Introduction to Protein Mass Spectrometry, Second Edition provides a comprehensive overview of this increasingly important, yet complex, analytical technique. This book enables readers to understand how determinations about protein identity from mass spectrometric data are made. Coverage begins with the technical basics, including preparations, instruments, and spectrometric analysis of peptides and proteins, before exploring applied use in biological applications, bioinformatics, database, and software resources. This new edition is fully updated to include the latest developments in the field and will feature new content covering recent progress in the areas where there have been the most exciting advances.
These include PNNL’s multilevel-PCB-based SLIM realization, SLIM-Agilent QQQ field trials; employment of SLIM-IMS-cryo-IR combination in molecular structure determination; proximity-labelling mass spectrometry, and applications in neuroscience.
1. Introduction to Protein Mass Spectrometry - p. iii 2. Cover - p. iii 3. Title Page - p. iii 4. Copyright Page - p. iv 5. Table of Contents - p. iv 6. Dedication - p. v 7. Preface - p. vii 8. Preface to the Second Edition - p. ix 9. Chapter 1 Introduction - p. 1 10. Chapter 2 Sample Preparation and Ionization for Mass Spectrometry - p. 9 11. Chapter 3 Instruments - p. 68 12. 3.1: Mass analysis - p. 68 13. 3.1.1: Mass analyzers: time-of-flight (TOF), 2D-quadrupole (Q), Linear Trap (q,LT), 3D-ion trap (IT), Fourier transform ion cyclotron resonance (FT-ICR), Orbitrap, ion mobility (IM), Structures for Lossless Ion Manipulation (SLIM), cyclic ion mobility (cIM) device on IM-MS system - p. 68 14. 3.1.2: Theoretical ion mobility cross-sections using PA, PSA - p. 116 15. 3.1.3: MS/MS instrumental supplements: CAD/CID, ECD, ETD, EDD, HCD, IRMPD - p. 120 16. 3.2: Some examples of instruments - p. 125 17. Chapter 4 Mass Spectrometry of Peptides and Proteins - p. 158 18. 4.1: Proteins - p. 159 19. 4.2: Alternative analysis methods - p. 173 20. 4.3: Quantitation - p. 173 21. 4.4: Peptide fragmentation: Experiments - p. 188 22. 4.5: Data mining scheme for identifying peptide structural motifs - p. 196 23. 4.6: Peptide fragmentation: mechanism - p. 198 24. 4.7: Possible pathways in the competitionmodel - p. 200 25. 4.8: Studying post translational modifications - p. 218 26. 4.9: Chemical cross-linking/massspectrometry - p. 222 27. 4.10: Manual de novo sequencing of peptides - p. 229 28. Chapter 5 Examples from Biological Applications - p. 243 29. 5.1: Mapping intact protein isoforms using top-down proteomics - p. 243 30. 5.2: Quantitative analysis of intact apolipoproteins in human HDL - p. 251 31. 5.3: Rapid sequence analysis of some conotoxins — combination of de novo, bottom-up methods - p. 254 32. 5.4: Mass spectrometry of ribosomes - p. 260 33. 5.5: Proteins in Purkinje cell post-synaptic densities - p. 266 34. 5.6: Neurexin-LRRTM2 interaction effect in synapse formation - p. 268 35. 5.7: Rapid analysis of human plasma proteome — an IMS-IMS-MS application - p. 270 36. 5.8: Topology of two transient virus capsid assembly intermediates - p. 274 37. 5.9: Mass spectrometry of intact V-type ATPases reveals bound lipids and the effects of nucleotide binding - p. 282 38. 5.10: Mass spectrometric imaging of biological material - p. 291 39. 5.11: Immunopeptidomics - p. 293 40. 5.12: Metaproteomics - p. 299 41. 5.13: Proteogenomics - p. 303 42. 5.14: Single-cell proteomics and single-cell metabolomics - p. 307 43. 5.15: Applications in neurobiology - p. 321 44. Chapter 6 Mass Spectrometry-Based Bioinformatics - p. 337 45. Index - p. 369
Introduction to Protein Mass Spectrometry, Second Edition provides a comprehensive overview of this increasingly important, yet complex, analytical technique. This book enables readers to understand how determinations about protein identity from mass spectrometric data are made. Coverage begins with the technical basics, including preparations, instruments, and spectrometric analysis of peptides and proteins, before exploring applied use in biological applications, bioinformatics, database, and software resources. This new edition is fully updated to include the latest developments in the field and will feature new content covering recent progress in the areas where there have been the most exciting advances.
