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E-grāmata: Proteomics in Systems Biology: Methods and Protocols

  • Formāts: PDF+DRM
  • Sērija : Methods in Molecular Biology 2456
  • Izdošanas datums: 25-May-2022
  • Izdevniecība: Springer-Verlag New York Inc.
  • Valoda: eng
  • ISBN-13: 9781071621240
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  • Formāts: PDF+DRM
  • Sērija : Methods in Molecular Biology 2456
  • Izdošanas datums: 25-May-2022
  • Izdevniecība: Springer-Verlag New York Inc.
  • Valoda: eng
  • ISBN-13: 9781071621240
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This detailed book highlights the diverse techniques and applications of proteomics in an accessible, informative, and concise manner. The collection features sample preparation from distinct extraction, quantification, enrichment, modification, as well as interactome methodology for the in-depth exploration of biological systems, and the application of proteomics to clinical, infectious disease, and agricultural practices. Moreover, cutting-edge bioinformatics tools, encompassing machine learning and data integration strategies, are explored, as are techniques expanding beyond proteomics into the realm of metabolomics. Written for the highly successful Methods in Molecular Biology series, 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 known pitfalls. 

Comprehensive and practical, Proteomics in Systems Biology: Methods and Protocols emphasizes the importance of proteomics and demonstrates a plethora of approaches for investigating diverse biological entities from a systems perspective.
Preface v
Contributors ix
1 Review of the Real and Sometimes Hidden Costs in Proteomics Experimental Workflows
1(14)
Aicha Asma Houfani
Leonard James Foster
2 High-Throughput Mass Spectrometry-Based Proteomics with dia-PASEF
15(14)
Patricia Skowronek
Florian Meier
3 Isolation of Detergent Insoluble Proteins from Mouse Brain Tissue or Quantitative Analysis Using Data Independent Acquisition (DIA)
29(24)
Cristen Molzahn
Lorenz Nierves
Philipp F. Lange
Thibault Mayor
4 Rodent Lung Tissue Sample Preparation and Processing for Shotgun Proteomics
53(10)
Hadeesha Piyadasa
Ying Lao
Oleg Krokhin
Neeloffer Mookherjee
5 Protein Purification and Digestion Methods for Bacterial Proteomic Analyses
63(8)
Nicole Hansmeier
Samrachana Sharma
Tzu-Chiao Chao
6 Mapping Cell Surface Proteolysis with Plasma Membrane-Targeted Subtiligase
71(14)
Aspasia A. Amiridis
Amy M. Weeks
7 N-Terminomics/TAILS of Tissue and Liquid Biopsies
85(10)
Anthonia Anowai
Sameeksha Chopra
Barbara Mainoli
Daniel Young
Antoine Dufour
8 HUNTER: Sensitive Automated Characterization of Proteolytic Systems by N Termini Enrichment from Microscale Specimen
95(28)
Anuli C. Uzozie
Janice Tsui
Philipp F. Lange
9 Phosphoproteomics and Organelle Proteomics in Pancreatic Islets
123(18)
Oziim Sehnaz Caliskan
Giorgia Massacci
Natalie Krahmer
Francesca Sacco
10 Phosphoproteomic Sample Preparation for Global Phosphorylation Profiling of a Fungal Pathogen
141(12)
Brianna Ball
Jonathan R. Krieger
Jennifer Geddes-McAlister
11 Glycopeptide-Centric Approaches for the Characterization of Microbial Glycoproteomes
153(20)
Nichollas E. Scott
12 Integrated Network Discovery Using Multi-Proteomic Data
173(12)
Rafe Helwer
Vincent C. Chen
13 Targeted Cross-Linking Mass Spectrometry on Single-Step Affinity Purified Molecular Complexes in the Yeast Saccharomyces cerevisiae
185(26)
Christian Trahan
Marlene Oeffinger
14 A Crosslinking Mass Spectrometry Protocol for the Structural Analysis of Microtubule-Associated Proteins
211(12)
Atefeh Rafiei
David C. Schriemer
15 Comprehensive Interactome Mapping of Nuclear Receptors Using Proximity Biotinylation
223(18)
Lynda Agbo
Sophie Anne Blanchet
Pata-Eting Kougnassoukou Tchara
Amelie Fradet-Turcotte
Jean-Philippe Lambert
16 Mining Proteomics Datasets to Uncover Functional Pseudogenes
241(12)
Anna Meller
Francois-Michel Boisvert
17 Proteomic Profiling of the Interplay Between a Bacterial Pathogen and Host Uncovers Novel Anti-Virulence Strategies
253(10)
Arjun Sukumaran
Jennifer Geddes-McAlister
18 Affinity Enrichment of Salmonella-Modified Membranes from Murine Macrophages for Proteomic Analyses
263(12)
Tzu-Chiao Chao
Samina Thapa
Nicole Hansmeier
19 Proteomic Profiling of Interplay Between Agrobacterium tumefaciens and Nicotiana benthamiana for Improved Molecular Pharming Outcomes
275(12)
Nicholas Prudhomme
Jonathan R. Krieger
Michael D. McLean
Doug Cossar
Jennifer Geddes-McAlister
20 Label-Free Quantitative Proteomic Profiling of Fusarium Head Blight in Wheat
287(12)
Boyan Liu
Danisha Johal
Mitra Serajazari
Jennifer Geddes-McAlister
21 DIA Proteomics and Machine Learning for the Fast Identification of Bacterial Species in Biological Samples
299(20)
Florence Roux-Dalvai
Michael Leclercq
Clarisse Gotti
Arnaud Droit
22 Novel Bioinformatics Strategies Driving Dynamic Metaproteomic Studies
319(20)
Caitlin M. A. Simopoulos
Daniel Figeys
Mathieu Lavallee-Adam
23 MaxQuant Module for the Identification of Genomic Variants Propagated into Peptides
339(10)
Pavel Sinitcyn
Maximilian Gerwien
Jurgen Cox
24 Untargeted Metabolomic Profiling of Fungal Species Populations
349(18)
Thomas E. Witte
David P. Overy
Index 367