly deploy quality control (QC) standards. In this workshop, an expert panel of laboratory scientists and clinical chemists, with active discussion of the participating audience, will discuss how we might begin to address these challenges.

Topics Covered:

  • A review of CAP/CLIA Quality Control Standards as deployed for small scale assays.
  • Identification of the barriers current standards may present to the deployment of large omics panels in the CAP/CLIA regulated clinical laboratory environment.
  • Expert panel and audience-driven discussion of potential strategies for ensuring proper assay QC, i.e. how panels can be adapted to current regulatory frameworks and/or proposing novel QC strategies that may satisfy CAP/CLIA regulatory frameworks.

Table 8: Roche - The Future and Beyond: A discussion on future assay menu needs for mass spectrometry in the busy clinical laboratory
Alex Chin and Allyson Kozak

For decades, immunoassays were considered by many the gold standard for analyte detection in the clinical lab. However, the need for improved sensitive and accurate complementary clinical laboratory methods grew in response to certain challenges in immunoassay performance. Mass spectrometry is renowned for its high sensitivity and accuracy and is therefore considered the gold standard in several clinical indications and has steadily become more prominent in today’s busy clinical laboratories. However gaps need to be addressed in the demands for a diverse test menu to serve a variety of clinical specialties and emerging disease areas. This roundtable will be an open forum to discuss gaps and pain points in current mass spectrometry assay test menus, what can be done to address current unmet and future needs in the clinical laboratory and to facilitate its adoption for improved patient outcomes.

Objectives:
1. Define what gaps exist in current mass spectrometry testing
2. Describe the pain points in current mass spectrometry testing
3. Identify potential future clinical indications for mass spectrometry testing

Table 9: Ionpath - From Bench to Map: Simplifying the MSi Spatial Proteomics Workflow
Sean Pawlowski

Multiplexed ion beam imaging (MIBI) is a technique that has simplified numerous issues present in MS workflows within spatial imaging. Compared to other MSi techniques, MIBI ™ presents a sample preparation workflow identical to fluorescence microscopy while also eliminating the need for messy spectral deconvolution to identify antibody targets. ToF-SIMS as the backbone of MIBI allows for multiple scans on a single ROI to glean more than surface-level information. Coupled with existing and custom data analytics tools, Ionpath’s spatial proteomics services help biologists answer fundamental questions about cellular and spatial interactions. Join this interactive session to discuss the spatial proteomics workflows used to extract information from this complex data and how MIBI can complement it.

Attendees of this session will:

  • Discuss the growing pains of MSi in the spatial biology world
  • Examine how MIBI technology can strengthen their spatial biology capabilities
  • Look at the current state of spatial workflows
  • Discuss the gains where MIBI technology can simplify the difficulties present in other MSi workflows
  • Discuss the gaps present in the analysis of data in spatial biology

Table 10: Forever and Always - PFAS Monitoring in Human Matrix
Carrie Adler

Is human testing of per- and polyfluoroalkyl substances (PFAS) the next frontier for detecting and quantifying the “forever chemicals” that are now everywhere? PFAS regulations have been proposed or currently exist for drinking water, food packaging, and consumer products. PFAS cleanup and remediation are now being proposed for the 400+ PFAS compounds on the Environmental Protection Agency (EPA) list, however thousands of compounds exist. This brainstorming roundtable will focus on how biomonitoring would best be achieved.

Key Discussion Points:

  • What are the drivers for human PFAS testing?
    • Current and anticipated regulations.
    • Direct to consumer requests.
    • With proposed environmental remediations, will repeat monitoring be required?
  • Who is currently performing PFAS biomonitoring? Why?
  • What are the challenges for targeted PFAS assays?
  • What are the future PFAS research topics?
    • Untargeted discovery approaches.
    • Excretion profile and matrix considerations.
2220
Thursday
915
1030
Poster Session 3 with Poster Tours
@ Exhibit Hall - Serra (Conference Ctr > Ground Floor)

