Mass Spectrometry Data Analysis in Proteomics

1. Front Matter

   Pages i-x

   PDF

2. Introduction to Proteomics

   • Rune Matthiesen, Kudzai E. Mutenda

   Pages 1-35

3. Extracting Monoisotopic Single-Charge Peaks From Liquid Chromatography-Electrospray Ionization-Mass Spectrometry

   • Rune Matthiesen

   Pages 37-48

4. Calibration of Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Peptide Mass Fingerprinting Spectra

   • Karin Hjernø, Peter Højrup

   Pages 49-60

5. Protein Identification by Peptide Mass Fingerprinting

   • Karin Hjernø

   Pages 61-75

6. Generating Unigene Collections of Expressed Sequence Tag Sequences for Use in Mass Spectrometry Identification

   • Jeppe Emmersen

   Pages 77-86

7. Protein Identification by Tandem Mass Spectrometry and Sequence Database Searching

   • Alexey I. Nesvizhskii

   Pages 87-119

8. Virtual Expert Mass Spectrometrist v3.0

   • Rune Matthiesen

   Pages 121-138

9. Quantitation With Virtual Expert Mass Spectrometrist

   • Albrecht Gruhler, Rune Matthiesen

   Pages 139-152

10. Sequence Handling by Sequence Analysis Toolbox v1.0

    • Christian Ravnsborg Ingrell, Rune Matthiesen, Ole Nørregaard Jensen

    Pages 153-168

11. Interpretation of Collision-Induced Fragmentation Tandem Mass Spectra of Posttranslationally Modified Peptides

    • Jakob Bunkenborg, Rune Matthiesen

    Pages 169-194

12. Retention Time Prediction and Protein Identification

    • Magnus Palmblad

    Pages 195-207

13. Quantitative Proteomics by Stable Isotope Labeling and Mass Spectrometry

    • Sheng Pan, Ruedi Aebersold

    Pages 209-218

14. Quantitative Proteomics for Two-Dimensional Gels Using Difference Gel Electrophoresis

    • David B. Friedman

    Pages 219-239

15. Proteomic Data Exchange and Storage

    • Per Gärdén, Rikard Alm

    Pages 241-259

16. Proteomic Data Exchange and Storage

    • Sandra Orchard, Philip Jones, Chris Taylor, Weimin Zhu, Randall K. Julian Jr., Henning Hermjakob et al.

    Pages 261-270

17. Organization of Proteomics Data With YassDB

    • Allan L. Thomsen, Kris Laukens, Rune Matthiesen, Ole Nørregaard Jensen

    Pages 271-287

18. Analysis of Carbohydrates by Mass Spectrometry

    • Kudzai E. Mutenda, Rune Matthiesen

    Pages 289-301

19. Useful Mass Spectrometry Programs Freely Available on the Internet

    • Rune Matthiesen

    Pages 303-305

20. Back Matter

    Pages 307-320

    PDF

Mass Spectrometry Data Analysis in Proteomics is an in-depth guide to the theory and practice of analyzing raw mass spectrometry (MS) data in proteomics. As MS is a high throughput technique, proteomic researchers must attend carefully to the associated field of data analysis, and this volume outlines available bioinformatics programs, algorithms, and databases available for MS data analysis. General guidelines for data analysis using search engines such as Mascot, Xtandem, and VEMS are provided, with specific attention to identifying poor quality data and optimizing search parameters. Several different types of MS data are discussed, followed by a description of optimal methods for conversion of raw data into peak lists for input to search engines. Choosing the most accurate and complete databases is emphasized, and a report of available sequence databases is included. Methods for assembling expressed sequence tags (ESTs) into assembled nonredundant databases are provided, along with protocols for further processing the sequences into a format suitable for MS data. Mass Spectrometry Data Analysis in Proteomics describes publicly available applications whenever possible.

• Mascot
• Proteomics
• Translation
• algorithms
• bioinformatics
• databases
• sequence analysis

• Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark

  Rune Matthiesen

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