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Mass Spectrometry [2019]

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