Sign-up and meet at Tour Rally Point in Booth 8 for Poster Tours.
2233

Scientific Session 3

Steinbeck 1

Data Analytics

Chair
Angela Fung
St. Paul's Hospital
2nd
Nicholas Spies
University of Utah, ARUP Laboratories

Steinbeck 2

Proteomics for Disease Diagnosis

Chair
Carrie Adler
Agilent Technologies
2nd
Kwasi Mawuenyega
MilliporeSigma

Steinbeck 3

Small Molecule Analysis

Chair
Lindsay Bazydlo
University of Virginia
2nd
Jessica Colón-Franco
Cleveland Clinic Foundation

Colton

Practical Training : Quantitative Metabolomics

Chair
Grace van der Gugten
Provincial Health Services Authority, BCCDC Toxicology Lab

De Anza 1

Intraoperative MS : iKnife/REIMS

Chair
Ruben Y. Luo
Stanford University
2nd
Keziah Liebenberg
Baylor College of Medicine

Thursday
1030
1050
The Old Assay in the New Era: Re-Evaluation of Mass Spectrometric Immunosuppressant Assay
Junyan Shi
Vancouver Coastal Health, University of British Columbia
Classifying Membranous Nephropathy Using Mass Spectrometry
Aaron Storey
Arkana Laboratories
Laboratory Implementation of a Newly-Developed LC-MS/MS Assay for Assessment of Acute Porphyria
Laura Sinden
ARUP Laboratories
Translating Quantitative LC-MS Metabolomics Assays To The Clinic
David Wishart
University of Alberta
15 Years of iKnife; Applications, Advances, and Breakthroughs
Lauren Ford
Imperial College London
Thursday
1050
1110
Of Peaks and Valleys: Deconvolution in the Service of Clinical Reference Intervals
Ahmed Najar
UCSF
Phage-display of Whole Proteome Enables Rapid Discovery of CAVIN4 as a Novel Antigen for Immune Mediated Rippling Muscle Disease
Surendra Dasari
Mayo Clinic
High Sensitivity Measurement of Free T4 in Serum by Equilibrium Dialysis-LC-MS/MS
Julie Ray
ARUP Laboratories
...
Extended Talk
...
MS Imaging-Based Prediction of Cell Population Ratio: Towards Real-Time Digital Twins for Margin Delineation and Cancer Prognosis
Léa Ledoux
Laboratoire Prism Inserm U1192
Thursday
1110
1130
Fully Automated LC/MS Data Processing Built on the Advantages of a Closed System
Andreas Reichert
Roche Diagnostics GmbH
Molecular Characterization of Antithrombin by Mass Spectrometry: Lessons Learned From Antithrombin Deficiency and CDG Cohorts
Mirjam Kruijt
Amsterdam UMC
A C18 is a C18 is a C18…? Effects Of Different Types Of C18 Columns On The Separation Of Bile Acids From Interferences In Matrix Samples
Kat Iacob
ARUP Institute for Clinical and Experimental Pathology
...
Extended Talk
...
Navigated 3D MS for Intra-operative Tissue Margin Assessment during Breast Cancer Surgery – Changing the Standard of Cancer Care through Metabolic Image Guidance
John Rudan
Queen's University
Thursday
1030
1130
Exhibitor Feedback Meeting
@ De Anza 3 (Portola Hotel > Ground Floor)

Exhibitors invited to join MSACL admin to provide feedback on MSACL 2024 and begin planning for MSACL 2025 in Montreal (September 21-26, 2025).
2227
Thursday
1130
1330
Exhibits & Lunch Buffet
@ Exhibit Hall - Serra (Conference Ctr > Ground Floor)
2234
Thursday
1215
1330
Poster Session 4
@ Exhibit Hall - Serra (Conference Ctr > Ground Floor)

Meet at Tour Rally Point in Booth 8.
2236
Thursday
1330
Exhibits Close
@ Exhibit Hall - Serra (Conference Ctr > Ground Floor)
2237

Scientific Session 4

Steinbeck 1

Toxicology

Chair
Christopher Chouinard
Clemson University
2nd
Difei Sun
LifeLabs Medical Laboratory Services

