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1
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Mass Spectrometry for Proteomics-Based Investigation
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2
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MALDI Profiling and Applications in Medicine
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3
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Applications of Matrix-Assisted Laser Desorption Ionization In-Source Decay Mass Spectrometry
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4
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Proteome Imaging: From Classic to Modern Mass Spectrometry-Based Molecular Histology
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5
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Mass Spectrometry-Based Tissue Imaging of Small Molecules
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6
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Sequencing Proteins from Bottom to Top: Combining Techniques for Full Sequence Analysis of Glucokinase
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7
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Proteomics and Non-proteomics Approaches to Study Stable and Transient Protein-Protein Interactions
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8
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Contribution of Mass Spectrometry-Based Proteomics to Discoveries in Developmental Biology
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9
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Profiling Optimal Conditions for Capturing EDEM Proteins Complexes in Melanoma Using Mass Spectrometry
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10
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The Methods Employed in Mass Spectrometric Analysis of Posttranslational Modifications (PTMs) and Protein–Protein Interactions (PPIs)
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11
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Identification of Posttranslational Modifications (PTMs) of Proteins by Mass Spectrometry
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12
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Sequence Variant and Posttranslational Modification Analysis During Cell Line Selection via High-Throughput Peptide Mapping
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13
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Selective Derivatization of Hexahistidine-Tagged Recombinant Proteins
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14
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Investigation of Antibody-Drug Conjugates by Mass Spectrometry
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15
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Mass Spectrometry- and Computational Structural Biology-Based Investigation of Proteins and Peptides
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16
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Strategies for Membrane Protein Analysis by Mass Spectrometry
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17
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The Potential for Ion Mobility in Pharmaceutical and Clinical Analyses
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18
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Application of Ion Mobility Mass Spectrometry in Lipidomics
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19
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Mass Spectrometry in Advancement of Redox Precision Medicine
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20
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Applications for Mass Spectrometry in the Study of Ion Channel Structure and Function
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21
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Immuno-Affinity Mass Spectrometry: A Novel Approaches with Biomedical Relevance
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22
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Developing Well-Annotated Species-Specific Protein Databases Using Comparative Proteogenomics
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23
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Stoichiometry of Heavy Metal Binding to Peptides Involved in Alzheimer’s Disease: Mass Spectrometric Evidence
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24
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Role of Mass Spectrometry in Investigating a Novel Protein: The Example of Tumor Differentiation Factor (TDF)
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25
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Mass Spectrometry-Based Biomarkers in Drug Development
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26
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Combinatorial Electrophoresis and Mass Spectrometry-Based Proteomics in Breast Milk for Breast Cancer Biomarker Discovery
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27
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Proteomic Approaches to Dissect Neuronal Signalling Pathways
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28
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Mass Spectrometry for the Study of Autism and Neurodevelopmental Disorders
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29
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Simplifying the Proteome: Analytical Strategies for Improving Peak Capacity
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30
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Exploration of Nicotine Metabolism in <italic>Paenarthrobacter nicotinovorans</italic> pAO1 by Microbial Proteomics
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31
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Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) for Quantitative Proteomics
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32
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Mass Spectrometry Based Comparative Proteomics Using One Dimensional and Two Dimensional SDS-PAGE of Rat Atria Induced with Obstructive Sleep Apnea
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33
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2D SDS PAGE in Combination with Western Blotting and Mass Spectrometry Is a Robust Method for Protein Analysis with Many Applications
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34
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Pulse SILAC Approaches to the Measurement of Cellular Dynamics
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35
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Protein Biomarkers in Major Depressive Disorder: An Update
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36
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A Pilot Exploratory Proteomics Investigation of Mental Fatigue and Mental Energy
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37
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Metabolomics and Biomarker Discovery
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38
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Analytical Methods for Mass Spectrometry-Based Metabolomics Studies
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39
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Trends in Analysis of Cortisol and Its Derivatives
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40
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Detection of Biomedically Relevant Stilbenes from Wines by Mass Spectrometry
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41
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Mass Spectrometry as a Complementary Approach for Noncovalently Bound Complexes Based on Cyclodextrins
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42
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Trends in Glycolipid Biomarker Discovery in Neurodegenerative Disorders by Mass Spectrometry
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43
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Non-targeted Screening in Environmental Monitoring Programs
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44
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Mass Spectrometric DNA Adduct Quantification by Multiple Reaction Monitoring and Its Future Use for the Molecular Epidemiology of Cancer
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45
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Bottlenecks in Proteomics: An Update
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46
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Recent Applications of Mass Spectrometry at Clarkson University
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47
