Proteomics in systems biology : methods and protocols / edited by Jorg Reinders.

Includes bibliographical references and index.

Multiplexed quantitative proteomics for high-throughput comprehensive proteome comparisons of human cell lines / Amanda Edwards and Wilhelm Haas -- Sample preparation approaches for iTRAQ labeling and quantitative proteomic analyses in systems biology / Christos Spanos and J. Bernadette Moore -- Two birds with one stone : parallel quantification of proteome and phosphoproteome using iTRAQ / Fiorella A. Solari [and others] -- Selected reaction monitoring to measure proteins of interest in complex samples : a practical guide / Yuehan Feng and Paola Picotti -- Monitoring PPARG-induced changes in glycolysis by selected reaction monitoring mass spectrometry / Andreas Hentschel and Robert Ahrends -- Targeted MRM approach for tempo-spatial proteomics analyses / Annie Moradian [and others] -- Targeted phosphoproteome analysis using selected/multiple reaction monitoring (SRM/MRM) / Jun Adachi, Ryohei Narumi, and Takeshi Tomonaga -- Testing suitability of cell cultures for SILAC-experiments using SWATH-mass spectrometry / Yvonne Reinders [and others] -- Combining amine-reactive cross-linkers and photo-reactive amino acids for 3D-structure analysis of proteins and protein complexes / Philip Lössl and Andrea Sinz -- Tissue MALDI mass spectrometry imaging (MALDI MSI) of peptides / Birte Beine [and others] -- Ethyl esterification for MALDI-MS analysis of protein glycosylation / Karli R. Reiding [and others] -- Characterization of protein N-glycosylation by analysis of ZIC-HILIC-enriched intact proteolytic glycopeptides / Gottfried Pohlentz, Kristina Marx, and Michael Mormann -- Simple and effective affinity purification procedures for mass spectrometry-based identification of protein-protein interactions in cell signaling pathways / Julian H.M. Kwan and Andrew Emili -- Systems approach to understand antigen presentation and the immune response / Nadine L. Dudek [and others] -- Profiling of small molecules by chemical proteomics / Kilian V.M. Huber and Giulio Superti-Furga -- Generating sample-specific databases for mass spectrometry-based proteomic analysis by using RNA sequencing / Toni Luge and Sascha Sauer -- Proteomic workflow using high-throughput de novo sequencing towards complementation of genome information for improved comparative crop science / Reinhard Turetschek [and others] -- From phosphoproteome to modeling of plant signaling pathways / Maksim Zakhartsev, Heidi Pertl-Obermeyer, and Waltraud X. Schulze -- Interpretation of quantitative shotgun proteomic data / Elise Aasebø [and others] -- Simple workflow for large scale shotgun glycoproteomics / Astrid Guldbrandsen [and others] -- Systemic analysis of regulated functional networks / Luis Francisco Hernández Sánchez [and others].

Online resource; title from PDF title page (springerLink, viewed December 28, 2015).

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.