Proteomics of Biological Systems - Protein Phosphorylation Using Mass Spectrometry Techniques

Informationen zum Autor BRYAN M. HAM, PhD, is a member of the American Society for Mass Spectrometry and the American Chemical Society. He has conducted proteomics and lipidomics research at The Ohio State University and Pacific Northwest National Laboratory in Richland, Washington. He is currently working for the Department of Homeland Security at the U.S. Customs and Border Protection New York Laboratory. He has published numerous research papers in peer-reviewed journals, and is the author of Even Electron Mass Spectrometry with Biomolecule Applications (Wiley). Klappentext Obtain protein phosphorylation knowledge using mass spectrometry techniquesA practical introduction to mass spectrometry-based phosphoproteomic studies, this book addresses various concepts including the protocols necessary for sample preparation through mass spectral interpretation of protein phosphorylation events. It delves into the determining factors for whether or not a protein has been correctly modified by the addition of a phosphate group. Highlighting both basic and significant principles, as well as specific applications using examples, Proteomics of Biological Systems covers:* Key fundamentals of mass spectrometry including mass analyzers, ionization, and nano-electrospray/nano-flow liquid chromatography* Optimized methodologies for performing post translational modification (PTM) of protein studies using tried and tested sample preparation and analysis methods and approaches* Specific examples of eukaryote and prokaryote normal state and perturbed state phosphoproteomic studies* Use of the most recent systems biology bioinformatic Internet tools for interpreting complex data such as the Blast2GO gene ontology tool* Step-by-step methodology for phosphoproteomic studies of both eukaryote and prokaryote systemsThis unique resource contains specific chapters devoted to normal state HeLa cell phosphoproteomes, DNA damage response state HeLa cell phosphoproteomes, Caulobacter crescentus normal state phosphoproteomes, and more. A core guide for scientists and researchers in academic laboratories and pharmaceutical, chemical, and biotech companies, Proteomics of Biological Systems is a useful text for expanding comprehension of mass spectrometry-based phosphoproteomic study. Zusammenfassung Phosphorylation is the addition of a phosphate (PO 4) group to a protein or other organic molecule. Phosphorylation activates or deactivates many protein enzymes, causing or preventing the mechanisms of diseases such as cancer and diabetes. Inhaltsverzeichnis Preface xvii Acknowledgments xxi About the Author xxiii 1 Posttranslational Modification (PTM) of Proteins 1 1.1 Over 200 Forms of PTM of Proteins 1 1.2 Three Main Types of PTM Studied by MS 2 1.3 Overview of Nano-Electrospray/Nanofl ow LC-MS 2 1.3.1 Defi nition and Description of MS 2 1.3.2 Basic Design of Mass Analyzer Instrumentation 3 1.3.3 ESI 7 1.3.4 Nano-ESI 11 1.4 Overview of Nucleic Acids 15 1.5 Proteins and Proteomics 20 1.5.1 Introduction to Proteomics 20 1.5.2 Protein Structure and Chemistry 22 1.5.3 Bottom-Up Proteomics: MS of Peptides 27 1.5.3.1 History and Strategy 27 1.5.3.2 Protein Identifi cation through Product Ion Spectra 30 1.5.3.3 High-Energy Product Ions 36 1.5.3.4 De Novo Sequencing 37 1.5.3.5 Electron Capture Dissociation (ECD) 40 1.5.4 Top-Down Proteomics: MS of Intact Proteins 42 1.5.4.1 Background 42 1.5.4.2 GP Basicity and Protein Charging 42 1.5.4.3 Calculation of Charge State and Molecular Weight 44 1.5.4.4 Top-Down Protein Sequencing 46 1.5.5 Systems Biology and Bioinformatics 48 1.5.6 Biomarkers in Cancer 52 Reference 56 2 Glycosylation of Proteins 59 2.1 Production of a Glyc...

