Shotgun Proteomics Methods and Protocols 1st Edition by Daniel Martins-De-Souza ISBN 1493946951 978-1493946952

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Product details: 

ISBN 10: 1493946951

ISBN 13:  978-1493946952

Author: Daniel Martins-De-Souza

Shotgun Proteomics: Methods and Protocols serves as a vital collection of protocols through which thousands of proteins can be simultaneously identified, quantified and characterized in a high throughput manner. Beginning with the history of proteomics centered on the vital role of mass spectrometry in its development, this detailed volume continues with chapters on sample pre-fractionation, in vivo and in vitro stable isotope labeling, label-free proteomics, informatics, protein-protein interactions, targeted proteomics and post-translational modifications. Written for the highly successful Methods in Molecular Biology series, 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.

Practical and comprehensive, Shotgun Proteomics: Methods and Protocols is an ideal and up-to-date guide for researchers seeking to understand the proteome of any given species.

Table of contents: 

PART I INTRODUCTION
1 Survey of Shotgun Proteomics
Fabio Cesar Sousa Nogueira and Gilberto B. Domont

PART II SAMPLE PRE-FRACTIONATION
2 LC-MALDI-TOF/TOF for Shotgun Proteomics
Patricia Fernández-Puente, Jesús Mateos, Francisco J. Blanco, and Cristina Ruiz-Romero

3 Fully Automatable Multidimensional Reversed Phase Liquid Chromatography with Online Tandem Mass Spectrometry
Maggie P.Y. Lam, Chun Hin Lam, Quan Quan, Yun Zhao, and Ivan K. Chu

4 GeLC-MS/MS Analysis of Complex Protein Mixtures
Monika Dzieciatkowska, Ryan Hill, and Kirk C. Hansen

5 IPG Strip Based Peptide Fractionation for Shotgun Proteomics
Murat Eravci, Christian Sommer, and Matthias Selbach

PART III IN VIVO STABLE ISOTOPE LABELING
6 SILAC Yeast: From Labeling to Comprehensive Proteome Quantification
Lyris M.E. de Godoy

7 Analysis of Proteome Dynamics in Mice by Isotopic Labeling
John C. Price and Sina Ghaemmaghami

8 Stable Isotope Labeling in Mammals (SILAM)
Daniel B. McClatchy and John R. Yates III

9 Analysis of Individual Protein Turnover in Live Animals on a Proteome Wide Scale
Stefan Reckow and Christian Webhofer

PART IV IN VITRO STABLE ISOTOPE LABELING
10 Determining Protein Subcellular Localization in Mammalian Cell Culture with Biochemical Fractionation and iTRAQ & Pex Quantification
Andy Christoforou, Alfonso Martinez Arias, and Kathryn S. Lilley

PART V LABEL-FREE PROTEOMICS
14 Spectral Counting Label Free Proteomics
Liis Arike and Lauri Peil

15 Quantification of Proteins by Label-Free LC-MS²
Alon Savidor and Tzachi Levin

PART VI PROTEOMICS INFORMATICS AND QUANTITATION
16 Bioinformatics for Proteomics: Opportunities at the Interface Between the Scientists, Their Experiments, and the Community
Marc Vaudel, Harald Barsnes, Lennart Martens, and Frode S. Berven

PART VII PROTEIN–PROTEIN INTERACTIONS
17 Identification of DNA Damage Checkpoint Dependent Protein Interactions in Saccharomyces cerevisiae Using Quantitative Mass Spectrometry
Francisco M. Bastos de Oliveira and Marcus B. Smolka

18 Application of Shotgun Proteomics for Discovery-Driven Protein–Protein Interaction
Livia Goto-Silva, Zlatan Maliga, Mikolaj Slabicki, Jimmy Rodríguez Murillo, and Magno Junqueira

19 Mapping Protein Complexes Using Covalently Linked Antibodies and Isobaric Mass Tags
Antje Dittmann, Sonja Ghidelli-Disse, Carsten Hopf, and Marcus Bantscheff

PART VIII TARGETED PROTEOMICS
20 Biomarker Verification Using Selected Reaction Monitoring and Shotgun Proteomics
Ángel Mauricio Castro-Gamero, Clarice Isumi, and José César Rosa

21 Use of Universal Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) Based Selected Reaction Monitoring (SRM) Approach for Verification of Breast Cancer Related Protein Markers
Ning Qing Lin, Lennard J.M. Dekker, Martijn M. Van Duijn, and Arzu Umar

PART IX POSTTRANSLATIONAL MODIFICATIONS
24 One Source Peptide/Phosphopeptide Ratio Standards for Accurate and Site-Specific Determination of the Degree of Phosphorylation
Martin E. Beehn, Bettina Hahn, and Wolf D. Lehmann

25 Quantitative Glycoproteomics for N-Glycoproteome Profiling
Sheng Pan

26 A Practical Recipe to Survey Phosphoproteomes
William C. Edelman, Kelsey M. Haas, Joanne L. Hsu, Robert T. Lawrence, and Judit Villén

27 Quantitation of the Phosphoproteome Using the Library Assisted Extracted Ion Chromatogram (LAXIC) Strategy
Justine V. Arrington, Liang Xue, and W. Andy Tao

28 Fast, Efficient, and Quality-Controlled Phosphopeptide Enrichment from Minute Sample Amounts Using Titanium Dioxide
Clarissa Dittrich, Sonja Radus, and René F. Zahedi

29 Quantifying Small Molecule-Induced Changes in Cellular Protein Expression and Posttranslational Modifications Using Isobaric Mass Tags
Lisette Becher, Maria Fathi Savitski, and Marcus Bantscheff

PART X MASS SPECTROMETRY FOR PROTEIN ANALYSIS
30 Analysis of Protein Structure by Cross-Linking Combined with Mass Spectrometry
Evgeny N. Petrotchenko, Karl A. T. Makepeace, Jason Y. Serpa, and Christoph H. Borchers

31 Top-Down Proteomics by Means of Orbitrap Mass Spectrometry
Kai Scheffler

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