Steinbeck 2

Metabolomics and Lipidomics in Rare Disease

Chair
Elizabeth Want
Imperial College London
2nd
Virag Sagi-Kiss
Imperial College London

Steinbeck 3

TaMADOR

Chair
Ruben Y. Luo
Stanford University
2nd
Stefani Thomas
University of Minnesota

Colton

Practical Training : Internal Standards

Chair
Deborah French
UCSF

De Anza 1

Spatial MS : Case Studies Using Fresh Tissue Samples

Chair
Erin Seeley
The University of Texas MD Anderson Cancer Center
2nd
Jessica Moore
Discovery Life Sciences

Thursday
1330
1350
Quantitation and Abundance of Xylazine and Xylazine Metabolites in Human Urines by LC-MS/MS
Yanchun Lin
Washington University School of Medicine in St louis
UPLC-MS/MS Analysis of Urinary Oligosaccharides and Glycoamino Acids for the Diagnosis of Mucopolysaccharidosis and Glycoproteinosis
Xinying Hong
The Children’s Hospital of Philadelphia
Quantification of Glucagon and Oxyntomodulin by Protein Precipitation-Immunoaffinity Enrichment-LC-MS/MS
Andy Hoofnagle
University of Washington
Everything you wanted to know about Internal Standards, but were too afraid to ask
Russell Grant
Labcorp
Intraoperative Workflows, MALDI MSI of Tissue, and Data Visualization in MRI
Michael Regan
Brigham and Women's Hospital
Thursday
1350
1410
Monitoring the San Francisco Drug Supply: Results from a Bio-Surveillance Project of Opiate Treatment Patients Using High Resolution Mass Spectrometry
John Halifax
UCSF
Lipidomics Analysis Reveals Metabolic Lipid Biomarkers of Plexiform Neurofibromas in NF1 Patients
Xueheng Zhao
Cincinnati Children’s Hospital Medical Center
A Multiplex Assay of Leptin, Resistin and Adiponectin by Immunoaffinity Enrichment and Targeted Mass Spectrometry
Jun Qu
SUNY,Pharmaceutical Sciences Department
...
Extended Talk
...
Imaging of Brain Signaling Molecules
Per Andrén
Uppsala University
Thursday
1410
1430
Combining Toxicology Testing with Field Sobriety Test Results to Improve Impairment Classification for Cannabis
Robert Fitzgerald
University of California San Diego
Nucleotide Sugars Correlate with Telomere Length and Are Part of a Highly Sensitive Dyskeratosis Congenita Metabolomic Plasma Signature
Yufeng Li
Imperial College London
Interlaboratory Comparison of Antibody-Free LC-MS/MS Measurements of C-peptide and Insulin
Annie Moradian
Precision Biomarker Laboratories/Cedars-Sinai Medical Center
...
Extended Talk
...
Discussion on the Pros and Cons of Working with Fresh Frozen versus FFPE Tissue
Discussion Session
Thursday
1430
1445
Intermission
@ Steinbeck Foyer (Conference Ctr > 2nd Floor)
2242

Scientific Session 5

Steinbeck 1

Toxicology Cases

Chair
Xander van Wijk
University of California San Francisco
2nd
Michael Pikulski
Sonic Reference Laboratory

Steinbeck 2

Implementation of Unique Ionization Methods

Chair
Nicolás Morato
Purdue University

Steinbeck 3

Microbes, the Microbiome and Metabolites

Chair
Emma Guiberson
Middlebury College
2nd
Elizabeth Want
Imperial College London

Colton

Practical Training : Automated Liquid Handling

Chair
Jacqueline Hubbard
Beth Israel Deaconess Medical Center, Harvard Medical School

