1. Analysis of protein-protein interactions using high-throughput yeast two-hybrid screens / Seesandra V. Rajagopala and Peter Uetz -- 2. Identification of mammalian protein complexes by lentiviral-based affinity purification and mass spectrometry / Zuyao Ni, Jonathan B. Olsen, Andrew Emili, and Jack F. Greenblatt -- 3. Protein networks involved in vesicle fusion, transport, and storage revealed by array-based proteomics / Mikael Bauer, Magdalena Maj, Ludwig Wagner, Dolores J. Cahill, Sara Linse, and David J. O'Connell -- 4. Identification and relative quantification of native and proteolytically generated protein C-termini from complex proteomes: C-terminome analysis / Oliver Schilling, Pitter F. Huesgen, Olivier Barreجپ and Christopher M. Overall -- 5. Construction of protein interaction networks based on the label-free quantitative proteomics / Mihaela E. Sardiu and Michael P. Washburn -- 6. Studying binding specificities of peptide recognition modules by high-throughput phage display selections / Haiming Huang and Sachdev S. Sidhu -- 7. Array-based synthetic genetic screens to map bacterial pathways and functional networks in escherichia coli / Mohan Babu, Alla Gagarinova, and Andrew Emili -- 8. Advanced methods for high-throughput microscopy screening of genetically modified yeast libraries / Yifat Cohen and Maya Schuldiner -- 9. Pooled lentiviral shRNA screening for functional genomics in mammalian cells / Kim Blakely, Troy Ketela, and Jason Moffat.