Computational Methods for Mass Spectrometry

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.

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

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
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Computational Methods for Mass Spectrometry Proteomics

Summary

Author Biography

Table of Contents

Supplemental Materials