De Anza 1

Spatial MS : Case Studies of FFPE Analysis

Chair
Surendra Dasari
Mayo Clinic
2nd
Angela Kruse
Ohio State University

Thursday
1445
1505
The Utility of High-Resolution Mass Spectrometry in Cases of Acute Polydrug Exposure: A Case of Flubromazepam and Fentanyl Overdose
Lilly Lim
University of California, San Francisco
Translating Biomarkers of Breast Cancer Tissue Samples to Targeted Desorption Electrospray Ionization Mass Spectrometry Imaging
Virag Sagi-Kiss
Imperial College London
Unveiling the Gut Metabolome: Insights into the Pathogenesis of Necrotising Enterocolitis through Advanced Mass Spectrometry Techniques
Maria Sani
Imperial College London

Cancelled following presenter WD on 3.16. To be replaced by Thomas Horvath on From Mice to Man: Techniques to Surveil Host-Microbe Gut-Brain Interactions

Practical Guidance and Examples of Automated Liquid Handling for LDT Mass Spectrometry Assays
Kelly Doyle
University of Utah Health / ARUP Laboratories
The Extracellular Microenvironment as a Pathological Differentiator
Peggi Angel
MUSC Proteomics Center
Thursday
1505
1525
Untargeted Analysis Using LC-QTOF in a Pediatric Clinical Toxicology Case
Lindsay Bazydlo
University of Virginia
Rapid Clinical Albuminuria Diagnostics Using Paper Spray Mass Spectrometry: High Throughput ACr Measurements and Non-Targeted Approaches Utilizing Machine Learning
Chris Gill
Vancouver Island University
A Combined Lipid- and Metabolomic Workflow for Differentiation of Bacteria Species and Strains
Jana Carpenter
University of Georgia
...
Extended Talk
...
Integration of Multiplexed Spatial Multi-omics for Deeper Understanding of Cancer Biology
Erin Seeley
The University of Texas MD Anderson Cancer Center
Thursday
1525
1545
Clinical Utility of High-Resolution Mass Spectrometry in a Pediatric Case of Altered Mental Status
Adina Badea
Lifespan/Rhode Island Hospital & the Warren Alpert Medical School of Brown University
Liquid Chromatography or Paper Spray? Quantifying Tyrosine Kinase Inhibitors with Tandem Mass Spectrometry
Rich Lahr
Mayo Clinic
LC-MS as a Platform for Precision Medicine: Accurately Predicting Survival from Bloodstream Infections Using a Training Set of 38,000 Microbial Proteomes
Ian Lewis
University of Calgary
...
Extended Talk
...
Spatial Framework for Understanding Immune Tolerance in Human Health and Disease
Michael Angelo
Stanford University School of Medicine
Thursday
1545
1600
Intermission
@ Steinbeck Foyer (Conference Ctr > 2nd Floor)
2247

Scientific Session 6

Steinbeck 1

Impending FDA Regulation of Clinical Lab LDTs

Chair
Briana Fitch
University of Southern California

Steinbeck 2

Biomarkers : ID and Model Development

Chair
Guinevere Lageveen-Kammeijer
University of Groningen
2nd
Tamás Pongrácz
Karolinska Institute

Steinbeck 3

Proteomics: Advances in Structural Characterization, Global Quantification, and Clinical Applications

Chair
Timothy Collier
Quest Diagnostics
2nd
David Colquhoun
SCIEX

Colton

Practical Training : Cross Platform Method Transfer

Chair
Jacqueline Hubbard
Beth Israel Deaconess Medical Center, Harvard Medical School

