Covering a wide-ranging facet of a “gold-standard” targeted mass spectrometry (MS) method for the consistent detection and accurate quantification of preselected proteins in complex biological matrices, Selected Reaction Monitoring Mass Spectrometry (SRM-MS) in Proteomics: A Comprehensive View describes:
- The knowledge-based development of highly efficient SRM methodology including assay workflow, selection of proteins, peptides, transitions and its validation, and quality assessment
- Available bioinformatic tools – for both pre-acquisition method development and post-MS acquisition data analysis and data repositories
- Various relative and absolute quantification techniques
- SRM-MS’ widespread applications in biomarker development and in clinical studies, as well as in the analysis of various posttranslational modifications (PTMs)
- Current challenges and contemporary trends to overcome those difficulties
In addition, it features the historical development of modern-day mass spectrometry with its vivid applications and also covers basic MS instrumentation, ionization techniques, and various proteomics approaches.
Comprehensive discussion, extensive references at the end of each chapter, and the list of review articles in the bibliography offer invaluable resources for advanced readings. Researchers from the undergraduate to postgraduate level and beyond in both academic or industry settings studying and working on mass spectrometry and/or proteomics will benefit from this book.
Author(s): Mahmud Hossain
Edition: 1st ed. 2020
Publisher: Springer
Year: 2020
Language: English
Pages: 300
Preface
Contents
Abbreviations
Chapter 1: Introduction
1.1 Introduction to Mass Spectrometry
1.1.1 Mass Spectrometer
1.1.2 Mass Spectrum
1.2 General Applications of Mass Spectrometry
1.2.1 Proteomics
1.2.2 Other Biological Applications
1.2.3 Pharmaceuticals
1.2.4 Clinical
1.2.5 Environmental
1.2.6 Geological
1.3 History of Mass Spectrometry
1.3.1 The Early Years of Mass Spectrometry
1.3.2 Use of Mass Spectrometry Pre– and Post–World War II Era
1.3.3 Beginning of Biomolecule Research by Mass Spectrometry
1.3.4 Paradigm Shift in Mass Spectrometry Analysis
1.3.5 The Development of Proteomics
References
Chapter 2: The Mass Spectrometer and Its Components
2.1 Major Components of the Mass Spectrometer
2.1.1 Ion Source
2.1.1.1 Electron Ionization (EI)
2.1.1.2 Chemical Ionization (CI)
2.1.1.3 Electrospray Ionization (ESI)
2.1.1.4 Matrix-Assisted Laser Desorption/Ionization (MALDI)
2.1.2 Mass Analyzers
2.1.2.1 Quadrupole Mass Analyzers
2.1.2.2 Quadrupole Ion Trap Mass Analyzer
2.1.2.3 Time-of-Flight Mass Analyzer
2.1.2.4 FT-ICR Mass Analyzers
2.1.2.5 Orbitrap Mass Analyzer
2.1.3 Detectors of Mass Spectrometry
2.1.3.1 Characteristics of an Ideal Detector
2.1.3.2 Photoplate Detector
2.1.3.3 Faraday Cup Detector
2.1.3.4 Electron Multiplier Detectors
2.1.3.5 Microchannel Plate (MCP) Detector
2.1.3.6 Microsphere Plate (MSP) Detector
2.1.4 Other Components of Mass Spectrometer: Vacuum System
2.2 Tandem Mass Spectrometry (MS/MS)
2.2.1 MS/MS Instrumentation
2.2.2 Scan Modes in Tandem Mass Spectrometry
2.3 Dissociation Methods in Mass Spectrometry
2.3.1 Collision-Induced Dissociation (CID)
2.3.2 High-Energy Collisional Dissociation (HCD)
2.3.3 Electron Capture Dissociation
2.3.4 Electron Transfer Dissociation (ETD)
References
Chapter 3: Selected Reaction Monitoring Mass Spectrometry
3.1 Proteomics
3.1.1 Bottom-Up, Top-Down, and Middle-Down Proteomics
3.1.2 Shotgun/Discovery and Targeted Proteomics
3.2 Selected Reaction Monitoring Mass Spectrometry (SRM-MS)
3.2.1 SRM-MS in Comparison to Non-MS Analytical Technique
3.2.2 Instrumentation for SRM-MS
3.2.3 Commercial Triple Quadrupole Instruments
3.2.4 Distinctive Features of SRM-MS
3.3 Variations of the Conventional SRM-MS
3.3.1 Constrained SRM-MS
3.3.2 MRM3
3.3.3 Dynamic SRM-MS
3.3.4 Photo-SRM
3.3.5 MALDI-SRM
3.3.6 MSIA-SRM
3.4 Other Targeted MS Methodologies
3.4.1 Selected Ion Monitoring
3.4.2 Accurate Inclusion Mass Screening (AIMS)
3.4.3 pSRM (pseudo-Selected Reaction Monitoring)
