Peptide and Protein Bioanalysis Boot Camp
Building Proficiency in LC-MS Large Molecule Quantification
Waters’ team of bioanalysis experts developed the Peptide & Protein Bioanalysis Boot Camp – a series of short, recorded presentations – to help you and your colleagues acquire a fundamental and practical proficiency in large molecule quantification.
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Introduction to Peptide & Protein Bioanalysis Boot Camp
Quantifying large molecules in matrix is new to many of us and presents a variety of challenges that we don’t see with small molecules. Peptides and proteins have a more diverse set of chemical properties and tend to be much more complex. Kelly Doering, Director, Discovery & DMPK, explains the goals of the Peptide and Protein Bioanalysis Bootcamp.
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Dr. Kelly Doering leads a business team within Waters’ Global Marketing group that focuses on the promotion of mass spectrometry solutions to Discovery and DMPK labs. Prior to Waters, she worked in a variety of commercial roles including product management, business development and new product development. She earned her doctorate from the University of Connecticut, studying nutrient regulation of hepatic gene expression in mice and then completed a post-doctoral fellowship in the Department of Endocrinology at Boston Childrens Hospital, studying the effects of glycemic index on body composition, also in rodent models. Before graduate school, she worked in Nutrition Research within the Division of Preventive & Behaviorial Medicine at UMass Medical Center, where she worked on a number of NIH funded projects, mainly centered around lifestyle interventions to improve cardiovascular outcomes.
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Introduction to Peptides and Proteins for Bioanalysis Using LC-MS
Khalid Khan, Senior Manager Business Development, discusses the basic structure of amino acids, peptides, and proteins, including specific examples like monoclonal antibodies. The ionization and fragmentation of peptides and how they differ from small molecules is also discussed.
- Access additional resources on this topic below:
- Simplifying Peptide Bioanalysis
- Generic Protein and Peptide Level Sample Preparation for Protein...
Khalid Khan is a senior manager with Waters Global Marketing, focusing on clinical and biomedical research applications. He has been involved in mass spectrometry technology for over 25 years since his postgraduate research studies where high resolution GC-MS data played a key role in the identification of novel organic compounds. Khalid joined Waters in 2001 and has been involved in both technical and business development roles in clinical diagnostics, toxicology and biomedical research applications of LC-MS. Khalid is currently focused on biomarker translation and quantification, with a particular interest in utilizing LC-MS in combination with advanced informatics to aid protein and peptide quantification to help advance biomedical research and drug development.
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Contrasting LBAs and LC-MS for Peptide and Protein Bioanalysis
Kelly Doering discusses ligand binding assays (LBAs) and compares the advantages and limitations of this technology to LC-MS. She'll then present three examples of when LC-MS is the preferred method for quantification of insulin analogs based on specificity requirements and the need to multiplex.
Dr. Kelly Doering leads a business team within Waters’ Global Marketing group that focuses on the promotion of mass spectrometry solutions to DMPK/Bioanalysis labs. Prior to Waters, she worked in a variety of commercial roles including product management, business development and new product development. She earned her doctorate from the University of Connecticut, studying nutrient regulation of hepatic gene expression in mice and then completed a post-doctoral fellowship in the Department of Endocrinology at Boston Childrens Hospital, studying the effects of glycemic index on body composition, also in rodent models. Before graduate school, she worked in Nutrition Research within the Division of Preventive & Behaviorial Medicine at UMass Medical Center, where she worked on a number of NIH funded projects, mainly centered around lifestyle interventions to improve cardiovascular outcomes.
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LC-MS/MS for Bioanalytical Peptide and Protein Quantification: MS Considerations
Caitlin Dunning, Associate Scientist, discusses how to use mass spectrometry to develop sensitive, selective, and robust quantification methods for peptide and protein quantification, including: basic mass spectrometry considerations, MS tuning, and best practices for success. In addition, practical considerations are provided to achieve greater MRM specificity for your peptides of interest.
Caitlin received her bachelor’s in Chemistry from Northeastern University (Boston, MA) where she participated in their signature cooperative education program. Leveraging her co-op experiences into a full-time position, Caitlin started her career in the field of proteomics. In this position, she learned that she loved bioanalytical chemistry, especially mass spectrometry. Caitlin joined Waters in 2016 as an Associate Applications Scientist where she provides support for new product development and discovery bioanalysis of proteins and peptides. She is responsible for all aspects of method development, including sample preparation, liquid chromatography, and mass spectrometry. She enjoys working on solutions to challenging bioanalytical applications and sharing her work with customers.
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LC-MS/MS for Bioanalytical Peptide and Protein Quantification: Chromatographic Considerations
Bioanalytical scientists are faced with developing robust, reliable, and sensitive methods. This is especially challenging when we deal with peptides and proteins. Mary Lame, Principal Applications Chemist, walks you through a basic LC screening method designed specifically with peptides in mind.
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- Development of a High Sensitivity SPE-LC-MS/MS Assay for the Quan...