These include PNNL’s multilevel-PCB-based SLIM realization, SLIM-Agilent QQQ field trials; employment of SLIM-IMS-cryo-IR combination in molecular structure determination; proximity-labelling mass spectrometry, and applications in neuroscience.
1. Introduction to Protein Mass Spectrometry - p. iii 2. Cover - p. iii 3. Title Page - p. iii 4. Copyright Page - p. iv 5. Table of Contents - p. iv 6. Dedication - p. v 7. Preface - p. vii 8. Preface to the Second Edition - p. ix 9. Chapter 1 Introduction - p. 1 10. Chapter 2 Sample Preparation and Ionization for Mass Spectrometry - p. 9 11. Chapter 3 Instruments - p. 68 12. 3.1: Mass analysis - p. 68 13. 3.1.1: Mass analyzers: time-of-flight (TOF), 2D-quadrupole (Q), Linear Trap (q,LT), 3D-ion trap (IT), Fourier transform ion cyclotron resonance (FT-ICR), Orbitrap, ion mobility (IM), Structures for Lossless Ion Manipulation (SLIM), cyclic ion mobility (cIM) device on IM-MS system - p. 68 14. 3.1.2: Theoretical ion mobility cross-sections using PA, PSA - p. 116 15. 3.1.3: MS/MS instrumental supplements: CAD/CID, ECD, ETD, EDD, HCD, IRMPD - p. 120 16. 3.2: Some examples of instruments - p. 125 17. Chapter 4 Mass Spectrometry of Peptides and Proteins - p. 158 18. 4.1: Proteins - p. 159 19. 4.2: Alternative analysis methods - p. 173 20. 4.3: Quantitation - p. 173 21. 4.4: Peptide fragmentation: Experiments - p. 188 22. 4.5: Data mining scheme for identifying peptide structural motifs - p. 196 23. 4.6: Peptide fragmentation: mechanism - p. 198 24. 4.7: Possible pathways in the competitionmodel - p. 200 25. 4.8: Studying post translational modifications - p. 218 26. 4.9: Chemical cross-linking/massspectrometry - p. 222 27. 4.10: Manual de novo sequencing of peptides - p. 229 28. Chapter 5 Examples from Biological Applications - p. 243 29. 5.1: Mapping intact protein isoforms using top-down proteomics - p. 243 30. 5.2: Quantitative analysis of intact apolipoproteins in human HDL - p. 251 31. 5.3: Rapid sequence analysis of some conotoxins — combination of de novo, bottom-up methods - p. 254 32. 5.4: Mass spectrometry of ribosomes - p. 260 33. 5.5: Proteins in Purkinje cell post-synaptic densities - p. 266 34. 5.6: Neurexin-LRRTM2 interaction effect in synapse formation - p. 268 35. 5.7: Rapid analysis of human plasma proteome — an IMS-IMS-MS application - p. 270 36. 5.8: Topology of two transient virus capsid assembly intermediates - p. 274 37. 5.9: Mass spectrometry of intact V-type ATPases reveals bound lipids and the effects of nucleotide binding - p. 282 38. 5.10: Mass spectrometric imaging of biological material - p. 291 39. 5.11: Immunopeptidomics - p. 293 40. 5.12: Metaproteomics - p. 299 41. 5.13: Proteogenomics - p. 303 42. 5.14: Single-cell proteomics and single-cell metabolomics - p. 307 43. 5.15: Applications in neurobiology - p. 321 44. Chapter 6 Mass Spectrometry-Based Bioinformatics - p. 337 45. Index - p. 369
