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  • 1
    Keywords: Life sciences ; Mass spectrometry ; Biochemistry ; Life sciences ; Protein Science ; Mass spectrometry ; Springer eBooks
    Description / Table of Contents: Introduction to Mass Spectrometry-Based Proteomics -- LC-MS Spectra Processing -- Isotopic Distributions -- Retention Time Prediction and Protein Identification -- Algorithms for Database Dependent Search of MSMS Data -- Interpretation of Tandem Mass Spectra of Post-Translationally Modified Peptides -- Improving Peptide Identification Using Empirical Scoring Systems -- Methods and Algorithms for Quantitative Proteomics by Mass Spectrometry -- Computational Approaches to Selected Reaction Monitoring (SRM) Assay Design -- Feature Selection and Machine Learning with Mass Spectrometry Data -- Considerations in the Analysis of Hydrogen Exchange Mass Spectrometry Data -- Permethylated N-Glycan Analysis with Mass Spectrometry -- Mass Spectrometry Methods for Studying Glycosylation in Cancer -- Proteomics Data Exchange and Storage: The Need for Common Standards and Public Repositories -- Tools for Protein Post Translational Modifications Analysis: FAK, A Case Study -- Proteomic Strategies to Characterize Signaling Pathways -- Simple Proteomics Data Analysis in the Object-Oriented PowerShell
    Abstract: Since the publishing of the first edition, the methodologies and instrumentation involved in the field of mass spectrometry-based proteomics has improved considerably.℗ Fully revised and expanded, Mass Spectrometry Data Analysis in Proteomics, Second Edition presents expert chapters on specific MS-based methods or data analysis strategies in proteomics. The volume covers data analysis topics relevant for quantitative proteomics, post translational modification, HX-MS, glycomics, and data exchange standards, among other topics.℗ Written in the highly successful Methods in Molecular Biology series format, chapters include brief introductions to their respective subjects, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. ℗ Updated and authoritative, Mass Spectrometry Data Analysis in Proteomics, Second Edition serves as a detailed guide for all researchers seeking to further our knowledge in the field of proteomics
    Pages: X, 405 p. 93 illus., 59 illus. in color. : digital.
    Edition: 2nd ed. 2013.
    ISBN: 9781627033923
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  • 2
    Keywords: Life sciences ; Plant science ; Botany ; Life sciences ; Plant Sciences ; Springer eBooks
    Description / Table of Contents: Approaches to Determine Protein Ubiquitination Residue Types -- Immunoprecipitation of Cullin Ring Ligases (CRLs) in Arabidopsis Thaliana Seedlings -- Radioligand Binding Assays for Determining Dissociation Constants of Phytohormone Receptors -- Measuring the Enzyme Activity of Arabidopsis Deubiquitylating Enzymes -- Fluorescent Reporters for Ubiquitin-Dependent Proteolysis in Plants -- Generation of Artificial N-end Rule Substrate Proteins In Vivo and In Vitro -- Peptide Arrays for Binding Studies of E3 Ubiquitin Ligases -- SUMO Chain Formation by Plants Enzymes -- Kinetic Analysis of Plant SUMO Conjugation Machinery -- Expression, Purification, and Enzymatic Analysis Of Plant SUMO Proteases -- Quantitative Analysis of Subcellular Distribution of the SUMO Conjugation System by Confocal Microscopy Imaging -- Biochemical Analysis of Autophagy in Algae and Plants by Monitoring the Electrophoretic Mobility of ATG8 -- Detection of Autophagy in Plants by Fluorescence Microscopy -- Protocols for Studying Protein Stability in a Arabidopsis Protoplast Transient Expression System -- Detection and Quantification of Protein Aggregates in Plants -- Determination of Protein Carbonylation and Proteasome Activity in Seeds -- Isobaric Tag for Relative and Absolute Quantitation (iTRAQ)-based Protein Profiling in Plants.-Use of a Phosphatidylinositol phosphate Affinity Chromatography (PIP - chromatography) for the Isolation of Proteins Involved in Protein Quality Control and Proteostasis Mechanisms in Plants -- In vivo Radiolabeling of Arabidopsis Leaves and Separation of Thylakoid Membrane Complexes by Blue Native PAGE -- Normalized Quantitative Western Blotting Based on Standardized Fluorescent Labeling -- Sequence Search and Comparative Genomic Analysis of SUMO-Activating Enzymes using CoGe -- Studying Evolutionary Dynamics of Gene Families Encoding SUMO-Activating Enzymes with SeaView and ProtTest -- Bioinformatics Tools for Exploring the SUMO Gene Network
    Abstract: This volume is a collection of detailed protocols describing state-of-art approaches that will facilitate the understanding of protein homeostasis in plant stress responses and development. Plant Proteostasis: Methods and Protocols is broken into four parts focusing on the study of ubiquitin-dependent post-translational modifications, protocols focused on Ubl post-translational modifications, protein homeostasis, and protocols for the in silico analysis. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Plant Proteostasis: Methods and Protocols aims to address next challenges in agriculture such as precision horticulture
    Pages: XI, 307 p. 73 illus., 40 illus. in color. : online resource.