- LC-MS/MS Quantification of Intact Insulin-Like Growth Factor I (I...
Mary received her B.S. in Chemistry from the Western Connecticut State University and her M.S. in Chemistry from Central Connecticut State University. She began her bioanalytical career in 1997 with a global Pharmaceutical company where she supported research and discovery efforts by performing DMPK studies and conducting various bioanalytical assays until 2011. Mary joined Waters in 2011, providing pharmaceutical applications development and support for the Waters Scientific Operations Group. Mary’s primary role is to support discovery bioanalysis, and develop bioanalytical methods for drug molecules, both large and small. She is responsible for sample preparation, mass spectrometry, and LC method development.
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LC-MS/MS for Bioanalytical Peptide and Protein Quantification: Peptide Level Sample Clean-up
Bioanalytical laboratories are continually pressed to attain increasing levels of performance and productivity in the development of robust, reliable, and sensitive methods for accurate quantification. The challenge is the high sensitivity quantification of peptides and proteins from complex biological matrices. Mary Lame, Principal Applications Chemist, presents the starting universal solid phase extraction protocol for therapeutic, endogenous, and tryptic peptides. The value of incorporating a mixed mode SPE strategy into the overall LC-MS quantitative workflow is demonstrated.
Mary received her B.S. in Chemistry from the Western Connecticut State University and her M.S. in Chemistry from Central Connecticut State University. She began her bioanalytical career in 1997 with a global Pharmaceutical company where she supported research and discovery efforts by performing DMPK studies and conducting various bioanalytical assays until 2011. Mary joined Waters in 2011, providing pharmaceutical applications development and support for the Waters Scientific Operations Group. Mary’s primary role is to support discovery bioanalysis, and develop bioanalytical methods for drug molecules, both large and small. She is responsible for sample preparation, mass spectrometry, and LC method development.
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Peptide Sample Preparation Optimization and Troubleshooting
Mass spectrometry, chromatography, and sample preparation are all leveraged to facilitate the development of sensitive, selective, and robust bioanalytical methods for the quantification of peptides in biological matrices. In this module, Erin Chambers, Vice President, Chemistry and Technology, focuses on peptide sample prep optimization and the fundamental characteristics of peptides.
As a principal scientist and now vice president of chemistry, Erin has worked at Waters for more than 14 years and has been in bioanalysis for almost 25. While at Yale, Erin recalls a conversation with her college dean that changed the course of her career and put her on the path of scientific study. Ultimately, she graduated from Yale University with a degree in chemistry focusing on molecular biochemistry and biophysics, and earned her doctoral degree from Kings College London. Erin loves the dynamic nature of her job, developing new extraction methods, and helping to design new analytical systems that have a profound influence on illnesses like diabetes and Alzheimer’s disease. She loves to play with her kids and being outdoors. Her favorite authors are Lincoln Child and Douglas Preston.
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Identification of Surrogate Peptides for LC-MS Protein Quantification
In this module Nikunj Tanna, Waters' Senior Scientist, discusses the circumstances in which it's necessary to perform a surrogate peptide approach for protein quantification; the differences between generic and unique surrogate peptides; and he outlines various steps in identifying peptides, and the available software tools to aid the process.
As a senior scientist, Nikunj Tanna is responsible for developing applications to support bioanalysis of large molecules, including therapeutic monoclonal antibodies, ADC’s, proteins and peptides as well as biomarkers. His past experience included method development and validation under GLP/CLIA guidelines for pharmacokinetic study of small molecule drugs, endogenous molecules for CPT code tests, and immunoaffinity extraction of protein biomarkers. He also led the routine analysis & data review of clinical samples in support of pharmacokinetics study and oversaw experimental design and data review for analytical and clinical validation of ELISA assays used in biomarker panels.
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MRM Optimization for Surrogate Peptides for LC-MS Protein Quantification
Paula Orens, Application Scientist, examines a typical workflow for surrogate peptide approach via LC-MS with tandem quadrupole mass spectrometry. Identifying transitions and optimizing MS conditions is a key focus of this module. By the end, you will understand how mass spectrometry informatics systesm combined with an open-source client MRM application can work together to simplify MRM method development. Using Infliximab as an example, Ms. Orens demonstrates the development and optimization of MRM transitions to establish sensitivity needs and discusses sample prep and LC considerations.
Paula began her career at a contract research organization supporting the high-throughput bioanalysis of small molecules and peptides. When she joined Waters in 2015, she transitioned into an Applications Scientist role, focused on new product development and discovery bioanalysis of peptides and proteins. With the ever changing and advancing Waters’ technologies, Paula’s kept busy with method development of therapeutic peptides and proteins.
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Protein Level Sample Purification and Digestion for LC-MS Quantification
Waters Product Manager, Steven Calciano, discusses the bioanalytical challenges of protein level sample purification and digestion.
