Location: Salon Ville-Marie, Hotel Level

Annie Moradian, PhD Precision Biomarker Laboratories/Cedars-Sinai Medical Center Annie Moradian is a Lead Biomedical Scientist at Precision Biomarker Laboratories at Cedars-Sinai Medical Center. Annie obtained her PhD in Analytical Chemistry from University of British Columbia. She has extensive background in both quantitative and discovery proteomics. Currently her focus is on development and optimization of new high-throughput LC-MS methods for biomarker candidate discovery and verification.

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

Objectives

1. Introduce and Evaluate Tools for Unbiased Biomarker Identification
   • Discuss recent advancements and techniques in discovery proteomics.
   • Analyze the effectiveness of various methodologies and instrumentation.
2. Utilize and Mine Discovery Proteomics Data for Targeted Method Development
   • Explore strategies for data mining from discovery proteomics.
   • Develop targeted proteomics methods based on mined data.
3. Demonstrate Software Tools and Applications for Targeted Proteomics
   • Provide hands-on demonstrations of software tools such as Skyline.
   • Apply these tools in the development of targeted proteomics assays.

Summary

In this workshop, we will thoroughly explore the journey from gathering and utilizing comprehensive data from various discovery proteomics analyses to developing targeted proteomics methods for protein biomarker verification. The workshop is divided into two sections.

In the first section, we will cover the fundamentals of discovery proteomics, including the latest trends in methodology and instrumentation, with comparative analyses. We will then delve into a Data Independent Acquisition (DIA) discovery proteomics strategy, focusing on study design, quality control approaches, and the data analysis pipeline for biomarker selection. Additionally, we will present and discuss a case study involving a large cohort. In the second section, once a set of target proteins has been determined, we will walk through the process of data mining from various sources such as public data repositories as well as in-house acquired data for the targeted proteomics assay development. A brief introduction on Skyline and various 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. Furthermore, a quality control strategy for large scale targeted proteomics measurement will be introduced and analyzed.

Syllabus

Section 1: Fundamentals of Discovery Proteomics

• Introduction to Discovery Proteomics
• Data Independent Acquisition (DIA) Strategy
• Case Study Presentation (design, execution, data analysis)

• Data Mining for Targeted Proteomics
• Introduction to Skyline
• Technical Aspects of Assay Development
• Quality Control in Targeted Proteomics

Location: Salon Bonaventure, Hotel Level

	Andy Hoofnagle, MD, PhD University of Washington Dr. Hoofnagle's laboratory focuses on the precise quantification of recognized protein biomarkers in human plasma using LC-MRM/MS. In addition, they have worked to develop novel assays for the quantification of small molecules in clinical and research settings. His laboratory also studies the role that the systemic inflammation plays in the pathophysiology of obesity, diabetes, and cardiovascular disease.
	Michael MacCoss, PhD University of Washington The focus of the MacCoss laboratory is in the development and application of cutting-edge mass spectrometry-based technologies for the analysis of complex protein mixtures. Dr. MacCoss’ primary area of expertise is in protein biochemistry, nanoflow liquid chromatography, mass spectrometry instrumentation, and computational analysis of mass spectrometry data. He has ~30 years of mass spectrometry experience that bridges the fields of protein mass spectrometry, isotope ratio mass spectrometry, and quantitative mass spectrometry. The MacCoss laboratory has been actively applying these tools to important areas of biology including but not limited to, the basic biology of aging, neurodegenerative disease, protein-protein interactions, insulin signaling, cancer, measurement of protein half-life, transcriptional regulation, characterization of post-translational modifications, proteogenomics, and clinical diagnostics. The MacCoss laboratory is widely known for its expertise in the development and support of proteomics software tools. This expertise in mass spectrometry and the support of open-source software tools will be critical to the success of this project. Dr. MacCoss has been actively involved in the scientific direction and management of NIH centers, program projects, consortia, and large quantitative proteomics data production efforts since he arrived at UW in 2004. The MacCoss lab has worked on proteomics application of the biology of aging for the last 20 years and has been working in the analysis of samples of relevance to Alzheimer’s disease for the last decade. The MacCoss lab has trained 15 Ph.D. students and 15 postdoctoral fellows. There have been 1000s of individuals who have attended the Quantitative Proteomics Courses co-taught by MacCoss lab personnel.
	Jun Qu, PhD SUNY,Pharmaceutical Sciences Department Jun Qu is a professor in the Department of Pharmaceutical Sciences of SUNY-Buffalo, and the director of Proteomics and Pharmaceutical Analysis Group in NY Center of Excellence in Life Sciences. His research focus is the development of protein bioanalysis strategies, both on global and targeted level, for quantitative investigation of pharmaceutical/clinical systems. Qu lab is also one of the leaders in LC-MS-based characterization of protein drugs and their targets in pre-clinical models.

