Proteomics in Systems Biology: Methods and Protocols

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 Ren é 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 V ö ller, 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 ö ssl 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. Ramara thinam, 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 Aaseb ø, 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 á ndez S á nchez, Elise Aaseb ø, Frode Selheim , Frode S. Berven, Helge R æ der, Harald Barsnes, and Marc Vaudel