Quantitative Methods in Proteomics

ISBN-13: 9781071610237 / Angielski / Twarda / 2021 / 483 str.

Katrin Marcus; Martin Eisenacher; Barbara Sitek

Spis treści

1. Important Issues in Planning a Proteomics Experiment: Statistical Considerations of Quantitative Proteomic Data

Karin Schork, Katharina Podwojski, Michael Turewicz, Christian Stephan, and Martin Eisenacher

 

2. Good Old-Fashioned Protein Concentration Determination by Amino Acid Analysis

Caroline May, Bettina Serschnitzki, and Katrin Marcus

 

3. Protein Quantification using the “Rapid Western Blot” Approach

Katalin Barkovits, Kathy Pfeiffer, Britta Eggers, and Katrin Marcus

 

4. The Whereabouts of 2D Gels in Quantitative Proteomics

Thierry Rabilloud and Cécile Lelong

 

5. Proteome Analysis with Classical 2D‑PAGE

Caroline May, Frederic Brosseron, Kathy Pfeiffer, Kristin Fuchs, Helmut E. Meyer, Barbara Sitek, and Katrin Marcus

 

6. Silver Staining of 2D Electrophoresis Gels

Thierry Rabilloud

 

7. Differential Proteome Analysis using 2D-DIGE

Caroline May, Frederic Brosseron, Piotr Chartowski, Kristin Fuchs, Helmut E. Meyer, Barbara Sitek, and Katrin Marcus

 

8. Quantitative Mass Spectrometry-Based Proteomics: An Overview

Svitlana Rozanova, Miroslav Nikolov, Carla Schmidt, Henning Urlaub, and Katrin Marcus

 

9. Tandem Mass Tags for Comparative and Discovery Proteomics      

Oliver Pagel, Laxmikanth Kollipara, and Albert Sickmann

 

10. An Approach for Triplex-IPTL

Christian J. Koehler and Bernd Thiede

 

11. Targeted Protein Quantification Using Parallel Reaction Monitoring (PRM)

Katalin Barkovits-Boeddinghaus, Weiqiang Chen, Michael Kohl, and Thilo Bracht

 

12. Quantitative Approach using Matrix Assisted Laser Desorption/Ionization Time of Flight (MALDI-ToF) Mass Spectrometry

Brooke A. Dilmetz, Peter Hoffmann, and Mark R. Condina

 

13. Application of SILAC Labeling in Phosphoproteomics Analysis

Markus Stepath and Thilo Bracht

 

14. Relative Quantification Of Phosphorylated and Glycosylated Peptides from the Same Sample using Isobaric Chemical Labelling with a Two-step Enrichment Strategy

Ivan Silbern, Pan Fang, Yanlong Ji, Henning Urlaub, and Kuan-Ting Pan

 

15. High Throughput Profiling of Proteome and Posttranslational Modifications by 16-plex TMT Labeling and Mass Spectrometry

Kaiwen Yu, Zhen Wang, Zhiping Wu, Haiyan Tan, Ashutosh Mishra, and Junmin Peng

 

16. Quantification and Identification of Post-Translational Modifications using Modern Proteomics Approaches

Anja Holtz, Nathan Basisty, and Birgit Schilling

 

17. Affinity-enrichment Chemoproteomics for Target Deconvolution and Selectivity Profiling

Thilo Werner, Michael Steidel, H. Christian Eberl, and Marcus Bantscheff

 

18. 2nSILAC for Quantitative Proteomics of Prototrophic Baker's Yeast

Stefan Dannenmaier, Silke Oeljeklaus, and Bettina Warscheid

 

19. Metabolic Labeling of Clostridioides difficile Proteins

Anke Trautwein-Schult, Jürgen Bartel, Sandra Maaß, and Dörte Becher

 

20. Application of Label-Free Proteomics for Quantitative Analysis of Urothelial Carcinoma and Cystitis Tissue

Kathrin E. Witzke, Frederik Großerueschkamp, Klaus Gerwert,and Barbara Sitek

 

21. Quantitative MS Workflow for a High-Quality Secretome Analysis by a Quantitative Secretome-proteome Comparison

Gereon Poschmann, Nina Prescher, and Kai Stühler

 

22. Establishing a Custom-Fit Data Independent Acquisition Method for Label Free Proteomics

Britta Eggers, Martin Eisenacher, Katrin Marcus, and Julian Uszkoreit

 

23. Label-free Proteomics Of Quantity-Limited Samples Using Ion Mobility-Assisted Data-Independent Acquisition Mass Spectrometry

Ute Distler, Malte Sielaff, and Stefan Tenzer

 

24. DIA-MS^E to Study Microglial Function in Schizophrenia

Guilherme Reis-de-Oliveira, Victor Corasolla Carregari, and Daniel Martins-de-Souza

 

25. Detailed Method for Performing the ExSTA Approach in Quantitative Bottom-up Plasma Proteomics

Andrew J. Percy and Christoph H. Borchers

 

26. Quantitative Cross-Linking of Proteins and Protein Complexes

Marie Barth and Carla Schmidt

 

27. Missing Value Monitoring to Address Missing Values in Quantitative Proteomics

Vittoria Matafora and Angela Bachi

 

28. Quantitative Proteome Data Analysis of Tandem Mass Tags Labeled Samples       

Oliver Pagel, Laxmikanth Kollipara, and Albert Sickmann

29. Mining Protein Expression Databases Using Network Meta-Analysis

Christine Winter and Klaus Jung

 

30. A Tutorial for Variance-sensitive Clustering And The Quantitative Analysis Of Protein Complexes

Veit Schwämmle and  Christina E Hagensen

 

31. Automated Workflow for Peptide-level Quantitation from DIA/ SWATH-MS Data

Shubham Gupta and Hannes Röst

 

 

Blurb

This second edition provides new and updated methods on the principles underlying modern protein analysis, from statistical issues to gel-based and mass spectrometry-based applications. Chapters detail protein quantification as basis for realisation of quantitative studies, gel-based and mass spectrometry-based quantification techniques, TMT, IPTL, PRM, MALDI Imaging, SILAC, PTM analysis, DIA, cross-linking, and the up-to-date topics of software and data analysis. Written in the highly successful Methods in Molecular Biology series format, 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.

 

Authoritative and cutting-edge,  Quantitative Methods in Proteomics, Second Edition aims to provide comprehensive and competent overview in the important and still growing field of quantitative proteomics.