Objectives

1. Outline the potential utility of biomarkers in clinical research and clinical care in diabetes
2. Provide the rationale for the use of LC-MS/MS methods in the quantification of peptide and protein biomarkers, including proteoform-specific biomarkers
3. List the advances in sample preparation and instrumentation that enable the development of assays to peptide and protein biomarkers in human serum/plasma
4. Identify the hurdles that exist for the development of novel protein and peptide biomarker assays

Summary

The precise and accurate quantification of proteins and peptides involved in diabetes will help facilitate research into disease pathogenesis and ultimately improve the diagnosis, prognosis, and therapeutic management of patients with diabetes. Unfortunately, most of the studies to date have relied on immunoassays, with little effort put into demonstrating the specificity of the reagents or the robustness of the assays. Furthermore, recent publications have highlighted the limitations of many commercial assays, including a failure to detect the intended target. Rigor and reproducibility could be substantially improved by applying mass spectrometry to the quantification of these biomarkers. Major improvements in sample preparation and instrumentation have made mass spectrometry–based targeted proteomics a highly reproducible methodology for detecting and quantifying proteins and peptides. In addition, the ability to quantify specific proteoforms provides insight into prohormone processing and post-translational modifications and creates an opportunity to identify and validate new biomarkers that can be used for disease stratification.

The NIDDK recently funded several projects that aim to use targeted mass spectrometry to quantify human plasma/serum proteins and peptides of interest to the diabetes clinical research community. During this workshop, the presenters will provide an overview of the recent advances toward this goal that have been made by the Targeted Mass spectrometry Assays for Diabetes and Obesity Research (TaMADOR) consortium, with a special focus on biomarkers important in type 1 diabetes.

Syllabus

1. Detecting proteins and peptides in human serum and plasma
2. Preparing samples for targeted proteomic analysis
3. The role of antibodies in the quantification of protein and peptide biomarkers
4. Examples of assays that can be translated to clinical research or clinical care

Location: Montreal 1-2

Rejwi Dahal, PhD Indiana University School of Medicine Rejwi Dahal is a clinical assistant professor in the department of Pathology and Laboratory Medicine at Indiana University School of Medicine. Her research interests include development of analytical methods for detecting small molecules, in diverse biological matrices using advanced mass spectrometry techniques, which can be translated to patient care. She is also passionate about creating diagnostics tests tailored for at-home sample collection, particularly using dried blood spot technology, to enhance healthcare accessibility for patients in remote and underserved settings.

Objectives

1. Discuss laboratory test development processes: deepen knowledge of essential CLSI and ISO standards that provide the framework for laboratory processes during pre-validation phase.
2. Describe risk management framework: learn how to establish a systematic risk management framework in a medical laboratory setting, including risk identification, assessment, mitigation, and monitoring.
3. Review patient safety and laboratory accuracy: learn how risk management practices directly enhance patient safety and ensure laboratory results' accuracy and reliability.
4. Give examples of practical solutions: analyze case studies highlighting challenges in FDA compliance, test development, and risk assessment.
5. Report regulatory expectations: gain a comprehensive understanding of the FDA's classification of clinical laboratories as manufacturers and the corresponding regulatory requirements: CLSI and CLIA.

Summary

Since clinical laboratories developing tests are classified as manufacturers, strict regulatory guidelines from the FDA have been implemented. A thorough understanding of the various phases of test development is crucial in this evolving regulatory landscape, as laboratorians develop tests to meet clinical needs. This workshop will focus on the critical steps focusing on pre-validation stages and the determination of risk tolerance during the feasibility study. The session will explore foundational guidelines from CLSI and ISO standards, equipping participants with the knowledge and tools needed for effective navigation of regulatory and quality requirements. To reinforce the learning, the workshop will integrate case studies and practical applications that provide real-world insights into overcoming challenges and ensuring compliance.

Syllabus

1. Regulatory guidelines from CLSI and ISO for pre-validation phase of laboratory developed tests.
2. Risk management framework: identifying, assessing, mitigating, and monitoring risks.
3. Examples of practical solutions.

