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)

Section 2: Targeted Proteomics Assay Development

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

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

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.

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.

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

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

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