Proteome Bioinformatics

1. Front Matter

   Pages i-xi

   PDF

2. An Introduction to Proteome Bioinformatics

   • Andrew R. Jones, Simon J. Hubbard

   Pages 1-5

3. Bioinformatics Methods for Protein Identification Using Peptide Mass Fingerprinting

   • Zhao Song, Luonan Chen, Dong Xu

   Pages 7-22

4. Computational Approaches to Peptide Identification via Tandem MS

   • Simon J. Hubbard

   Pages 23-42

5. Scoring and Validation of Tandem MS Peptide Identification Methods

   • Markus Brosch, Jyoti Choudhary

   Pages 43-53

6. Target-Decoy Search Strategy for Mass Spectrometry-Based Proteomics

   • Joshua E. Elias, Steven P. Gygi

   Pages 55-71

7. Understanding and Exploiting Peptide Fragment Ion Intensities Using Experimental and Informatic Approaches

   • Ashley C. Gucinski, Eric D. Dodds, Wenzhou Li, Vicki H. Wysocki

   Pages 73-94

8. Spectral Library Searching for Peptide Identification via Tandem MS

   • Henry Lam, Ruedi Aebersold

   Pages 95-103

9. De Novo Sequencing Methods in Proteomics

   • Christopher Hughes, Bin Ma, Gilles A. Lajoie

   Pages 105-121

10. Cross Species Proteomics

    • J. C. Wright, R. J. Beynon, S. J. Hubbard

    Pages 123-135

11. Gene Model Detection Using Mass Spectrometry

    • Bindu Nanduri, Nan Wang, Mark L. Lawrence, Susan M. Bridges, Shane C. Burgess

    Pages 137-144

12. Signal Processing in Proteomics

    • Rene Hussong, Andreas Hildebrandt

    Pages 145-161

13. A High-Performance Reconfigurable Computing Solution for Peptide Mass Fingerprinting

    • Daniel Coca, Istvan Bogdan, Robert J. Beynon

    Pages 163-185

14. Mining Proteomic MS/MS Data for MRM Transitions

    • Jennifer A. Chem (Mead), Luca Bianco, Conrad Bessant

    Pages 187-199

15. OpenMS and TOPP: Open Source Software for LC-MS Data Analysis

    • Knut Reinert, Oliver Kohlbacher

    Pages 201-211

16. Trans-Proteomic Pipeline: A Pipeline for Proteomic Analysis

    • Patrick G. A. Pedrioli

    Pages 213-238

17. Informatics and Statistics for Analyzing 2-D Gel Electrophoresis Images

    • Andrew W. Dowsey, Jeffrey S. Morris, Howard B. Gutstein, Guang-Zhong Yang

    Pages 239-255

18. Automated Generic Analysis Tools for Protein Quantitation Using Stable Isotope Labeling

    • Wen-Lian Hsu, Ting-Yi Sung

    Pages 257-272

19. An Overview of Label-Free Quantitation Methods in Proteomics by Mass Spectrometry

    • Jason W. H. Wong, Gerard Cagney

    Pages 273-283

20. The PeptideAtlas Project

    • Eric W. Deutsch

    Pages 285-296

The feld of proteomics moves rapidly. New methods, techniques, applications, standards, models and software appear almost on a daily basis. Accompanying this are plenty of texts on the experimental side of the feld and a few appearing on the informatic and data analysis side. This latterly includes one in the Methods in Molecular Biology series tackling the specifc analysis of “Mass spectrometry data in proteomics” in MMB vol. 376. This current collection builds on this, but takes a broader view of proteome data analysis covering data analysis essentials, but also the databases and data models, as well as practical consid- ations for analysing database search results, annotating genomes, and speeding up searches. It also digs deeper into some topics, such as decoy database searching and aspects of signal processing in proteomic mass spectrometry. The aim of the volume is to provide the reader with a mix of reviews and methodology chapters, which build from the essentials of database searching in proteomics, on through specifc data processing challenges to databases, data standards and data models.

• Proteomics
• algorithms
• bioinformatics
• databases
• genes
• genome
• molecular biology

• Fac. Life Sciences, University of Manchester, Manchester, United Kingdom

  Simon J. Hubbard

• Fac. Veterinary Science, University of Liverpool, Liverpool, United Kingdom

  Andrew R. Jones