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Library | Item Barcode | Call Number | Material Type | Item Category 1 | Status |
|---|---|---|---|---|---|
Searching... | 30000010160684 | QP551 C65 2007 | Open Access Book | Book | Searching... |
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Summary
Summary
Proteomics is the study of the subsets of proteins present in different parts of an organism and how they change with time and varying conditions. Mass spectrometry is the leading technology used in proteomics, and the field relies heavily on bioinformatics to process and analyze the acquired data. Since recent years have seen tremendous developments in instrumentation and proteomics-related bioinformatics, there is clearly a need for a solid introduction to the crossroads where proteomics and bioinformatics meet.
Computational Methods for Mass Spectrometry Proteomics describes the different instruments and methodologies used in proteomics in a unified manner. The authors put an emphasis on the computational methods for the different phases of a proteomics analysis, but the underlying principles in protein chemistry and instrument technology are also described. The book is illustrated by a number of figures and examples, and contains exercises for the reader. Written in an accessible yet rigorous style, it is a valuable reference for both informaticians and biologists.
Computational Methods for Mass Spectrometry Proteomics is suited for advanced undergraduate and graduate students of bioinformatics and molecular biology with an interest in proteomics. It also provides a good introduction and reference source for researchers new to proteomics, and for people who come into more peripheral contact with the field.
Author Notes
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 |
| 1 Protein, Proteome, and Proteomics |
| 1.1 Primary goals for studying proteomes |
| 1.2 Defining the protein |
| 1.2.1 Protein identity |
| 1.2.2 Splice variants |
| 1.2.3 Allelic variants - polymorphisms |
| 1.2.4 Posttranslational modifications |
| 1.2.5 Protein isoforms |
| 1.3 Protein properties - attributes and values |
| 1.3.1 The amino acid sequence |
| 1.3.2 Molecular mass |
| 1.3.3 Isoelectric point |
| 1.3.4 Hydrophobicity |
| 1.3.5 Amino acid composition |
| 1.4 Posttranslational modifications |
| 1.5 Protein sequence databases |
| 1.5.1 UniProt KnowledgeBase (Swiss-Prot/TrEMBL, PIR) |
| 1.5.2 The NCBI non-redundant database |
| 1.5.3 The International Protein Index (IPI) |
| 1.5.4 Time-instability of sequence databases |
| 1.6 Identification and characterization of proteins |
| 1.6.1 Top-down and bottom-up proteomics |
| 1.6.2 Protein digestion into peptides |
| 1.7 Two approaches for bottom-up protein analysis by mass spectrometry |
| 1.7.1 MS - Peptide mass fingerprinting |
| 1.7.2 MS/MS - Tandem MS |
| 1.7.3 Combination approaches |
| 1.7.4 Reducing the search space |
| 1.8 Instrument calibration and measuring errors |
| 1.8.1 Calibration |
| 1.8.2 Accuracy and precision |
| 1.9 Exercises |
| 1.10 Bibliographic notes |
| 2 Protein Separation - 2D Gel Electrophoresis |
| 2.1 Separation on molecular mass - SDS-PAGE |
| 2.1.1 Estimating the protein mass |
| 2.2 Separation on isoelectric point - IEF |
| 2.3 Separation on mass and isoelectric point, 2D |
| 2.3.1 Transferring the proteins from the first to the second dimension |
| 2.3.2 Visualizing the proteins after separation |
| 2.3.3 Problems |
| 2.3.4 Excising the proteins |
| 2.4 2D SDS-PAGE for (complete) proteomics |
| 2.4.1 Identifying the proteins |
| 2.4.2 Quantification |
| 2.4.3 Programs for treating and comparing gels |
| 2.4.4 Comparing results from different experiments - DIGE |
| 2.5 Exercises |
| 2.6 Bibliographic notes |
| 3 Prote |