3.4.4 Parallel Reaction Monitoring
3.4.5 Data-Independent Acquisition (DIA)
3.4.6 Comparison of SRM with PRM and DIA/SWATH
References
Chapter 4: Development of SRM-MS Experiment
4.1 General Workflow of a Proteomic SRM-MS Assay
4.2 Selection of Protein
4.3 Selection of Peptide
4.3.1 Peptide Selection Criteria
4.3.2 Peptide Selection Techniques
4.4 Selection of Transition
4.4.1 Transition Selection Process
4.4.1.1 Empirically Determined from the Same Instrument Types Used for SRM-MS.
4.4.1.2 From Discovery Experiments Done on Different Types of Instruments
4.4.2 Validation of Selected Transitions
4.5 Optimization of Experimental Parameters
4.6 Assay Development and Data Acquisition
4.6.1 Development of an SRM-MS Assay Workflow
4.7 System Suitability Monitoring and Quality Control
References
Chapter 5: Bioinformatics Tools for SRM-MS
5.1 SRM Preacquisition Stage
5.1.1 MRMaid
5.1.2 ATAQS
5.1.3 TIQAM
5.1.4 MaRiMba
5.1.5 PChopper
5.1.6 Picky
5.1.7 Skyline
5.2 Databases Related to SRM-MS
5.2.1 SRMAtlas
5.2.1.1 Defining the Target Proteome
5.2.1.2 Selection of Proteotypic Peptides
5.2.1.3 Peptide Selection for Isoforms, SNPs, and N-Glycosylated Proteins
5.2.1.4 Development of SRM Assays Using Synthetic Peptides
5.2.1.5 Compiling the Results into SRMAtlas Database
5.2.2 CPTAC Assay Portal
5.2.3 MRMAssayDB
5.2.4 ProteomeTools
5.3 SRM-MS Data Acquisition on LC-MS
5.4 SRM Postacquisition Stage
5.4.1 Data Analysis with ATAQS
5.4.2 MRMer
5.4.3 Postacquisition Data Analysis with Skyline
5.4.4 SRMstats and MSstats
5.4.5 160 Automated SRM-MS Data Analysis Workflow for Large-Scale Studies
5.5 Commercial Software from Instrument Vendors
5.5.1 Pinpoint (ThermoScientific)
5.5.2 MRMPilot (AB Sciex)
5.5.3 TargetLynx (Waters)
5.5.4 MassHunter (Agilent)
References
Chapter 6: Quantification by SRM-MS
6.1 Protein Quantification by SRM-MS
6.2 Relative Quantification
6.2.1 Label-Free Approach
6.2.1.1 AUC or Signal Intensity Measurement
6.2.1.2 Spectral Counting (SC)
6.2.1.3 SRM MS as a Label-free Quantification Approach
6.2.2 Stable Isotope Labeling Approach
6.2.2.1 Metabolic Labeling
6.2.2.2 Chemical Stable isotope Labeling
6.3 Absolute Quantification
6.3.1 Absolute Quantification (AQUA)
6.3.2 Quantification Concatemer (QconCAT)
6.3.3 Protein Standard Absolute Quantification (PSAQ)
6.4 Calibration Reference Standards
6.5 Validation of Quantitative SRM Assay
References
Chapter 7: SRM-MS Applications in Proteomics
7.1 General Proteomic Applications
7.1.1 Applications in Systems Biology/Network Biology
7.2 Clinical/Biomarkers Applications
7.2.1 Application on Cancers
7.2.1.1 Lung Cancer
7.2.1.2 Prostate Cancer
7.2.1.3 Colorectal Cancer
7.2.1.4 Breast Cancer
7.2.2 Biomarker Quantification Using Dried Blood Spots (DBS)
7.3 PSA as a Model Biomarker
References
Chapter 8: SRM-MS for Posttranslational Modification Analysis
8.1 Posttranslational Modifications (PTMS) of Proteins
8.1.1 Posttranslational Modification
8.1.2 Determination of Posttranslational Modifications
8.1.3 PTM Analysis by Mass Spectrometry
8.2 Analysis of Phosphorylation
8.3 Analysis of Ubiquitination
8.4 Analysis of Glycosylation
8.4.1 Analytical Strategy of Protein Glycosylation by Mass Spectrometry
8.4.2 Protein Glycosylation by SRM-MS
8.5 Analysis of Acetylation
References
Chapter 9: Challenges, Current Trends, and Future Directions
9.1 Sensitivity Issue
9.1.1 Improvement in Sample Preparation
9.1.2 Utilization of Various Separation Methods
9.1.3 Advances in MS Instrumentation
9.2 Multiplexing Capability Issue
9.3 Reproducibility Issue
9.4 Global SRM-MS Data Repositories
9.5 Outlook
References
Glossary of SRM-MS-Related Terms
Bibliography
Review Articles/Book Chapters on Various Aspects of SRM-MS (In Chronological Order)
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Method of the Year 2012 | Nature Methods articles
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Index