Location: Montreal 3

Zoltan Takats, PhD Imperial College Professor Takats has obtained his PhD from Eötvös Loránd University, Budapest, Hungary. He has worked as a post-doctoral research associate at Purdue University, Indiana, USA. After returning to Hungary, he served as Director of Cell Screen Research Centre and also as Head of Newborn Screening and Metabolic Diagnostic Laboratory at Semmelweis University, Budapest. Professor Takats was awarded the Starting Grant by the European Research Council in 2008 and he subsequently, became a Junior Research Group Leader at Justus Liebig University, Gießen, Germany. He moved to the United Kingdom in 2012 and currently works as a Professor of Analytical Chemistry at Imperial College London. Professor Takats has pursued pioneering research in mass spectrometry and he is one of the founders of the field of ‘Ambient Mass Spectrometry’. He is the primary inventor of six mass spectrometric ionization techniques and author of 78 peer reviewed publications. He was the recipient of the prestigious Mattauch-Herzog Award of the German Mass Spectrometry Society and the Hungarian Star Award for Outstanding Innovators. He is the founder of Prosolia Inc, Medimass Ltd and Massprom Ltd, all companies pursuing analytical and medical device development.

Lauren Ford, BSc (Hons), PhD Imperial College London I am an early career researcher and have a background in materials chemistry, having studied for a PhD between the School of Chemistry and the School of Design at the University of Leeds I have experience in polymer technology, physical adsorption theory and purification. I am interested in using these skills to aid detection of disease using mass spectrometry detection. Since joining Imperial in 2019 I have been working as a post-doctoral research associate in the department of Surgery and Cancer, working on the iEndoscope project. This project utilised ambient ionisation mass spectrometry and allowed me to gain critical experience of ambient MS for early cancer detection.

Objectives

1. Discuss instrumentation requirements for interventional MS
2. Review instrument concepts and respective applications
3. Define a roadmap for the clinical translation/introduction of interventional MS

Summary

The clinical environment is a highly dynamic setting, and the decisions made can have huge downstream consequences for patient outcomes and ongoing care. To make these decisions clinical testing is used to reduce subjectivity, provide data, and ensure patient safety. Mass spectrometry is a useful tool in clinical care due to the high sensitivity and specificity for the detection of metabolites in bodily fluids such as blood, plasma, urine, saliva, stool, and mucus. Most mass spectrometry in the clinical setting is performed offline, with sample collection performed at the point of care setting and then transported to the laboratory for extraction and analysis. Ambient ionisation mass spectrometry revolutionized the use case for mass spectrometry in the clinic by enabling direct sample analysis, opening new clinical analysis opportunities. Coupling ambient ionisation mass spectrometry with machine learning techniques enables dynamic analysis of thousands of metabolites directly from clinical samples, without the need for sample preparation. These advances in technology have led to the development of novel uses of mass spectrometry for intervention and aiding clinical decision making, such as surgical margin detection, point of care testing, and mass spectrometry guided surgery. Interventional mass spectrometry describes a clinical assay from which the results steer a patients ongoing treatment. The decision to intervene in clinical care needs to be fast and robust, with the testing taking place at the point of care.

Syllabus

1. Interventional mass spectrometry methods: strengths, weaknesses, applications and future perspectives.
2. Hardware choices and the effect on interventional mass spectrometry progression.
3. Regulatory aspects surrounding the advancement of technology.

Location: Montreal 4

Christopher Chouinard, PhD Clemson University I received my PhD from University of Florida in 2016, where I developed ion mobility-mass spectrometry (IM-MS) methods for steroids and vitamin D metabolites. I then worked as a post-doctoral research at Pacific Northwest National Laboratory, building Structures for Loss Ion Manipulations (SLIM) ion mobility instrumentation for application in metabolomics and proteomics. In 2018, I began my independent career as an Assistant Professor at Florida Institute of Technology. I have since moved to Clemson University in August 2022. Work in my research group focuses on ion mobility-mass spectrometry (IM-MS)-based methods and technology, including structurally selective reactions for improved characterization of steroids and other controlled substances.

Robin Kemperman, PhD Children’s Hospital of Philadelphia Robin Kemperman received his Bachelor's in chemistry from the HAN University of Applied Sciences in The Netherlands. Thereafter, he fulfilled his MSc and PhD in analytical chemistry at the University of Florida under the direction of Dr. Richard Yost. Currently, he works at the Children's Hospital of Philadelphia as Sr. Mass Spectrometrist in the Metabolic and Advanced Diagnostics Lab. Dr. Kemperman's work has covered a variety of aspects in mass spectrometry, including targeted analysis of steroids and ketone bodies using LC-MS/MS, bile acid, opioid, and glycan isomer separations using ion mobility spectrometry, and metabolomics High-Resolution MS. Dr. Kemperman is experienced in clinical MS-based validations and has presented his work at a variety of national and international meetings. Focusing on the future, he is interested in working on novel innovations for biomedical and clinical applications.

