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Analysis of Protein Post-Translational Modifications by Mass Spectrometry

PrefacePost-translational Modification of ProteinsGlobal versus Targeted Analysis StrategiesMass Spectrometric Analysis Methods for the Detection of PTMsData-Dependent and Data-Independent AnalysesTargeted AnalysesMultiple Reaction MonitoringMultiple Reaction Monitoring Initiated Detection and SequencingThe Importance of BioinformaticsReferencesIdentification and Analysis of Protein Phosphorylation by Mass SpectrometryIntroduction to Protein PhosphorylationAnalysis of Protein Phosphorylation by Mass SpectrometryGlobal Analysis of Protein Phosphorylation by Mass SpectrometrySample Preparation and Enrichment Strategies for Phosphoprotein Analysis by Mass SpectrometryMultidimensional Separations for Deep Coverage of the PhosphoproteomeComputational and Bioinformatics Tools for PhosphoproteomicsConcluding RemarksReferencesAnalysis of Protein Glycosylation by Mass SpectrometryIntroductionGeneral Structures of CarbohydratesProtein-Linked GlycansIsolation and Purification of GlycoproteinsLectin Affinity ChromatographyBoronate-Based CompoundsHydrazide EnrichmentTitanium Dioxide Enrichment of Sialylated GlycoproteinsMass Spectrometry of Intact GlycoproteinsSite AnalysisGlycan ReleaseUse of HydrazineUse of Reductive-EliminationUse of EnzymesAnalysis of Released GlycansCleanup of Glycan SamplesDerivatizationDerivatization at the Reducing TerminusDerivatization of Hydroxyl Groups: PermethylationLinkage AnalysisDerivatization of Sialic AcidsExoglycosidase DigestionsHPLC and ESIMass Spectrometry of GlycansAspects of Ionization for Mass Spectrometry Specific to the Analysis of GlycansElectron Impact (EI)Fast Atom Bombardment (FAB)Matrix-Assisted Laser Desorption/Ionization (MALDI)Electrospray Ionization (ESI)Glycan Composition by Mass SpectrometryFragmentationNomenclature of Fragment IonsIn-Source Decay (ISD) IonsPostsource Decay (PSD) IonsCollision-Induced Dissociation (CID)Electron Transfer Dissociation (ETD)Infrared Multiphoton Dissociation (IRMPD)MSnFragmentation Modes of Different Ion Types[M+H]+ Ions[M+Metal]+ Ions[M-H]- and [M+Anion]- IonsIon MobilityQuantitative MeasurementsComputer Interpretation of MS DataTotal Glycomics MethodsConclusionsAbbreviationsReferencesProtein Acetylation and MethylationOverview of Protein Acetylation and MethylationProtein AcetylationProtein MethylationFunctional AspectsMass Spectrometry AnalysisMass Spectrometry Behavior of Modified PeptidesMS Fragmentation ModesAcetylation- and Methylation-Specific Diagnostic Ions in MS AnalysisApplication of MS Methodologies for the Analysis of PTM StatusQuantification StrategiesSingle Reaction Monitoring/Multiple Reaction MonitoringParallel Reaction MonitoringData-Independent Acquisition MSIon Mobility MSUse of Stable Isotope-Labeled PrecursorsDynamics of Acetylation and MethylationStoichiometry of Acetylation and MethylationGlobal AnalysisTop-Down ProteomicsMiddle DownEnrichmentImmunoaffinity EnrichmentReader Domain-Based CaptureKac-Specific Capture ReagentsMethyl-Specific Capture ReagentsBiotin Switch-Based CaptureEnrichment of N-Terminally Acetylated PeptidesBioinformaticsAssigning Acetylation and Methylation StatusPTM Repositories and Data Mining ToolsComputational Prediction Tools for Acetylation and Methylation SitesInformation for Design of Follow-Up ExperimentsSummaryReferencesTyrosine NitrationOverview of Tyrosine NitrationMS Behavior of Nitrated PeptidesGlobal Analysis of Tyrosine NitrationEnrichment StrategiesConcluding RemarksAcknowledgementsAbbreviationsReferencesMass Spectrometry Methods for the Analysis of Isopeptides Generated from Mammalian Protein Ubiquitination and SUMOylationOverview of Ub and SUMOBiological Overview of Ubiquitin-Like ProteinsBiological Overview of Ub and SUMOBiological Functions of Ub and SUMOMass Spectrometry Behavior of IsopeptidesTerminology of a Ub/Ubl isopeptideMass Spectrometry Analysis of SUMO-Isopeptides Derived from Proteolytic DigestionAnalysis of SUMO-Isopeptides with Typical Full-Length Tryptic Iso-chainsAnalysis of SUMO-Isopeptides with Atypical Tryptic Iso-chains and Shorter Iso-chains Derived from Alternative Digestion StrategiesSUMO-Isopeptides with Atypical Iso-chains Generated from Tryptic DigestionDual Proteolytic Enzyme Digestion with Trypsin and ChymotrypsinProteolytic Enzyme and Chemical Digestion with Trypsin and AcidMS Analysis of Modified Ub- and SUMO-Isopeptides under CID ConditionsSPITC ModificationDimethyl Modificationm-TRAQ ModificationEnrichment and Global Analysis of IsopeptidesOverview of Enrichment ApproachesK-GG AntibodySUMOylation EnrichmentConcluding Remarks and RecommendationsReferencesThe Deimination of Arginine to CitrullineOverview of Arginine to Citrulline Conversion: Biological ImportanceMass Spectrometry-Based ProteomicsLiquid Chromatography and Mass Spectrometry Behavior of Citrullinated PeptidesGlobal Analysis of CitrullinationEnrichment StrategiesBioinformaticsConcluding RemarksReferencesGlycation of ProteinsOverview of Protein GlycationMass Spectrometry Behavior of Glycated PeptidesGlobal Analysis of GlycationEnrichment StrategiesBioinformaticsConcluding RemarksReferencesBiological Significance and Analysis of Tyrosine SulfationOverview of Protein SulfationMass Spectrometry Behavior of Sulfated PeptidesEnrichment Strategies and Global Analysis of SulfationSulfation Site PredictionsSummaryReferencesThe Application of Mass Spectrometry for the Characterization of Monoclonal Antibody-Based TherapeuticsIntroductionAntibody StructureN-Linked GlycosylationAntibody-Drug ConjugatesBiosimilarsMass Spectrometry Solutions to Characterizing Monoclonal AntibodiesHyphenated Mass Spectrometry (X-MS) Techniques to Study Glycosylation ProfilesHydrogen/Deuterium Exchange Mass Spectrometry (HDX-MS) to Characterize Monoclonal Antibody StructureNative Mass Spectrometry and the Use of IM-MS to Probe Monoclonal Antibody StructureAdvanced ApplicationsQuantifying GlycosylationAntibody-Drug ConjugatesBiosimilar CharacterizationConcluding RemarksReferences

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