ESSENTIALS OF PROTEOMICS: A COMPREHENSIVE STUDY OF PROTEINS
ISBN: 978-1-83926-870-0
Year: 2022
Binding: HB
Price: US $ 305.00
About Book
Proteomics is an advanced approach that aims to characterize a large number of proteins (proteome) in a single assay, or single experiment. As opposed to single protein analysis using antibody-based techniques, such as western blotting, enzyme-linked immunosorbent assay (ELISA) and fluorescent microscopy, proteomics offers a valuable opportunity to study proteins “in bulk” in order to draw a clearer picture of the molecular biology of healthy and/or diseased cells. In its present state, it is dependent on decades of technological and instrumental developments. These developments have included advances in mass spectrometry (MS) technology, protein fractionation techniques, bioinformatics, etc. Advances in this technology have enabled thousands of proteins to be resolved in a single gel. No area of proteomics has evolved faster than bioinformatics. Proteomics is critically dependent on bioinformatics to process the raw mass spectral data into protein data. This book provides comprehensive insights into the field of proteomics. It talks extensively about food proteomics, antarctic bacterium, quantitative proteomics, phosphoproteomics, protein complexes, proteomics analysis, functional proteomics, thiol proteomics and proteomics approaches. The book aims to shed light on some of the unexplored aspects of proteomic. It is compiled in such a manner, that it will provide in-depth knowledge about the theory and practice of the subject. Different approaches, evaluations and methodologies have been included in it. For all those who are interested in this topic, this book can prove to be an essential guide.
Preface............................................................................................................v
Chapter 1 Mechanisms of aIIbb3 Biogenesis in the Megakaryocyte:
A Proteomics Approach ...........................................................................1
1. Introduction............................................................................................1
2. Materials and methods .......................................................................4
3. Results ....................................................................................................9
4. Discussion ...........................................................................................24
5. Conclusion ...........................................................................................26
Chapter 2 Protein Thiol Modification and Thiol Proteomics...........................30
1. Introduction..........................................................................................30
2. Analysis of redox-sensing and signalling thiols...........................30
3. Proteomics studies to analyse the oxidation state of proteins..36
4. Human diseases and early hints from redox proteomics..........38
5. Challenges to mapping the thiol proteome...................................42
6. Conclusion............................................................................................43
Chapter 3 Functional Proteomics: Mapping Lipid-Protein Interactomes.......49
1. Introduction..........................................................................................49
2. Metabolomics.......................................................................................50
3. Functional lipidomics: From lipidomics to lipid-protein
interactomics............................................................................................51
4. Chemical proteomics for lipid pathway drug specificity
validation..............................................................................................62
5. Comparison of PI interactomics data to whole genome genetic
screens...................................................................................................62
6. Conclusion: Challenges and future direction in lipid-protein
interactomics........................................................................................64
Chapter 4 Proteomics Analysis of Kinetically Stable Proteins.......................71
1. Introduction..........................................................................................71
2. Diagonal two-dimensional (D2D) SDS-PAGE:
A proteomics tool for identifying kinetically stable proteins....76
3. Proteomics analysis of KSPs by capillary electrophoresis ........87
4. Conclusion ...........................................................................................91
5. Acknowledgment................................................................................92
Chapter 5 Dynamics of Protein Complexes Tracked by Quantitative
Proteomics...................................................................................................97
1. Introduction..........................................................................................97
2. Towards a comprehensive map of the human protein
interactome...........................................................................................99
3. SILAC-based quantitative proteomics: A method of choice to
reliably analyze specific protein interactions and protein complex
dynamics.............................................................................................106
4. Optimization of experimental procedures ..................................114
5. An additional criterion to identify putative contaminants:
The Protein Frequency Library .....................................................117
6. Standardization of data analysis and storage ............................120
7. Conclusion .........................................................................................122
8. Acknowledgment .............................................................................123
Chapter 6 Phosphoproteomics: Detection, Identification and Importance of
Protein Phosphorylation........................................................................130
1. Introduction........................................................................................130
2. Phosphorylation.................................................................................131
3. Challenges, limitations, future directions and potential...........147
Chapter 7 Labeling Methods in Mass Spectrometry Based Quantitative
Proteomics.................................................................................................154
1. Introduction........................................................................................154
2. LC-MS-based quantitation methods..............................................157
3. Comparison of different methods for quantitation....................170
4. Data analysis......................................................................................174
5. Concluding remarks.........................................................................175
Chapter 8 F0F1 ATP Synthase: A Fascinating Challenge for Proteomics......183
1. Introduction........................................................................................183
2. The nano-motor enzyme F0F1ATP synthase.................................183
3. Mass spectrometry data of F0F1 ATP synthase...........................194
4. Native electrophoresis of F0F1 ATP synthase...............................199
5. Ectopic F0F1ATP synthase of mammalian cells...........................205
6. Conclusions........................................................................................208
Chapter 9 Life in the Cold: Proteomics of the Antarctic Bacterium
Pseudoalteromonas haloplanktis.........................................................220
1. Introduction........................................................................................220
2. Temperature dependence of growth.............................................222
3. Cold-induced versus cold-repressed proteins.............................224
4. Cold shock and heat shock proteins.............................................226
5. Protein folding at low temperature rescued by the trigger
factor ..................................................................................................228
6. Possible origins of heat shock protein repression at low
temperature .......................................................................................229
7. Structural properties of the psychrophilic trigger factor..........230
8. Protein synthesis and folding are limiting factors in the
cold.......................................................................................................234
9. Metabolism depression at low temperatures..............................234
10. Down-regulation of iron metabolism at low temperatures......235
11. Oxidative stress-related proteins....................................................236
12. Other proteomic studies..................................................................237
13. Conclusions .......................................................................................238
Chapter 10 Food Proteomics: Mapping Modifications........................................248
1. Introduction........................................................................................248
2. Proteins and nutrition .....................................................................249
3. Food proteomics ..............................................................................250
4. Protein modification ........................................................................259
5. Redox proteomics ............................................................................266
6. Redox proteomics case study.........................................................269
7. Future directions...............................................................................276
Citation......................................................................................................291
Index...........................................................................................................293