Objectives

1. Understand the basic operating principles of IMS and the differences between the different techniques (e.g., drift tube, traveling wave, FAIMS/DMS, etc.)
2. Understand potential benefits of integrating IM into clinical workflows for "high value" applications
3. Appreciate the remaining challenging to integrating ion mobility into a routine workflow

Summary

Ion mobility-mass spectrometry (IM-MS) has become commonplace in biological research over the last decade, yet its transition to a more "routine" tool in fields such as clinical, forensic, and toxicological applications has been hampered by challenges in sensitivity, ease of use, and software compatibility, etc. While the benefits of separation, especially for isobaric and isomeric compounds, have been extensively demonstrated, method development is still often required to maximize signal-to-noise (S/N). In this workshop, we will invite several leaders in Clinical Chemistry to provide their perspectives on the potential advantages of integrating ion mobility into clinical workflows and high value applications, but also highlight the challenges in technology, software, and interpretation, etc. The presenters will then provide recent examples of attempts to overcome these challenges, especially focusing on recent work (i.e., within the last year). A brief introduction to ion mobility fundamentals, the different techniques, and data interpretation will also 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. Clinical Chemistry Leaders: Perspectives on potential benefits and remaining challenges to ion mobility in the clinic
4. Discussion of recent method development attempts to overcome these challenges

Location: Montreal 5

	Margret Thorsteinsdottir, PhD University of Iceland Professor in Pharmaceutical Analytical Chemistry at the Faculty of Pharmaceutical Sciences, University of Iceland and R&D Director of ArcticMass LTd, Reykjavik, Iceland. Dr. Thorsteinsdóttir received her PhD from Uppsala University, Sweden in 1998. From 2000 to 2009 she was the managing director of Bioanalytical Laboratories at deCODE Genetics, Reykjavik, Iceland. She has extensive experience in development of analytical methods for metabolite profiling and quantification of clinical biomarkers in various biofluids utilizing chemometrics with the goal of improved clinical management of patients towards personalized patient care. Her current research interest includes studies of lipid metabolism in cancer cells and profiling plasma derived biomarkers for early detection of BRCA-related breast cancer. She is responsible for implementation of clinical mass spectrometry for support of diagnostics and therapeutic drug monitoring in collaboration with ArcticMass and the Landspitali University Hospital, Reykjavik, Iceland with major focus on quantitative targeted proteomics for clinical diagnosis. She is a principal investigator of the Icelandic Research Rannis projects, profiling metabolites for breast cancer diagnosis and search for novel biomarkers for early breast cancer diagnosis by metabolomics. Dr. Thorsteinsdóttir is a principal investigator for the Marine Biotechnology ERA-net project CYNOBESITY and the Horizon 2020 project MossTech, with the main task to isolate, identify and structurally characterize bioactive compounds from cyanobacteria, Icelandic mosses and liverworts. She is one of the founders of Females in Mass Spectrometry (FeMS), she is a vice-leader of the working group clinical significance and applications of (epi)lipidomics in the pan-European network, EpiLipidNET and vice-chair of the Nordic Metabolomics Society.
	Finnur Eiriksson, PhD ArticMass
	Mark Kushnir, PhD ARUP Institute for Clinical & Experimental Pathology Mark Kushnir is Scientific Director, Mass Spectrometry R&D at ARUP Institute for Clinical and Experimental Pathology and Adjunct Assistant Professor at the Department of Pathology, University of Utah School of Medicine. Mark received PhD in Analytical Chemistry from Uppsala University (Uppsala, Sweden); his main areas of interest include development, application and clinical evaluation of novel mass spectrometry based clinical diagnostic methods for small molecule, protein and peptide biomarkers. He is author/coauthor of over 100 scientific peer reviewed publications.

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 numerous experimental factors, which need to be simultaneously optimized to obtain a true maximum sensitivity with adequate resolution at minimum retention time. DoE offers an efficient 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 cost-effective benefit of DoE, which allows the effect of variables to be assessed with only a fraction of the experiments that would be required by changing one-separate-factor-at-time (COST) approach, two case studies will be presented. The first case is optimization of sample preparation in bottom-up targeted protein LC-MS workflow using DoE. The second case is an optimization of a UPLC-MS/MS assay for clinical diagnostic and therapeutic drug monitoring of patients with adenine phosphoribosyltransferase (APRT) deficiency, which is an inborn error of purine metabolism. 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 (PLS)-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

