Mass Spectrometry of Proteins and Peptides

1. Front Matter

   Pages i-xiv

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2. Generation and Analysis of Multidimensional Protein Identification Technology Datasets

   • Selene K. Swanson, Laurence Florens, Michael P. Washburn

   Pages 1-20

3. Quantitative Peptide and Protein Profiling by Mass Spectrometry

   • Alexander Schmidt, Birgit Bisle, Thomas Kislinger

   Pages 21-38

4. Label-Free Relative Quantitation of Prokaryotic Proteomes Using the Accurate Mass and Time Tag Approach

   • Kim K. Hixson

   Pages 39-63

5. Classical Proteomics: Two-Dimensional Electrophoresis/MALDI Mass Spectrometry

   • Ursula Zimny-Arndt, Monika Schmid, Renate Ackermann, Peter R. Jungblut

   Pages 65-91

6. The Use of Difference In-Gel Electrophoresis for Quantitation of Protein Expression

   • Rajat Sapra

   Pages 93-112

7. Liquid-Chromatography-Mass Spectrometry of Thylakoid Membrane Proteins

   • Christian G. Huber, Anna-Maria Timperio, Hansjörg Toll, Lello Zolla

   Pages 113-130

8. High Accuracy Mass Spectrometry in Large-Scale Analysis of Protein Phosphorylation

   • Jesper V. Olsen, Boris Macek

   Pages 131-142

9. Manual Validation of Peptide Sequence and Sites of Tyrosine Phosphorylation from MS/MS Spectra

   • Amy M. Nichols, Forest M. White

   Pages 143-160

10. Assigning Glycosylation Sites and Microheterogeneities in Glycoproteins by Liquid Chromatography/Tandem Mass Spectrometry

    • Yehia Mechref, Milan Madera, Milos V. Novotny

    Pages 161-180

11. Structure Analysis of N -Glycoproteins

    • Stefanie Henning, Jasna Peter-Katalinić, Gottfried Pohlentz

    Pages 181-200

12. Capillary Zone Electrophoresis-Mass Spectrometry for the Characterization of Isoforms of Intact Glycoproteins

    • Christian Neusüβ, Matthias Pelzing

    Pages 201-213

13. Top-Down Proteomics on a High-field Fourier Transform Ion Cyclotron Resonance Mass Spectrometer

    • Séverine A. Ouvry-Patat, Matthew P. Torres, Craig A. Gelfand, Hung Hiang Quek, Michael Easterling, J. Paul Speir et al.

    Pages 215-231

14. Capillary Isoelectric Focusing/Reversed Phase Liquid Chromatography/Mass Spectrometry

    • Cheng S. Lee, Brian M. Balgley

    Pages 233-240

15. Integrating Accelerated Tryptic Digestion into Proteomics Workflows

    • Gordon W. Slysz, David C. Schriemer

    Pages 241-254

16. Hydrogen/Deuterium Exchange Mass Spectrometry

    • Xuguang Yan, Claudia S. Maier

    Pages 255-271

17. Mass Spectrometry Detection and Characterization of Noncovalent Protein Complexes

    • Sheng Yin, Joseph A. Loo

    Pages 273-282

18. Chemical Cross-Linking for Protein–Protein Interaction Studies

    • Xiaoting Tang, James E. Bruce

    Pages 283-293

19. Tissue Analysis with High-Resolution Imaging Mass Spectrometry

    • A. F. Maarten Altelaar, Ron M. A. Heeren

    Pages 295-308

20. Proteomic Global Profiling for Cancer Biomarker Discovery

    • Vitor Faca, Hong Wang, Samir Hanash

    Pages 309-320

When the last edition of this book was published in 2000, the field of proteomics was in its infancy. At that time, multidimensional liquid chromatographic separations were being introduced as an alternative to traditional gel-based techniques for separating complex protein and peptide mixtures prior to mass spectrometric detection. Today, this approach – referred to as shotgun proteomics – is considered routine for lar- scale global analyses of protein mixtures. Now in its adolescence, proteomics is fundamentally transforming biological and medical research. Much of this transformation can be attributed to technological advancements, particularly in mass spectrometry. Much wider accessibility of hi- resolution and mass measurement accuracy instrumentation in recent years has ini- ated a new revolution in the field by providing more reliable data and shifting the focus from cataloging proteins to precisely quantifying changes in protein abundance over time and in response to stimuli. Advanced mass spectrometers and novel ion d- sociation schemes such as electron transfer/capture dissociation make it possible to venture boldly into the maze of protein posttranslational modifications, which are an integral component of understanding functional proteomics in the spatial and t- poral domains. Another area that has benefited from these advancements is top-down proteomics, an emerging method essential for characterizing various protein variants that has potentially high impact in biomedical research.

• Mass Spectrometry
• Microarray
• Proteomics
• Termination
• genes
• membrane proteins
• microorganisms
• molecular biology
• protein complexes
• protein structure

From the reviews of the second edition:

"This book … covers a wide range of applications of modern mass spectrometry in peptide and protein analysis. … Very useful is the presence of a final ‘Notes’ section within each chapter. These notes and laboratory tips help both beginners and experienced researchers to make their first steps into new fields … . The well balanced mixture … makes it a helpful resource for scientists working in analytical chemistry, biochemistry, biotechnology, and bioinformatics, and a valuable resource for everyone working in biologically oriented mass spectrometry." (Andreas Tholey, Analytical and Bioanalytical Chemistry, September, 2009)

• Fundamental & Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, USA

  Mary S. Lipton

• Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, USA

  Ljiljana Paša-Tolic

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