Mass Spectrometry Data Analysis in Proteomics

ISBN-13: 9781627033916 / Angielski / Twarda / 2013 / 405 str.

Rune Matthiesen

Opis

Since the publishing of the first edition, the methodologies and instrumentation involved in the field of mass spectrometry-based proteomics has improved considerably. Fully revised and expanded, Mass Spectrometry Data Analysis in Proteomics, Second Edition presents expert chapters on specific MS-based methods or data analysis strategies in proteomics. The volume covers data analysis topics relevant for quantitative proteomics, post translational modification, HX-MS, glycomics, and data exchange standards, among other topics. Written in the highly successful Methods in Molecular Biology series format, chapters include brief introductions to their respective subjects, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.Updated and authoritative, Mass Spectrometry Data Analysis in Proteomics, Second Edition serves as a detailed guide for all researchers seeking to further our knowledge in the field of proteomics.

Spis treści

1. Introduction to Mass Spectrometry-Based Proteomics

            Rune Matthiesen and Jakob Bunkenborg

 

2. LC-MS Spectra Processing

            Rune Matthiesen

 

3. Isotopic Distributions

            Alan L. Rockwood and Magnus Palmblad

 

4. Retention Time Prediction and Protein Identification

            Alex A. Henneman and Magnus Palmblad

 

5. Algorithms for Database Dependent Search of MSMS Data

            Rune Matthiesen

 

6. Interpretation of Tandem Mass Spectra of Post-Translationally Modified Peptides

            Jakob Bunkenborg and Rune Matthiesen

 

7. Improving Peptide Identification Using Empirical Scoring Systems

            Robert J. Chalkley

 

8. Methods and Algorithms for Quantitative Proteomics by Mass Spectrometry

            Rune Matthiesen and Ana Sofia Carvalho

 

9. Computational Approaches to Selected Reaction Monitoring (SRM) Assay Design

            Conrad Bessant and Jun Fan

 

10. Feature Selection and Machine Learning with Mass Spectrometry Data

            Susmita Datta

 

11. Considerations in the Analysis of Hydrogen Exchange Mass Spectrometry Data

            Thomas E. Wales, Michael J. Eggertson, and John R. Engen

 

12. Permethylated N-Glycan Analysis with Mass Spectrometry

            Zhenxin Lin and David M. Lubman

 

13. Mass Spectrometry Methods for Studying Glycosylation in Cancer

            Hugo Osório and Celso A. Reis

 

14. Proteomics Data Exchange and Storage: The Need for Common Standards and Public Repositories

            Rafael C. Jiménez and Juan Antonio Vizcaíno

 

15. Tools for Protein Post Translational Modifications Analysis: FAK, A Case Study

            Catarina Fonseca, Paula Voabil, Ana Sofia Carvalho, and Rune Matthiesen

 

16. Proteomic Strategies to Characterize Signaling Pathways

            H.C. Harsha, Sneha M. Pinto, and Akhilesh Pandey

 

17. Simple Proteomics Data Analysis in the Object-Oriented PowerShell

            Yassene Mohammed and Magnus Palmblad