Cover image for Protein Phosphorylation Analysis by Electrospray Mass Spectrometry : A guide to concepts and practice.
Protein Phosphorylation Analysis by Electrospray Mass Spectrometry : A guide to concepts and practice.
Title:
Protein Phosphorylation Analysis by Electrospray Mass Spectrometry : A guide to concepts and practice.
Author:
Lehmann, Wolf D.
ISBN:
9781849732208
Personal Author:
Edition:
1st ed.
Physical Description:
1 online resource (395 pages)
Contents:
Protein Phosphorylation Analysis by Electrospray Mass Spectrometry -- Contents -- Acknowledgements -- Chapter 1 Introduction -- 1.1 The Rise of Protein Phosphorylation in the Life Sciences -- 1.1.1 Reversible Covalent Protein Modification -- 1.1.2 The Phosphorus Content of a Cell -- 1.1.3 Nutritional Proteins Recognized as Phosphoproteins -- 1.1.4 Protein Phosphorylation Controls Metabolic Enzymes -- 1.1.5 Protein Kinase Cascades as Principle of Cellular Signal Transduction -- 1.1.6 Structural Consequences of Protein Phosphorylation -- 1.1.7 Dysregulation of Protein Kinases can Cause Cancer -- 1.1.8 Protein Kinase Inhibitors as Anticancer Drugs -- 1.2 The Rise of Mass Spectrometry in the Life Sciences -- 1.2.1 The Start-Electron Impact Ionization -- 1.2.2 The Intricate Ways towards Soft Ionisation Methods -- 1.2.3 Ionizing Analytes from the Liquid Phase -- 1.2.4 Ionizing Analytes from the Solid Phase -- 1.2.5 The Glamour of Large Ions -- 1.2.6 The Rise of Tandem Mass Spectrometry - Back to Small Ions -- 1.2.7 Element Mass Spectrometry -- 1.2.8 Mass Spectrometry and Bioinformatics -- References -- Chapter 2 Analysis of Phosphopeptides by Mass Spectrometry -- 2.1 Mass Analyzers, MS/MS Instrumentation and Scan Modes -- 2.1.1 Introduction -- 2.1.2 Mass Analyzers -- 2.1.3 Tandem Mass Spectrometers Overview -- 2.1.4 Triple Quadrupole -- 2.1.5 Ion Traps -- 2.1.6 Q-TOF -- 2.1.7 Q-Trap -- 2.1.8 LTQ-FTICR and LTQ-Orbitrap -- 2.2 LC-MS/MS Scan Modes for Phosphopeptide Detection -- 2.2.1 Product Ion Scans - Top X Method -- 2.2.2 LC-ESI-MS/MS with Exclusion/Inclusion Lists -- 2.2.3 LC-MSE -- 2.2.4 Precursor Ion Scanning -- 2.2.5 Ion Trap Neutral Loss-triggered MS3 -- 2.3 ESI MS and MS/MS of Peptides -- 2.3.1 Peptide Sequencing by Mass Spectrometry -- 2.3.2 The Mobile Proton Model -- 2.3.3 Nomenclature of Peptide Fragment Ions.

