Mass Spectrometry Data Analysis in Proteomics

ISBN-13: 9781493997435 / Angielski / Twarda / 2019 / 445 str.

Opis

The aim of this new edition is to provide detailed information on each topic and present novel ideas and views that can influence future developments in mass spectrometry-based proteomics. In contrast to the previous editions, this third edition aims to provide the most relevant computational methods, focusing on computational concepts. 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, Mass Spectrometry Data Analysis in Proteomics, Third Edition to ensure successful results in the further study of this vital field.

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 Henneman and Magnus Palmblad

 

5. Comparing Peptide Spectra Matches Across Search Engines

Rune Matthiesen, Gorka Prieto and Hans Christian Beck

 

6. Calculation of False Discovery Rate for Peptide and Protein Identification

Gorka Prieto and Jesús Vázquez

 

7. Methods and Algorithms for Quantitative Proteomics by Mass Spectrometry

Rune Matthiesen and Ana Sofia Carvalho

  8. Interpretation of Tandem Mass Spectra of Posttranslationally Modified Peptides

Jakob Bunkenborg, and Rune Matthiesen

 

9. Solution to Dark Matter Identified by Mass-tolerant Database Search

Rune Matthiesen

 

10. Phosphoproteomics Profiling to Identify Altered Signaling Pathways and Kinase-targeted Cancer Therapies

Barnali Deb, Irene A. George, Jyoti Sharma, and Prashant Kumar

 

11. Mass Spectrometry Based Characterization of Ub- and UbL-modified Proteins

Nagore Elu, Benoit Lectez, Juanma Ramirez, Nerea Osinalde, and Ugo Mayor

 

12. Targeted Proteomics as a Tool for Quantifying Urine-based Biomarkers

Sonali V Mohan, David S Nayakanti, Gajanan Sathe, Irene A Geroge, Harsha Gowda, PrashantKumar

 

13. Data Imputation in Merged Isobaric Labelling-based Relative Quantification Datasets

Nicolai Bjødstrup Palstrøm, Rune Matthiesen, and Hans Christian Beck

 

14. Clustering Clinical Data in R

Ana Pina, Maria Paula Macedo, and Roberto Henriques

  15. Review of Issues and Solutions to Data Analysis Reproducibility and Data Quality in Clinical Proteomics

Mathias Walzer and  Juan Antonio Vizcaíno

 

16. Review of Batch Effects Prevention, Diagnostics, and Correction Approaches

Jelena Čuklina, Patrick G. A. Pedrioli, and Ruedi Aebersold

 

17. Using the Object-oriented PowerShell for Simple Proteomics Data Analysis

Yassene Mohammed and Magnus Palmblad

 

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

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