Computational Methods for Mass Spectrometry Proteomics

by Eidhammer, Ingvar; Flikka, Kristian; Martens, Lennart; Mikalsen, Svein-Ole

• ISBN13: 9780470512975
• ISBN10: 0470512970
• Edition: 1st
• Format: Hardcover
• Copyright: 2008-01-22
• Publisher: Wiley-Interscience

Summary

This book uniquely provides basic knowledge and principles of proteomic bioinformatics and mass spectrometry. Computational Methods for Mass Spectrometry Proteomics covers the bioinformatics problems and how they are solved, which types of programs are used and the different principles / algorithms underlying these programs. A description of the instruments used is also given. The book includes many examples to help make the subject practical and accessible, and is an invaluable resource for all bioinformaticians, students, proteomic researchers, analytical chemists, and computer scientists.

Author Biography

Ingvar Eidhammer. Associate Professor, Department of Informatics, University of Bergen, Norway

Lennart Martens. European Bioinformatics Institute, EBI, Hinxton, Cambridge, UK

Svein-Ole Mikalsen. The Norwegian Radium Hospital, Oslo, Norway

Kristian Flikka. University of Bergen, Norway

Table of Contents

Preface

Protein, Proteome, and Proteomics

Primary goals for studying proteomes

Defining the protein

Protein identity

Splice variants

Allelic variants - polymorphisms

Posttranslational modifications

Protein isoforms

Protein properties - attributes and values

The amino acid sequence

Molecular mass

Isoelectric point

Hydrophobicity

Amino acid composition

Posttranslational modifications

Protein sequence databases

UniProt KnowledgeBase (Swiss-Prot/TrEMBL, PIR)

The NCBI non-redundant database

The International Protein Index (IPI)

Time-instability of sequence databases

Identification and characterization of proteins

Top-down and bottom-up proteomics

Protein digestion into peptides

Two approaches for bottom-up protein analysis by mass spectrometry

MS - Peptide mass fingerprinting

MS/MS - Tandem MS

Combination approaches

Reducing the search space

Instrument calibration and measuring errors

Calibration

Accuracy and precision

Exercises

Bibliographic notes

Protein Separation - 2D Gel Electrophoresis

Separation on molecular mass - SDS-PAGE

Estimating the protein mass

Separation on isoelectric point - IEF

Separation on mass and isoelectric point, 2D

Transferring the proteins from the first to the second dimension

Visualizing the proteins after separation

Problems

Excising the proteins

2D SDS-PAGE for (complete) proteomics

Identifying the proteins

Quantification

Programs for treating and comparing gels

Comparing results from different experiments - DIGE

Exercises

Bibliographic notes

Prote

Table of Contents provided by Publisher. All Rights Reserved.