List of contents

Preface xvii
 
Acknowledgments xxi
 
About the Author xxiii
 
1 Posttranslational Modification (PTM) of Proteins 1
 
1.1 Over 200 Forms of PTM of Proteins 1
 
1.2 Three Main Types of PTM Studied by MS 2
 
1.3 Overview of Nano-Electrospray/Nanofl ow LC-MS 2
 
1.3.1 Defi nition and Description of MS 2
 
1.3.2 Basic Design of Mass Analyzer Instrumentation 3
 
1.3.3 ESI 7
 
1.3.4 Nano-ESI 11
 
1.4 Overview of Nucleic Acids 15
 
1.5 Proteins and Proteomics 20
 
1.5.1 Introduction to Proteomics 20
 
1.5.2 Protein Structure and Chemistry 22
 
1.5.3 Bottom-Up Proteomics: MS of Peptides 27
 
1.5.4 Top-Down Proteomics: MS of Intact Proteins 42
 
1.5.5 Systems Biology and Bioinformatics 48
 
1.5.6 Biomarkers in Cancer 52
 
Reference 56
 
2 Glycosylation of Proteins 59
 
2.1 Production of a Glycoprotein 59
 
2.2 Biological Processes of Protein Glycosylation 59
 
2.3 N-Linked and O-Linked Glycosylation 60
 
2.4 Carbohydrates 60
 
2.4.1 Ionization of Oligosaccharides 64
 
2.4.2 Carbohydrate Fragmentation 65
 
2.4.3 Complex Oligosaccharide Structural Elucidation 70
 
2.5 Three Objectives in Studying Glycoproteins 72
 
2.6 Glycosylation Study Approaches 72
 
2.6.1 MS of Glycopeptides 73
 
2.6.2 Mass Pattern Recognition 75
 
2.6.3 Charge State Determination 76
 
2.6.4 Diagnostic Fragment Ions 76
 
2.6.5 High-Resolution/High-Mass Accuracy Measurement and Identification 76
 
2.6.6 Digested Bovine Fetuin 78
 
Reference 79
 
3 Sulfation of Proteins as Posttranslational Modification 81
 
3.1 Glycosaminoglycan Sulfation 81
 
3.2 Cellular Processes Involved in Sulfation 81
 
3.3 Brief Example of Phosphorylation 82
 
3.4 Sulfotransferase Class of Enzymes 82
 
3.5 Fragmentation Nomenclature for Carbohydrates 82
 
3.6 Sulfated Mucin Oligosaccharides 83
 
3.7 Tyrosine Sulfation 84
 
3.8 Tyrosylprotein Sulfotransferases TPST1 and TPST2 87
 
3.9 O-Sulfated Human Proteins 89
 
3.10 Sulfated Peptide Product Ion Spectra 89
 
3.11 Use of Higher Energy Collisions 93
 
3.12 Electron Capture Dissociation (ECD) 94
 
3.13 Sulfation versus Phosphorylation 95
 
Reference 97
 
4 Eukaryote PTM as Phosphorylation: Normal State Studies 99
 
4.1 Mass Spectral Measurement with Examples of HeLa Cell Phosphoproteome 99
 
4.1.1 Introduction 99
 
4.1.2 Protein Phosphatase and Kinase 99
 
4.1.3 Hydroxy-Amino Acid Phosphorylation 100
 
4.1.4 Traditional Phosphoproteomic Approaches 102
 
4.1.5 Current Approaches 103
 
4.1.6 The Ideal Approach 107
 
4.1.7 One-Dimensional (1-D) Sodium Dodecyl Sulfate (SDS) PAGE 108
 
4.1.8 Tandem MS Approach 108
 
4.1.9 Alternative Methods: Infrared Multiphoton Dissociation (IRMPD) and Electron Capture Dissociation (ECD) 115
 
4.1.10 Electron Transfer Dissociation (ETD) 115
 
4.2 The HeLa Cell Phosphoproteome 118
 
4.2.1 Introduction 118
 
4.2.2 Background of Study 118
 
4.2.3 What is Covered 119
 
4.2.4 Optimized Methods to Use for Phosphoproteomic Studies 119
 
4.2.5 Description of Instrumental Analyses 123
 
4.2.6 Current Approaches for Peptide Identification and False Discovery Rate (FDR) Determination 125
 
4.2.7 Results of the Protein Extraction and Preparation 126
 
4.2.8 HeLa Cell Phosphoproteome Methodology Comparison 128
 
4.2.9 Overall Conclusion 134

Product details

• Authors: Bm Ham, Bryan M Ham, Bryan M. Ham, HAM BRYAN M, Ham Bryan M.
• Publisher: Wiley, John and Sons Ltd
• Languages: English
• Product format: Hardback
• Released: 15.11.2011
• EAN: 9781118028964
• ISBN: 978-1-118-02896-4
• No. of pages: 392
• Subjects: Natural sciences, medicine, IT, technology > Chemistry; Chemie, Massenspektrometrie, Life Sciences, Biowissenschaften, chemistry, mass spectrometry, Pharmaceutical & Medicinal Chemistry, Pharmazeutische u. Medizinische Chemie, Genomforschung u. Proteomik, Genomics & Proteomics