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Leading researchers and innovators describe in step-by-step detail the latest techniques that promise to significantly impact the practice of proteomics, as well as its success in developing novel clinical agents. The methods span the entire spectrum of top-down and bottom-up approaches, including microarrays, gels, chromatography, and affinity separations, and address every aspect of the human proteome, both quantitatively and qualitatively. The techniques of protein detection utilized are diverse and range from fluorescence and resonance light scattering to surface plasmon resonance and mass spectrometry. The protocols follow the successful Methods in Molecular Biology(TM) series format, each offering step-by-step laboratory instructions, an introduction outlining the principles behind the technique, lists of the necessary equipment and reagents, and tips on troubleshooting and avoiding known pitfalls.

New and Emerging Proteomic Techniques

On-Chip Protein Synthesis for Making Microarrays

Niroshan Ramachandran, Eugenie Hainsworth, Gokhan Demirkan, and Joshua LaBaer



RCA-Enhanced Protein Detection Arrays

Brian B. Haab and Paul M. Lizardi



Antibody Microarrays Using Resonance Light-Scattering Particles for Detection

Bernhard H. Geierstanger, Petri Saviranta, and Achim Brinker



Chemical Proteomics Profiling of Proteasome Activity

Martijn Verdoes, Celia R. Berkers, Bogdan I. Florea, Paul F. van Swieten, Herman S. Overkleeft, and Huib Ovaa



Two-Dimensional Difference Gel Electrophoresis

Terence L. Wu



Oligomeric States of Proteins Determined by Size-Exclusion Chromatography Coupled With Light Scattering, Absorbance, and Refractive Index Detectors

Ewa Folta-Stogniew



Surface Plasmon Resonance Imaging Measurements of Protein Interactions With Biopolymer Microarrays

Terry T. Goodrich, Alastair W. Wark, Robert M. Corn, and Hye Jin Lee



Surface Plasmon Resonance Mass Spectrometry for Protein Analysis

Dobrin Nedelkov and Randall W. Nelson



High-Throughput Affinity Mass Spectrometry

Urban A. Kiernan, Dobrin Nedelkov, Eric E. Niederkofler, Kemmons A. Tubbs, and Randall W. Nelson



Isotope-Coded Affinity Tags for Protein Quantification

Christopher M. Colangelo and Kenneth R. Williams



Proteomic Analysis by Multidimensional Protein Identification Technology

Laurence Florens and Michael P. Washburn



Isolation of Glycoproteins and Identification of Their N-Linked Glycosylation Sites

Hui Zhang and Ruedi Aebersold



N-Glycosylation Analysis Using the StrOligo Algorithm

Martin Ethier, Daniel Figeys, and Hélene Perreault



MALDI-MS Data Analysis for Disease Biomarker Discovery

Weichuan Yu, Baolin Wu, Junfeng Liu, Xiaoye Li, Kathy Stone, Kenneth R. Williams, and Hongyu Zhao



Using the Global Proteome Machine for Protein Identification

Ronald C.Beavis



Index