1. Design of Experiments (DoE) – Get it right from the beginning
2. Basic concept and assessment of DoE
3. Optimization of sample preparation and UPLC-MS/MS clinical assay by DoE
4. Evaluation of robustness of an analytical method by DoE

Location: Montreal 6-8

	Enaksha Wickremsinhe, PhD Gates Medical Research Institute Enaksha has over 20 years of experience in Pharma R&D as a bioanalytical expert combined with ADME/DMPK project leadership. He is currently a Bioassay Development Lead at the Gates Medical Research Institute. Prior to that he served as a Research Advisor at Eli Lilly and Company where he was responsible for the development, validation, and execution of quantitative LC-MS/MS assays supporting the entire small molecule portfolio, spanning from discovery to registration. He is also an expert on novel blood sampling technologies and supporting Decentralized Clinical Trials (DCTs). Enaksha has numerous publications demonstrating the adoption of patient centric minimally invasive blood sampling for PK as well as safety panels supporting global trials including pediatric. He is the co-chair of the AAPS Microsampling and Patient Centric Sampling discussion group. Enaksha represented PhRMA as a member of the ICH M10 Expert Working Group. He received his Ph.D. from the Pennsylvania State University and his undergraduate from the University of Peradeniya (Sri Lanka).
	Emily Harari, BS Artyc PBC Based on a foundation of early wetlab experience, I've worked in both large pharma and small biotech. My experience is in study operations and I'm currently focused on solving the problem of reliable specimen handling in decentralized trials and point-of-care testing. I'm interested in reducing pre-analytical errors and maximizing sample quality using reliable temperature control and other safe-handling practices of specimens in transit to the lab.
	Dajana Vuckovic, PhD Concordia University Dr. Dajana Vuckovic is Professor and Concordia University Research Chair in Clinical Metabolomics and Biomarkers and the Director of Centre for the Biological Applications of Mass Spectrometry at Concordia University. Her research program focuses on the development of novel mass spectrometry and microextraction methods to accurately measure challenging low-abundance and unstable metabolites and improve metabolite coverage and data quality in clinical metabolomics and lipidomics. Dr. Vuckovic is the recipient of the 2023 Fred Beamish Award from the Canadian Society for Chemistry and the 2024 Metabolomics Society medal. She serves on the editorial boards of Bioanalysis and Analytical and Bioanalytical Chemistry and currently co-leads the Best Practices Working Group of Metabolomics Quality Assurance and Quality Control Consortium. She was elected as Secretary and member of the Board of Directors of Metabolomics Association of North America. She has co-organized numerous scientific symposia at leading national and international conferences and has co-chaired Metabolomics 2023 conference held in Niagara Falls, Canada.

Objectives

1. Learn about patient centric sampling technologies – what they are, what the benefits are and how they might be used to enable the patient journey.
2. Define the challenges for routine implementation of patient centric sampling technologies for diagnostic blood sampling and analysis.
3. Break out group discussions regarding the defined challenges and how they may be overcome.
4. Prioritize actionable next steps for improved patient outcomes.

Summary

Numerous technologies are now commercially available that facilitate the collection of human blood samples in locations away from the clinical setting. This approach is termed patient centric sampling, or microsampling and can involve the collection of samples from a finger stick, or from elsewhere on the body. The samples can be dried or liquid, and are often a smaller volume than those obtained by traditional phlebotomy.

The use of these approaches potentially enables samples to be collected from currently underserved communities (pediatric, elderly, remote areas, etc). Furthermore, the approach may enable more regular sampling of individuals to be performed and facilitates choice for the patient about how and where samples will be collected. These technologies also have the potential to overcome the discomfort, pain and fear that is encountered by many when collecting samples by traditional phlebotomy. This workshop will give the background to this approach for biological specimen collection. Workshop participants will then take part in a facilitated discussion focusing on the challenges of implementing these technologies. Participants will then take part in facilitated break-out groups to provide tractable solutions to overcome these challenges and what future activities are required to facilitate this.

Syllabus

1. Welcome and introduction to the workshop, including objectives – Russell Grant.
2. Presentation on patient centric remote sampling technologies, what they are what the benefits are and how they might be used as a part of healthcare. Primer on what to discuss as the challenges – regulatory hurdles; affordability; integrating into laboratory workflows (15 min) – Enaksha Wickremsinhe
3. Discussion of challenges of implementing this approach – entire workshop (25 min) - Dajana Vuckovic
4. Set-up breakout groups and subjects for discussion (10 min)
5. Discussion of potential solutions to the challenges – breakout groups (30 min) – Enaksha Wickremsinhe
6. Next steps and wrap-up (10 min) – Russell Grant