De Anza 1

MS Atlas Approaches to Histology

Chair
Zoltan Takats
Imperial College

Thursday
1600
1620
Discussion on Impending FDA Regulation of Clinical Lab LDTs
Discussion Session
Absolute Quantification of Protein Biomarkers in Human Plasma by UPLC-MRM-MS Assay for Early Breast Cancer Diagnosis
Margret Thorsteinsdottir
University of Iceland
How a Single Mutation in CFTR Causes the Systemic Disease Cystic Fibrosis: Interactions, PTMs, and Structure
John Yates
Scripps Research Institute
Cross-Platform LCMS Method Transfer
Gregory Buchan, Ryan Pearce
Molecular Heterogeneity in Human Pancreas, Kidney, and Eye Revealed by Multimodal Spatial Atlases
Angela Kruse
Ohio State University
Thursday
1620
1640
...
Extended Talk
...
Using Spatial Omics for the Identification of N-glycan Alterations as Biomarkers in Early Liver Disease and Primary Liver Cancer
Shaaron Ochoa-Rios
Medical University of South Carolina
Finding Solutions for Drug Development: Parkin Activator Mitigates Adverse Left Ventricular Remodeling After Myocardial Infarction
Jennifer van Eyk
Cedars-Sinai Heart Institute
...
Extended Talk
...
The Human Protein Atlas – an open access resource providing expression references in tissues and cells
Evelina Sjostedt
SciLifeLab
Thursday
1640
1700
...
Extended Talk
...
Urine Adenine: A Novel Precision Biomarker for Kidney and Heart Failure Identified by Orthogonal Metabolomics Platforms
Kumar Sharma
University of Texas Health San Antonio
A Novel Strategy For Absolute Quantitation Of Human Proteins
Christoph Borchers
Jewish General Hospital, McGill University Montreal, QC, Canada
...
Extended Talk
...
(Top-down) Mass Spectrometry Histochemistry on sections of FFPE Tissue Banks: current status and future perspectives
Peter Verhaert
ProteoFormiX
Thursday
1700
1730
Happy Half-Hour & Trivia Dinner Check-In
@ San Carlos Foyer (Marriott > Mezzanine > Stairs from Lobby or SkyBridge from Conference Ctr)

Enjoy a relaxing moment during check-in for the Closing Pub-Style Trivia Dinner in the San Carlos foyer.
2251
Thursday
1730
2000
Dinner & Pub-Style Trivia Night
@ San Carlos (Marriott > Mezzanine | Stairs from Lobby or SkyBridge from Conference Ctr)

Fee-based Pre-Registration Required for Entry

Includes presentation of Poster Awards and Closing statements by the Steering Committee Chair.

2252
Thursday
2000
2330
MSACL Hospitality Lounge
@ Club Room (Portola Hotel > Ground Floor)

Drinks provided.
2253
Thursday
2130
Monterey Conference Center Closes
@ Serra Foyer (Conference Ctr > Ground Floor)
2352

Friday
Friday
700
900
MSACL Sunrise Challenge Walk-Jog to Lover's Point
@ Club Room (Portola Hotel > Ground Floor)

Check in 7am @Club Room - water, orange juice, coffee, whole fruits, yogurts.

Group photo at 7:15 and run commences at 7:20 sharp.

Will follow the Monterey Recreation Trail for about a 5-mile round-trip to Lover's Point. About 1.5 hours walking, 45 min running. Or turn back at any point to shorten the distance.

Followed by breakfast in the MSACL Lounge (Portola Club Room).

2254
Friday
730
930
Farewell Breakfast
@ Club Room (Portola Hotel > Ground Floor)

Enjoy a farewell breakfast to either replenish your tank after the run/walk, prepare for your flight home, or both!
2255
Friday
900
1000
Closing Breakfast Seminar
@ Club Room (Portola Hotel > Ground Floor)

Anthony Molina, PhD
UCSD


Identifying Blood-Based Markers of Universal Resilience

UC San Diego and the Wellcome Leap Dynamic Resilience Program

Major Contract Funds Study on Drivers of Resilience Among Older Adults

A multi-disciplinary team of researchers at the University of California San Diego, led by Anthony J.A. Molina, a professor in the Department of Medicine, has launched a new project to better understand why older adults who share the same age and similar health characteristics can have vastly different trajectories following stress events such as fall-related injuries.

This project is funded through a contract with Wellcome Leap’s $60 million Dynamic Resilience program, which is jointly funded with Temasek Trust. The Dynamic Resilience program seeks to identify and validate markers of health resilience that can be used to develop and test preventative interventions that support resilience in people at risk of deterioration after a stress event.

During his presentation, Dr. Molina will delve into the journey that has brought the team to this pivotal point and outline their anticipated achievements in the years to come.

Moderated by:

David Herold, MD, PhD
MSACL, University of California San Diego and VA San Diego Medical Center

2324

Page generated in 0.5414 seconds.