Skip to main content
SpringerLink
Log in
Book cover

Mass Spectrometry Data Analysis in Proteomics

  • Book
  • © 2007

Overview

Editors:
  1. Rune Matthiesen

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

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Essential reference for mass spectrometry (MS) in proteomics and glycomics
  • Concise protocols for optimizing search parameters in MS search engines
  • Practical guide to MS data analysis and bioinformatics
  • Thorough review of available databases for proteomics researchers
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 367)

This is a preview of subscription content, log in via an institution to check access.

Access this book

Log in via an institution
eBook USD 149.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book USD 199.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book USD 199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Other ways to access

Licence this eBook for your library

Institutional subscriptions

Table of contents (18 protocols)

  1. Front Matter

    Pages i-x
    Download chapter 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
    Download chapter PDF
Back to top

Keywords

About this book

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.

Editors and Affiliations

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

    Rune Matthiesen

Bibliographic Information

  • Book Title: Mass Spectrometry Data Analysis in Proteomics

  • Editors: Rune Matthiesen

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1385/1597452750

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Humana Press 2007

  • Hardcover ISBN: 978-1-58829-563-7Published: 15 November 2006

  • Softcover ISBN: 978-1-61737-644-3Published: 19 November 2010

  • eBook ISBN: 978-1-59745-275-5Published: 02 February 2008

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: X, 320

  • Number of Illustrations: 87 b/w illustrations

  • Topics: Biochemistry, general, Cell Biology, Bioinformatics, Biotechnology, Proteomics

Publish with us

Policies and ethics

Back to top

Search

Navigation