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The Proteomics Protocols Handbook
Protein Identification and Analysis Tools on the ExPASy Server
other
Author(s):
Elisabeth Gasteiger
,
Christine Hoogland
,
Alexandre Gattiker
,
S'everine Duvaud
,
Marc R. Wilkins
,
Ron D. Appel
,
Amos Bairoch
Publication date
(Print):
2005
Publisher:
Humana Press
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Book Chapter
Publication date (Print):
2005
Pages
: 571-607
DOI:
10.1385/1-59259-890-0:571
PubMed ID:
10027275
SO-VID:
a037e2dc-895a-4ed4-80ed-5450175911ac
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Book chapters
pp. 1
Extraction and Solubilization of Proteins for Proteomic Studies
pp. 19
Preparation of Bacterial Samples for 2-D PAGE
pp. 27
Preparation of Yeast Samples for 2-D PAGE
pp. 31
Preparation of Mammalian Tissue Samples for Two-Dimensional Electrophoresis
pp. 37
Differential Detergent Fractionation of Eukaryotic Cells
pp. 49
Serum or Plasma Sample Preparation for Two-Dimensional Gel Electrophoresis
pp. 55
Preparation of Plant Protein Samples for 2-D PAGE
pp. 59
Laser-Assisted Microdissection in Proteomic Analyses
pp. 67
Purification of Cellular and Organelle Populations by Fluorescence-Activated Cell Sorting for Proteome Analysis
pp. 79
Purification of Nucleoli From Lymphoma Cells and Solubilization of Nucleolar Proteins for 2-DE Separation
pp. 87
Prefractionation of Complex Protein Mixture for 2-D PAGE Using Reversed-Phase Liquid Chromatography
pp. 97
Fractionation of Complex Proteomes by Microscale Solution Isoelectrofocusing Using ZOOM− IEF Fractionators to Improve Protein Profiling
pp. 119
Large-Format 2-D Polyacrylamide Gel Electrophoresis
pp. 133
Analysis of Membrane Proteins by Two-Dimensional Gels
pp. 145
2-D PAGE of High-Molecular-Mass Proteins
pp. 151
Using Ultra-Zoom Gels for High-Resolution Two-Dimensional Polyacrylamide Gel Electrophoresis
pp. 167
NEpHGE and pI Strip Proteomic 2-D Gel Electrophoretic Mapping of Lipid-Rich Membranes
pp. 177
Silver Staining of 2-D Gels
pp. 185
Zn2+Reverse Staining Technique
pp. 193
Multiplexed Proteomics Technology for the Fluorescence Detection of Glycoprotein Levels and Protein Expression Levels Using Pro-Q® Emerald and SYPRO® Ruby Dyes
pp. 201
Multiplexed Proteomics Technology for the Fluorescence Detection of Phosphorylation and Protein Expression Levels Using Pro-Q® Diamond and SYPRO® Ruby Dyes
pp. 209
Sensitive Quantitative Fluorescence Detection of Proteins in Gels Using SYPRO® Ruby Protein Gel Stain
pp. 215
Rapid, Sensitive Detection of Proteins in Minigels With Fluorescent Dyes
pp. 223
Differential In-Gel Electrophoresis in a High-Throughput Environment
pp. 239
Statistical Analysis of 2-D Gel Patterns
pp. 259
2-DE Databases on the World Wide Web
pp. 267
Computer Analysis of 2-D Images
pp. 279
Comparing 2-D Electrophoretic Gels Across Internet Databases
pp. 307
Sample Cleanup by Solid-Phase Extraction/Pipet-Tip Chromatography
pp. 311
Protein Identification by In-Gel Digestion and Mass Spectrometric Analysis
pp. 315
Peptide Sequences of 2-D Gel-Separated Protein Spots by Nanoelectrospray Tandem Mass Spectrometry
pp. 319
Identification of Proteins by MALDI-TOF MS
pp. 325
Sequencing of Tryptic Peptides Using Chemically Assisted Fragmentation and MALDI-PSD
pp. 341
The In Situ Characterization of Membrane-Immobilized 2-D PAGE-Separated Proteins Using Ink-Jet Technology
pp. 355
Protein Identification by Peptide Mass Fingerprinting
pp. 367
Analysis of the Proteomes in Human Tissues by In-Gel Isoelectric Focusing and Mass Spectrometry
pp. 375
Liquid Chromatography Coupled to MS for Proteome Analysis
pp. 385
Quantitative Analysis of Proteomes and Subproteomes by Isotope-Coded Affinity Tag and Solid-Phase Glycoprotein Capture
pp. 393
Amino Acid-Coded Mass Tagging for Quantitative Profiling of Differentially Expressed Proteins and Modifications in Cells
pp. 407
Mass-Coded Abundance Tagging for Protein Identification and Relative Abundance Determination in Proteomic Experiments
pp. 417
Virtual 2-D Gel Electrophoresis by MALDI Mass Spectrometry
pp. 431
Identification of Posttranslational Modification by Mass Spectrometry
pp. 439
Approaches to the O-Glycoproteome
pp. 459
Identification of Protein Phosphorylation Sites by Mass Spectrometry
pp. 467
Quantitative Analysis of Protein Phosphorylation Status and Protein Kinase Activity on Microarrays Using Pro-Q− Diamond Dye Technology
pp. 475
New Challenges and Strategies for Multiple Sequence Alignment in the Proteomics Era
pp. 493
The Clustal Series of Programs for Multiple Sequence Alignment
pp. 503
FASTA Servers for Sequence Similarity Search
pp. 527
Protein Sequence Analysis and Domain Identification
pp. 543
Mammalian Genes and Evolutionary Genomics
pp. 555
Computational Identification of Related Proteins
pp. 571
Protein Identification and Analysis Tools on the ExPASy Server
pp. 609
Protein Sequence Databases
pp. 619
In Silico Characterization of Proteins InterPro and Proteome Analysis
pp. 629
Computational Prediction of Protein-Protein Interactions
pp. 653
The Yeast Two-Hybrid System for Detecting Interacting Proteins
pp. 683
Antibody- Affinity Purification to Detect Interacting Proteins
pp. 689
Biomolecular Interaction Analysis Coupled With Mass Spectrometry to Detect Interacting Proteins
pp. 699
Assessment of Antibody-Antigen Interaction Using SELDI Technology
pp. 709
Protein and Peptide Microarray- Based Assay Technology
pp. 723
Production of Protein Microarrays Using Robotic Pin Printing Technologies
pp. 735
PCR-Directed Protein In Situ Arrays
pp. 743
Site-Specific Immobilization of Proteins in a Microarray
pp. 753
A Guide to Protein Interaction Databases
pp. 801
Deriving Function From Structure
pp. 831
Comparative Protein Structure Modeling
pp. 861
Classification of Protein Sequences and Structures
pp. 875
How to Use Protein 1- D Structure Predicted by PROFphd
pp. 903
Classification of Protein Folds
pp. 921
Protein Threading
pp. 939
High- Throughput Crystallography for Structural Proteomics
pp. 955
Automated High-Throughput Protein Crystallization
pp. 967
NMR- Based Structure Determination of Proteins in Solution
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