Proteomics in Systems Biology, Softcover reprint of the original 1st ed. 2016
Methods and Protocols
Methods in Molecular Biology Series, Vol. 1394

Language: English

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Proteomics in Systems Biology
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313 p. · 17.8x25.4 cm · Paperback

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Proteomics in Systems Biology
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This volume presents an overview of contemporary quantitative proteomics methods along with instructions on data interpretation, while providing examples on how to implement proteomics into systems biology. 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.

Thorough and practical, Proteomics in Systems Biology: Methods and Protocols is a valuable resource for researchers who are interested in using proteomics techniques to help answer biological and medical questions.

1. Multiplexed Quantitative Proteomics for High-Throughput Comprehensive Proteome Comparisons of Human Cell Lines
Amanda Edwards and Wilhelm Haas

2. Sample Preparation Approaches for iTRAQ Labelling and Quantitative Proteomic Analyses in Systems Biology
Christos Spanos and J. Bernadette Moore

3. Two Birds with One Stone: Parallel Quantification of Proteome and Phospho-Proteome Using iTRAQ
Fiorella A. Solari, Laxmikanth Kollipara, Albert Sickmann, and René P. Zahedi

4. Selected Reaction Monitoring to Measure Proteins of Interest in Complex Samples: A Practical Guide
Yuehan Feng and Paola Picotti

5. Monitoring PPARG Induced Changes in Glycolysis by Selected Reaction Monitoring Mass Spectrometry
Andreas Hentschel and Robert Ahrends

6. A Targeted MRM Approach for Tempo-Spatial Proteomics Analyses
Annie Moradian, Tanya R. Porras-Yakushi, Michael J. Sweredoski, and Sonja Hess

7.. Targeted Phospho-Proteome Analysis Using Selected/Mul
tiple Reaction Monitoring (SRM/MRM)
Jun Adachi, Ryohei Narumi, and Takeshi Tomonaga

8. Testing Suitability of Cell Cultures for SILAC-Experiments Us
ing SWATH-Mass Spectrometry
Yvonne Reinders, Daniel Völler, Anja-K. Bosserhoff, Peter J. Oefner, and Joerg Reinders

9. Combining Amine-Reactive Cross-Linkers and Photo-Reactive Amino Acids for 3D-Structure Analysis of Proteins and Protein Complexes
Philip L
össl and Andrea Sinz

10. Tissue MALDI Mass Spectrometry Imaging (MALDI MSI) of Peptides
Birte Beine, Hanna C. Diehl, Helmut E. Meyer, and Corinna Henkel

11. Ethyl Esterification for MALDI-MS Analysis of Protein Glycosylation
Karli R. Reiding, Emanuela Lonardi, Agnes L. Hipgrave Ederveen, and Manfred Wuhrer

12. Characterization of Protein N-Glycosylation by Analysis of ZIC-HILIC-Enriched Intact Proteolytic Glycopeptides
Gottfried Pohlentz, Kristina Marx, and Michael Mormann

13. Simple and Effective Affinity Purification Procedures for Mass Spectrometry-Based Identification of Protein-Protein Interactions in Cell Signaling Pathways
Julian H. M. Kwan and Andrea Emili

14. A Systems Approach to Understand Antigen Presentation and the Immune Response
Nadine L. Dudek, Nathan P. Croft, Ralf B. Schittenhelm, Sri H. Ramarathinam, and Anthony W. Purcell
15. Profiling of Small Molecules by Chemical Proteomics
Kilian HUber and Giulio Superti-Furga

16. Generating Sample Specific Databases for Mass Spectrometry Based Proteomic Analysis by Using RNA Sequencing
Toni Luge and Sascha Sauer

17. A Proteomic Workflow Using High Throughout De Novo Sequencing towards Complementation of Genome Information for Improved Comparative Crop Science
Reinhard Turetschek, David Lyon, Getinet Desalegn, Hans-Peter Kaul, and Stefanie Wienkoop

18. From Phospho-Proteome to Modelling of Plant Signalling Pathways
Maksim Zakhartsev, Heidi Pertl-Obermeyer, and Waltraud X. Schulze

19. Interpretation of Quantitative Shotgun Proteomic Data
Elise Aasebø, Frode S. Berven, Frode Selheim, Harald Barsnes, and Marc Vaudel

20. A Simple Workflow for Large Scale Shotgun Glycoproteomics
Astrid Guldbrandsen, Harald Barsnes, Ann Cathrine Kroksveen, Frode A. Berven, and Marc Vaudel

21. Systemic Analysis of Regulated Functional Networks
Luis Francisco Hern
ández Sánchez, Elise Aasebø, Frode Selheim, Frode S. Berven, Helge Ræder, Harald Barsnes, and Marc Vaudel
Dr. Joerg Reinders Institute of Functional Genomics University Regensburg Joseph-Engert-Strasse 9 93053 Regensburg Germany Phone: +49 941 943 5004 Fax: +49 941 943 5019 E-Mail: joerg.reinders@klinik.uni-regensburg.de

Includes cutting-edge methods and protocols

Provides step-by-step detail essential for reproducible results

Contains key notes and implementation advice from the experts

Includes supplementary material: sn.pub/extras