    ISBN: 9781493937592
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  • 3
    Keywords: Mass spectrometry ; Proteomics ; Mass spectrometry ; Proteomics ; Springer eBooks
    Description / Table of Contents: Introduction to Mass Spectrometry-based Proteomics -- LC-MS Spectra Processing -- Isotopic Distributions -- Retention Time Prediction and Protein Identification -- Comparing Peptide Spectra Matches Across Search Engines -- Calculation of False Discovery Rate for Peptide and Protein Identification -- Methods and Algorithms for Quantitative Proteomics by Mass Spectrometry -- Interpretation of Tandem Mass Spectra of Posttranslationally Modified Peptides -- Solution to Dark Matter Identified by Mass-tolerant Database Search -- Phosphoproteomics Profiling to Identify Altered Signaling Pathways and Kinase-targeted Cancer Therapies -- Mass Spectrometry Based Characterization of Ub- and UbL-modified Proteins -- Targeted Proteomics as a Tool for Quantifying Urine-based Biomarkers -- Data Imputation in Merged Isobaric Labelling-based Relative Quantification Datasets -- Clustering Clinical Data in R -- Review of Issues and Solutions to Data Analysis Reproducibility and Data Quality in Clinical Proteomics -- Review of Batch Effects Prevention, Diagnostics, and Correction Approaches -- Using the Object-oriented PowerShell for Simple Proteomics Data Analysis -- Considerations in the Analysis of Hydrogen Exchange Mass Spectrometry Data
    Abstract: The aim of this new edition is to provide detailed information on each topic and present novel ideas and views that can influence future developments in mass spectrometry-based proteomics. In contrast to the previous editions, this third edition aims to provide the most relevant computational methods, focusing on computational concepts. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Mass Spectrometry Data Analysis in Proteomics, Third Edition to ensure successful results in the further study of this vital field
    Pages: X, 445 p. 136 illus., 94 illus. in color. : online resource.
    Edition: 3rd ed. 2020.
    ISBN: 9781493997442
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  • 4
    Keywords: Life sciences ; Proteins ; Life sciences ; Protein Science ; Springer eBooks
    Description / Table of Contents: UPS Activation in the Battle against Aging and Aggregation-Related Diseases: An Extended Review -- Review And Literature Mining On Proteostasis Factors’ And Cancer -- Combining Zebrafish and Mouse Models to Test the Function of Deubiquitinating Enzyme (Dubs) Genes in Development: Role Of Usp45 in the Retina -- Immunodepletion and Immunopurification as Approaches for CSN Research -- Studying Protein Ubiquitylation in Yeast -- Strategies to Detect Endogenous Ubiquitination of a Target Mammalian Protein -- In Vitro Ubiquitination – Self-Ubiquitination, Chain Formation, and Substrate Ubiquitination Assays -- Isolation of the Ubiquitin-Proteome From Tumour Cell Lines and Primary Cells Using Tubes -- Tubes-Mass Spectrometry for Identification and Analysis of the Ubiquitin-Proteome -- Isolation of Ubiquitinated Proteins to High Purity from In Vivo Samples -- Method for the Purification of Endogenous Unanchored Polyubiquitin Chains -- Fluorescent Tools for In Vivo Studies on the Ubiquitin-Proteasome System -- Bimolecular Fluorescence Complementation to Assay the Interactions of Ubiquitylation Enzymes in Living Yeast Cells -- Monitoring Ubiquitin-Coated Bacteria Via Confocal Microscopy -- Detection and Analysis of Cell Cycle-Associated Apc/C-Mediated Cellular Ubiquitylation In Vitro and In Vivo -- Detection and Analysis Of Sumoylation Substrates In Vitro and In Vivo. - Detection of Protein-Protein Interactions and Post-Translational Modifications using the Proximity Ligation Assay: Application to the Study of the Sumo Pathway -- Dissecting of Sumo Dynamics by Mass Spectrometry -- Isolation of Lysosomes from Mammalian Tissues and Cultured Cells -- Analysis Of Relevant Parameters For Autophagic Flux Using Hela Cells Expressing Egfp-Lc3 -- Analysis of Protein Oligomeric Species by Sucrose Gradients -- Analysis of Protein Oligomerization by Electrophoresis.-Blot-Ms of Carbonylated Proteins: A Tool to Identify Oxidized Proteins -- Quantitation of Protein Translation Rate In Vivo with Bioorthogonal Click-Chemistry -- A Simple Protocol for High Efficiency Protein Isolation after RNA Isolation from Mouse Thyroid and Other Very Small Tissue Samples -- Monitoring Target Engagement Of Deubiquitylating Enzymes Using Activity Probes: Past, Present, and Future -- Activity Based Profiling of Deubiquitylating Enzymes and Inhibitors in Animal Tissues -- High-Throughput Sirna Screening Applied to the Ubiquitin-Proteasome System -- High-Throughput Yeast-Based Reporter Assay to Identify Compounds with Anti-Inflammatory Potential -- Using Alphascreen ® to Identify Small Molecule Inhibitors Targeting a Conserved Host-Pathogen Interaction -- Global MS-Based Proteomics Drug Profiling
    Abstract: This volume highlights the role of proteostasis in human health and associated disease model systems, reflecting its rising importance which has led to the development of new technologies to obtain insight into underling protein mechanistic events. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Proteostasis: Methods and Protocols aims to become a reference book on proteostasis in human health
    Pages: XVI, 488 p. 94 illus., 60 illus. in color. : online resource.
    ISBN: 9781493937561
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