2.3.4 Mass Values of Amino Acid Building Blocks -- 2.3.5 y Ions -- 2.3.6 b Ions -- 2.3.7 Immonium Ions -- 2.3.8 Neutral Loss Fragmentations of Protonated Peptides -- 2.4 ESIMS and MS/MS of Phosphopeptides, Positive Ions -- 2.4.1 General -- 2.4.2 Electrospray Ionization Efficiency of Phosphopeptides -- 2.4.3 ESI-MS/MS of pSer/pThr Phosphopeptides, Positive Ions -- 2.4.4 Pinpointing of Phosphorylation Sites -- 2.4.5 MS3 of pSer/pThr Phosphopeptides -- 2.4.6 Phosphopeptides with Competing Neutral Losses -- 2.4.7 Peptides with Multiple pSer/pThr Sites -- 2.4.8 Mechanism of H3PO4 Loss from pSer/pThr Phosphopeptides -- 2.4.9 MS/MS of pTyr Phosphopeptides -- 2.4.10 Phosphohistidine -- 2.4.11 Accurate Mass-Based Recognition of Phosphopeptides -- 2.5 Negative Ion ESI MS and MS/MS of Phosphopeptides -- 2.5.1 NanoESI Precursor Ion Scanning -- 2.5.2 Marker Ion Information and LC-MS -- 2.5.3 High Mass Marker Fragments of Phosphopeptides -- 2.5.4 Phosphate Group Shift in Monoanions of pTyr Peptides -- 2.6 Electron Capture Dissociation and Electron Transfer Dissociation of Phosphopeptides -- 2.6.1 Principles of ECD and ETD -- 2.6.2 ECD and ETD in Proteomic Studies -- 2.6.3 ECD and ETD in Analysis of Phosphopeptides -- 2.6.4 ETD combined with CID for Phosphopeptide Analysis -- 2.7 LC-MS of Peptides -- 2.7.1 Instrumental Basis -- 2.7.2 Reversed Phase LC of Peptides -- 2.7.3 Proteotypic Peptides -- 2.7.4 LC-MS/MS Work Flow -- 2.7.5 Prediction of Peptide LC Retention Times -- 2.7.6 Details of Peptide Separation in Reversed Phase LC -- 2.8 LC-MS of Phosphopeptides -- 2.8.1 Challenges of LC-ESI-MS of Phosphopeptides -- 2.8.2 β-Casein Digest as Model Analyte -- 2.8.3 Metal Ion Chelators as Sample Additives -- 2.8.4 LC Retention Times of Peptide/Monophosphopeptide Pairs -- 2.9 Terms and Abbreviations for MS/MS Analyses -- References -- Chapter 3 Phosphopeptide Enrichment.

3.1 Introduction -- 3.2 Enrichment of Phosphopeptides by IMAC -- 3.2.1 IMAC Mechanism -- 3.2.2 IMAC Protocols -- 3.2.3 Sequential IMAC (SIMAC) -- 3.2.4 IMAC Side Reactions -- 3.2.5 Methyl Esterification and IMAC -- 3.2.6 Metal Ion Elution from IMAC Columns -- 3.3 Enrichment of Phosphopeptides by Metal Oxides -- 3.4 Enrichment of Phosphopeptides based on pKa or pI -- 3.4.1 General -- 3.4.2 Ion Exchange Chromatography -- 3.4.3 Isoelectric Focusing -- 3.5 Other Phosphopeptide Enrichment Methods -- 3.5.1 Immunoaffinity Enrichment -- 3.5.2 Covalent Phosphopeptide Capture -- 3.5.3 HILIC and ERLIC -- 3.5.4 Coated Magnetic Beads -- 3.5.5 Coprecipitation with Alkaline Earth Ions -- 3.5.6 Intact Phosphoproteins and Metal Oxides/Hydroxides -- 3.5.7 Gel-immobilzed Phosphoprotein Ligands -- 3.6 Combination of Enrichment Methods -- 3.6.1 Comparison of PAC, IMAC, and TiO2 -- 3.6.2 Combination of Calcium Phosphate Coprecipitation with two-step IMAC -- 3.6.3 SIMAC -- 3.6.4 Combination of SCX with IMAC or TiO2 -- References -- Chapter 4 Dephosphorylation -- 4.1 Introduction -- 4.2 Enzymatic Dephosphorylation -- 4.3 Base-catalyzed Dephosphorylation-β-Elimination of H3PO4 from pS/pT -- 4.4 HF Catalyzed Dephosphorylation -- 4.5 Analytical Work Flows with Integrated Dephosphorylation Step -- 4.5.1 β-Elimination and Phosphorylation Site Pinpointing -- 4.5.2 β-Elimination and Phosphoprotein Enrichment -- 4.5.3 In-gel Peptide/Protein Dephosphorylation -- 4.5.4 LC-ESI-MS/MS and Dephosphorylation -- References -- Chapter 5 Protein Phosphorylation and Element Mass Spectrometry -- 5.1 Introduction -- 5.2 Technical Details -- 5.2.1 P and S detection by ICP-MS -- 5.2.2 microLC-ICP-MS -- 5.3 Phosphoprotein Digests -- 5.4 Quantitative Determination of the P/S Ratio -- 5.4.1 μLC-ICP-MS -- 5.4.2 Laser Ablation ICP-MS and P/S Ratio Detection -- 5.5 Preparation of Peptide Standards.