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Correction to: 2D SDS PAGE in Combination with Western Blotting and Mass Spectrometry Is a Robust Method for Protein Analysis with Many Applications
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1
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Introduction
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1
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Introduction and Scope of the Thesis
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1
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Introduction to Mass Spectrometry-Based Proteomics
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1
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Protein Analysis by Shotgun Proteomics
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5
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A Brief History of Mass Spectrometry
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5
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Fundamentals
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9
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Basic Definitions
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13
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Instrumentation
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27
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State of the Art
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39
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Quantitative Proteomics for Analyses of Multiple Samples in Parallel with Chemical Perturbation
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45
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Experimental and Instrumental Setup
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53
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Advantages of Correlation Loadings for MVA of ToF-SIMS Data
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59
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LC-MS Spectra Processing
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67
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Chemoproteomic Analyses by Activity‐Based Protein Profiling
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73
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Required Number of Replicate Measurements - A Case Study
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79
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Isotopic Distributions
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89
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Selection of an Efficient Peak List in Root Cause Analysis
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101
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Activity‐Based Probes for Profiling Protein Activities
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115
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Retention Time Prediction and Protein Identification
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115
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Scaling, Normalization and Centering for MVA on Spectra
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127
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Chemical Probes for Proteins and Networks
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133
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Comparing Peptide Spectra Matches Across Search Engines
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145
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Calculation of False Discovery Rate for Peptide and Protein Identification
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147
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Presentation of PCA Results
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159
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Probing Biological Activities with Peptide and Peptidomimetic Biosensors
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161
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Methods and Algorithms for Quantitative Proteomics by Mass Spectrometry
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167
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MVA of Li-ion Battery Samples - A Case Study
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177
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Concluding Remarks and Future Perspectives
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181
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Hyphenated Techniques
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187
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Chemoselective Tagging to Promote Natural Product Discovery
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199
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Interpretation of Tandem Mass Spectra of Posttranslationally Modified Peptides
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207
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Identification and Quantification of Newly Synthesized Proteins Using Mass Spectrometry‐Based Chemical Proteomics
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217
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Mass Spectrometry Imaging
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231
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Solution to Dark Matter Identified by Mass-Tolerant Database Search
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231
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Tandem Mass Spectrometry
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231
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Tracing Endocytosis by Mass Spectrometry
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241
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Phosphoproteomics Profiling to Identify Altered Signaling Pathways and Kinase-Targeted Cancer Therapies
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257
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Functional Identification of Target by Expression Proteomics (<fc>FITExP</fc>)
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261
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Mass Spectrometry Applications
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265
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Mass Spectrometry-Based Characterization of Ub- and UbL-Modified Proteins
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267
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Target Discovery Using Thermal Proteome Profiling
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277
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Targeted Proteomics as a Tool for Quantifying Urine-Based Biomarkers
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293
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Chemical Strategies to Glycoprotein Analysis
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297
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Data Imputation in Merged Isobaric Labeling-Based Relative Quantification Datasets
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309
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Clustering Clinical Data in R
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317
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Proteomic Analysis of Protein–Lipid Modifications: Significance and Application
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345
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Review of Issues and Solutions to Data Analysis Reproducibility and Data Quality in Clinical Proteomics
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349
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Site‐Specific Characterization of <fc>Asp</fc>‐ and <fc>Glu</fc>‐<fc>ADP</fc>‐Ribosylation by Quantitative Mass Spectrometry
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363
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<fc>MS</fc>‐Based Hydroxyl Radical Footprinting: Methodology and Application of Fast Photochemical Oxidation of Proteins (<fc>FPOP</fc>)
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373
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Review of Batch Effects Prevention, Diagnostics, and Correction Approaches
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389
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Appendix
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389
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Using the Object-Oriented PowerShell for Simple Proteomics Data Analysis
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407
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Abbreviations