Timothy D. Veenstra, PhD, is the Director of the Laboratory of Proteomics and Analytical Technologies, Department of Applied Science, Maranatha Baptist University,Watertown, Wisconsin, USA. John R. Yates III, PhD, is in the Department of Molecular Medicine and Neurobiology, The Scripps Research Institute, La Jolla, California, USA.

• Foreword viiList of Contributors ix1. Quantitative Proteomics for Differential Protein Expression Profiling 1Christian K. Frese, Henk van den Toorn, Albert J.R. Heck, and Shabaz Mohammed2. Protein Microarrays 29Fernanda Festa and Joshua LaBaer3. Protein Biomarker Discovery: An Integrated Concept 63Andrei P. Drabovich, Eduardo Martinez‐Morillo, and Eleftherios P. Diamandis4. Biomarker Discovery with Mass Spectrometry Imaging and Profiling 89Sage J.B. Dunham, Elizabeth K. Neumann, Eric J. Lanni, Ta-Hsuan Ong, and Jonathan V. Sweedler5. Protein–Protein Interactions 125Claire M. Delahunty and John R. Yates III6. Mass Spectrometry of Intact Protein Complexes 145Jonathan T.S. Hopper and Carol V. Robinson7. Cross‐linking Applications in Structural Proteomics 175Evgeniy V. Petrotchenko, Jason J. Serpa, and Christoph H. Borchers8. Functional Proteomics: Systematic Characterization of the Physical and Functional Organization of Cell Systems 197Pierre C. Havugimana, Pingzhao Hu, and Andrew Emili9. High‐Resolution Interrogation of Biological Systems via Mass Cytometry 215Heather M. Grundhofer, Michelle M. Kuhns, and Edgar A. Arriaga10. Characterization of Drug–Protein Interactions by Chemoproteomics 247Markus Schirle, Marcus Bantscheff, and Bernhard Kuster11. Phosphorylation 265Timothy D. Veenstra12. Large‐Scale Phosphoproteomics 291John R. Yates III13. Probing Glycoforms of Individual Proteins Using Antibody‐Lectin Sandwich Arrays: Methods and Findings from Studies of Pancreatic Cancer 311Brian B. HaabIndex 329

Timothy D. Veenstra, PhD, is the Director of the Laboratory of Proteomics and Analytical Technologies, Department of Applied Science, Maranatha Baptist University,Watertown, Wisconsin, USA. John R. Yates III, PhD, is in the Department of Molecular Medicine and Neurobiology, The Scripps Research Institute, La Jolla, California, USA.

• Foreword viiList of Contributors ix1. Quantitative Proteomics for Differential Protein Expression Profiling 1Christian K. Frese, Henk van den Toorn, Albert J.R. Heck, and Shabaz Mohammed2. Protein Microarrays 29Fernanda Festa and Joshua LaBaer3. Protein Biomarker Discovery: An Integrated Concept 63Andrei P. Drabovich, Eduardo Martinez‐Morillo, and Eleftherios P. Diamandis4. Biomarker Discovery with Mass Spectrometry Imaging and Profiling 89Sage J.B. Dunham, Elizabeth K. Neumann, Eric J. Lanni, Ta-Hsuan Ong, and Jonathan V. Sweedler5. Protein–Protein Interactions 125Claire M. Delahunty and John R. Yates III6. Mass Spectrometry of Intact Protein Complexes 145Jonathan T.S. Hopper and Carol V. Robinson7. Cross‐linking Applications in Structural Proteomics 175Evgeniy V. Petrotchenko, Jason J. Serpa, and Christoph H. Borchers8. Functional Proteomics: Systematic Characterization of the Physical and Functional Organization of Cell Systems 197Pierre C. Havugimana, Pingzhao Hu, and Andrew Emili9. High‐Resolution Interrogation of Biological Systems via Mass Cytometry 215Heather M. Grundhofer, Michelle M. Kuhns, and Edgar A. Arriaga10. Characterization of Drug–Protein Interactions by Chemoproteomics 247Markus Schirle, Marcus Bantscheff, and Bernhard Kuster11. Phosphorylation 265Timothy D. Veenstra12. Large‐Scale Phosphoproteomics 291John R. Yates III13. Probing Glycoforms of Individual Proteins Using Antibody‐Lectin Sandwich Arrays: Methods and Findings from Studies of Pancreatic Cancer 311Brian B. HaabIndex 329

Timothy D. Veenstra, PhD, is the Director of the Laboratory of Proteomics and Analytical Technologies, Department of Applied Science, Maranatha Baptist University,Watertown, Wisconsin, USA. John R. Yates III, PhD, is in the Department of Molecular Medicine and Neurobiology, The Scripps Research Institute, La Jolla, California, USA.

• Foreword viiList of Contributors ix1. Quantitative Proteomics for Differential Protein Expression Profiling 1Christian K. Frese, Henk van den Toorn, Albert J.R. Heck, and Shabaz Mohammed2. Protein Microarrays 29Fernanda Festa and Joshua LaBaer3. Protein Biomarker Discovery: An Integrated Concept 63Andrei P. Drabovich, Eduardo Martinez‐Morillo, and Eleftherios P. Diamandis4. Biomarker Discovery with Mass Spectrometry Imaging and Profiling 89Sage J.B. Dunham, Elizabeth K. Neumann, Eric J. Lanni, Ta-Hsuan Ong, and Jonathan V. Sweedler5. Protein–Protein Interactions 125Claire M. Delahunty and John R. Yates III6. Mass Spectrometry of Intact Protein Complexes 145Jonathan T.S. Hopper and Carol V. Robinson7. Cross‐linking Applications in Structural Proteomics 175Evgeniy V. Petrotchenko, Jason J. Serpa, and Christoph H. Borchers8. Functional Proteomics: Systematic Characterization of the Physical and Functional Organization of Cell Systems 197Pierre C. Havugimana, Pingzhao Hu, and Andrew Emili9. High‐Resolution Interrogation of Biological Systems via Mass Cytometry 215Heather M. Grundhofer, Michelle M. Kuhns, and Edgar A. Arriaga10. Characterization of Drug–Protein Interactions by Chemoproteomics 247Markus Schirle, Marcus Bantscheff, and Bernhard Kuster11. Phosphorylation 265Timothy D. Veenstra12. Large‐Scale Phosphoproteomics 291John R. Yates III13. Probing Glycoforms of Individual Proteins Using Antibody‐Lectin Sandwich Arrays: Methods and Findings from Studies of Pancreatic Cancer 311Brian B. HaabIndex 329