LC-MS/MS in Proteomics

In this cutting-edge book, experts in the field provide protocols and up-to-date reviews of the applications of LC-MS/MS. There is particular focus on MS-based methods of protein and peptide quantification and the analysis of post-translational modifications.

With the development of new quantitative strategies and powerful bioinformatics tools to cope with the analysis of the large amounts of data generated in proteomics experiments, liquid chromatography with tandem mass spectrometry (LC-MS/MS) is making possible the analysis of proteins on a global scale, meaning that proteomics can now start competing with cDNA microarrays for the analysis of whole genomes. In LC-MS/MS in Proteomics: Methods and Applications, experts in the field provide protocols and up-to-date reviews of the applications of LC-MS/MS, with a particular focus on MS-based methods of protein and peptide quantification and the analysis of post-translational modifications. Beginning with overviews of the use of LC-M/MS in protein analysis, the book continues with topics such as protocols for the analysis of post-translational modifications, with particular focus on phosphorylation and glycosylation, popular techniques for quantitative proteomics, such as multiple reaction monitoring, metabolic labelling, and chemical tagging, biomarker discovery in biological fluids, as well as novel applications of LC-MS/MS. Written in the highly successful Methods in Molecular Biology™ series format, chapters include introductions to their respective subjects, lists of necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Comprehensive and cutting-edge, LC-MS/MS in Proteomics: Methods and Applications presents the techniques and concepts necessary in order to aid proteomic practitioners in the application of LC-MS/MS to essentially any biological problem.

Examines current LC-MS technologies, instrumentation, applications, and analysis solutions used in quantitative proteomics Details protocols for isobaric tagging, in vivo stable isotopic labelling, label-free quantification, and multiple reaction monitoring Covers the analysis of protein post-translational modifications, protein complexes, organelles, and kinase activities Includes supplementary material: sn.pub/extras

Inhalt
Overviews of Techniques and Approaches in LC-MS-Based Proteomics.- Approaches and Applications of Quantitative LC-MS for Proteomics and Activitomics.- Overview of Quantitative LC-MS Techniques for Proteomics and Activitomics.- Instrumentation for LC-MS/MS in Proteomics.- Bioinformatics for LC-MS/MS-Based Proteomics.- Analysis of Post-translational Modifications by LC-MS/MS.- Structural Analysis of Post-Translational Modifications.- In-Depth Analysis of Protein Phosphorylation by Multidimensional Ion Exchange Chromatography and Mass Spectrometry.- Mapping of Phosphorylation Sites by LC-MS/MS.- Analysis of Carbohydrates on Proteins by Offline Normal-Phase Liquid Chromatography MALDI-TOF/TOF-MS/MS.- Techniques for Quantitative LC-MS.- Selected Reaction Monitoring Applied to Quantitative Proteomics.- Basic Design of MRM Assays for Peptide Quantification.- Proteome-Wide Quantitation by SILAC.- Quantification of Proteins by iTRAQ.- Quantification of Proteins by Label-Free LC-MS/MS.- Analysis of Protein Complexes and Organelles.- Protocol for Quantitative Proteomics of Cellular Membranes and Membrane Rafts.- Organelle Proteomics by Label-Free and SILAC-Based Protein Correlation Profiling.- Mapping ProteinProtein Interactions by Quantitative Proteomics.- Analysis of Biological Fluids and Clinical Samples.- Analysis of Serum Proteins by LC-MS/MS.- Urinary Proteome Profiling Using 2D-DIGE and LC-MS/MS.- Analysis of Peptides in Biological Fluids by LC-MS/MS.- Novel Applications of LC-MS.- Quantification of Protein Kinase Activities by LC-MS.- A Protocol for Top-Down Proteomics Using HPLC and ETD/PTR-MS.