5.6 Preparation of Protein Standards -- References -- Chapter 6 Structural Phosphorylation Analysis -- 6.1 Introduction -- 6.1.1 Protein Phosphorylation at Ser, Thr, and Tyr -- 6.1.2 Intrinsically Disordered Protein Regions and Phosphorylation -- 6.2 NanoESI-MS -- 6.2.1 nanoESI-MS/MS of Phosphoprotein Digests -- 6.2.2 NanoESI and Neutral Loss of H3PO4 -- 6.2.3 NanoESI and Data-Directed MS/MS Analysis -- 6.2.4 NanoESI-MS and QTOF Precursor Ion Scanning -- 6.2.5 NanoESI-MS/MS and Targeted Analysis of pTyr Sites -- 6.2.6 Positive Ion nanoESI and Precursor Ion Scanning -- 6.2.7 Negative Ion nanoESI and Precursor Ion Scanning -- 6.3 Structural Phosphoprotein Analysis by LC-ESI-MS/MS -- 6.3.1 Introduction -- 6.3.2 Use of Multiple Proteases -- 6.3.3 Multi-method Phosphopeptide Enrichment -- 6.3.4 Metal Ion-Mobilizing LC -- 6.3.5 Phosphopeptide-targeted MS/MS -- 6.3.6 Phosphopeptide-dedicated Search Tools -- 6.3.7 Manual Control of Automated Phosphopeptide Annotation -- 6.3.8 Isotopic Patterns of Peptide/Phosphopeptide Pairs -- 6.3.9 Cooperativity of Phosphorylation Events -- 6.4 Structural Phosphoproteome Analysis and Databases -- 6.4.1 Introduction -- 6.4.2 Methods for Structural Phosphoproteomic Analysis -- 6.4.3 Bacterial Phosphoproteome Databases -- 6.4.4 Eukaryotic Phosphoproteome Databases -- References -- Chapter 7 Quantitative Protein Phosphorylation Analysis -- 7.1 General -- 7.2 Label-free Methods -- 7.3 Isotope Dilution Methods -- 7.3.1 Accuracy of Peptide Isotopic Pattern Measurements -- 7.3.2 Chemical Labelling of Analytes -- 7.3.3 Enzymatic Labelling of Analytes -- 7.3.4 Metabolic Labelling of Analytes -- 7.3.5 Labelled Peptide Standards -- 7.3.6 Labelled Protein Standards -- 7.4 Phosphorylation Degree Analysis by ESI-MS -- 7.4.1 General -- 7.4.2 Bottom-up Approach -- 7.4.3 Relative Ionization Efficiency of Peptide/Phosphopeptides.

7.4.4 Use of Correction Factors -- 7.4.5 Standard-free Method -- 7.4.6 Differential Labelling and Dephosphorylation -- 7.4.7 Separate Peptide and Phosphopeptide Standards -- 7.4.8 One-Source Peptide/Phosphopeptide Standards -- 7.4.9 Phosphopeptides with Multiple Modifications -- 7.5 Top-down Approach -- 7.5.1 Overview -- 7.5.2 FLEXIQuant Protein -- 7.5.3 RISQ Protein -- 7.5.4 Separation of Phosphoprotein Isoforms -- 7.5.5 Summary Phosphorylation Degree Analysis -- 7.6 Quantitative and Dynamic Phosphoproteomics -- 7.6.1 Introduction -- 7.6.2 Tyrosine Phosphorylation Analysis and EGFR Signaling -- 7.6.3 Tyrosine Kinase Inhibition and Tyrosine Labelling -- 7.6.4 Comprehensive Testing of Protein Kinase Inhibitors -- 7.6.5 Multiplexed in vitro Kinase Activity Testing -- 7.6.6 In vivo Phosphoproteome Analysis and EGFR stimulation -- 7.6.7 The Spindle Phosphoproteome during Mitosis -- References -- Outlook -- Subject Index.
Abstract:
This unique book describes the concepts and practice of protein phosphorylation analysis by tandem mass spectrometry and related techniques.
Local Note:
Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, 2017. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries.
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