Steven Calciano joined Waters Corporation in 2015 and is responsible bringing innovative large molecule chromatography and mass spectrometry sample preparation solutions to market. Prior to his current role, Steven supported analytical standards and reagents products across pharmaceutical, environmental, chemical and food industries, gaining an understanding of a variety of complex analytical workflows. He strives to bring enabling technology to LC-MS users which simplify complex sample preparation methods.
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Internal Standard Options for Peptide LC-MS Quantification
An internal standard is a compound that displays physical and chemical characteristics similar to that of the analyte of interest, but at the same time generates a response that can be distinguished from that of the analyte. In Part 1 of "Internal Standard (IS) Options," Erin Chambers focuses on Peptide LC-MS quantification. She discusses various IS options when, where, and how to implement various strategies, and accurate peptide quantification with various options.
As a Principal Scientist and now Vice President, Chemistry and Technology, Erin has worked at Waters for more than 14 years and has been in bioanalysis for almost 25. While at Yale, Erin recalls a conversation with her college dean that changed the course of her career and put her on the path of scientific study. Ultimately, she graduated from Yale University with a degree in chemistry focusing on molecular biochemistry and biophysics, and earned her doctoral degree from Kings College London. Erin loves the dynamic nature of her job, developing new extraction methods, and helping to design new analytical systems that have a profound influence on illnesses like diabetes and Alzheimer’s disease. She loves to play with her kids and being outdoors. Her favorite authors are Lincoln Child and Douglas Preston.
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Internal Standard Options for Protein LC-MS Quantification
In Part 2 of "Internal Standard (IS) Options," Erin Chambers focuses on Protein LC-MS quantification. She discusses when, where, and how to implement various strategies and accurate protein quantification with various IS options.
As a Principal Scientist and now Vice President, Chemistry and Technology, Erin has worked at Waters for more than 14 years and has been in bioanalysis for almost 25. While at Yale, Erin recalls a conversation with her college dean that changed the course of her career and put her on the path of scientific study. Ultimately, she graduated from Yale University with a degree in chemistry focusing on molecular biochemistry and biophysics, and earned her doctoral degree from Kings College London. Erin loves the dynamic nature of her job, developing new extraction methods, and helping to design new analytical systems that have a profound influence on illnesses like diabetes and Alzheimer’s disease. She loves to play with her kids and being outdoors. Her favorite authors are Lincoln Child and Douglas Preston.
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Integrated Microflow LC-MS for Peptide & Protein Quantification
In this module, Waters' Market Development Manager, Logan Umberger explains how to apply microflow LC-MS in your large molecule bioanalysis efforts.
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An Introduction to High Resolution Mass Spectrometry versus Tandem Quad Mass Spectrometry for Large Molecule Bioanalysis
This presentation, presented by Ian Edwards, is designed as a primer for those new to mass spec and want to apply it to large molecule bioanalysis. It also appeals to those using triple quad MS and are exploring the benefits of HRMS for quantification of challenging samples.
Ian has a doctorate in the application of mass spectrometry and stable isotope labelling to measure protein turnover in animals, and in his early career as an application specialist in industry worked with MALDI-TOF MS systems for protein identification, molecular imaging and microbial identification. Ian spent several years in the Waters European Applications Laboratory working on a range of high resolution mass spectrometry applications including metabolomics, proteomics, molecular imaging and large molecule bioanalysis (therapeutics and biomarkers) before moving into marketing roles at a regional and global level. In his current business role he is focused on the application of LC-MS for large molecule bioanalysis including the emerging area of intact protein quantification.
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High Resolution Mass Spectrometry: Introduction to Quantitative Data Acquisition Modes on a Waters QTof for Large Molecule Bioanalysis
Hear from Mark Wrona as he discusses this next module in a series of training presentations discussing LC-MS–based quantification for large molecules using high resolution mass spectrometers.
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Case Studies in High Resolution Mass Spectrometry (HRMS) for Large Molecule Bioanalytical Quantification
In this presentation, Caitlin Dunning demonstrates the sensitivity and selectivity that can be achieved with HRMS for the quantification of peptides and proteins, speaks to some of the practical considerations to keep in mind for successful method development and more.
Caitlin received her bachelor’s in Chemistry from Northeastern University (Boston, MA) where she participated in their signature cooperative education program. Leveraging her co-op experiences into a full-time position, Caitlin started her career in the field of proteomics. In this position, she learned that she loved bioanalytical chemistry, especially mass spectrometry. Caitlin joined Waters in 2016 as an Associate Applications Scientist where she provides support for new product development and discovery bioanalysis of proteins and peptides. She is responsible for all aspects of method development, including sample preparation, liquid chromatography, and mass spectrometry. She enjoys working on solutions to challenging bioanalytical applications and sharing her work with customers.
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High Resolution Mass Spectrometry for Quantification of Intact Monoclonal Antibodies in Plasma
In this short presentation we will go over an introduction to intact level protein quantification using LC-MS, then we will cover some of the challenges and best practices associated with this application and more.