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Dedication; Preface; Contents; Contributors; Part 1: Rebranding Classical Protein Chemistry: Proteomics of the Past; Chapter 1: Introduction: HIV-1 Proteomics, Why Should One Care?; References; Chapter 2: HIV-1 Biology at theßProtein Level; The Benefits ofßHIV-1 Protein Study; Evolution ofßRetroviral Biochemistry; HIV-1 Virus Genome andßIts Proteins: Basics; Viral Proteins inßHIV-1 Virions; HIV-1 Assembly: Why Gag Polyproteins?; The HIV-1 Proteins; Gag (http://www.uniprot.org/uniprot/P12493); MA, Matrix, p17MA; CA, Capsid, or p24CA; SP1, Spacer Protein 1, p2Gag.
Nucleocapsid, NC, p7NC p6Gag; GagPol (http://www.uniprot.org/uniprot/P12497); p6Pol, Preprotease, Transframe Protein; PR, Protease; RT, Reverse Transcriptase; IN, Integrase; Env (http://www.uniprot.org/uniprot/P03377); Accessory Proteins; Vpr (http://www.uniprot.org/uniprot/P12520); Nef (http://www.uniprot.org/uniprot/P03406); Regulatory Proteins; Incorporation ofßCellular Proteins intoßHIV-1: Bystanders, Partners, Captives, andßAssassins; The Purity Problem; HIV-1 Proteome Summary; References; Chapter 3: 25 Years ofßHIV-1 Biochemistry; Aspects ofßHIV-1 Particle Biochemistry.
HIV-1 Proteomics Before There WasßProteomics Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis; Immunoblotting/Western Blotting; Reversed-Phase High-Pressure Chromatography; Automated N-Terminal (Edman Degradation) Protein Sequencing; Amino Acid Analysis; References; Part 2: Modern HIV-1 Proteomics; Chapter 4: Proteomic Studies ofßHIV-1; Introduction; Proteomic Studies ofßHIV-1; Proteomics: "A Three-Legged Stool"; Sample Preparation; Protein andßPeptide Quantitation; Sample Cleanup: Beware ofßTraditional Detergents; Mass Spectrometry: TheßBasics; Vacuum System andßSource.
The Mass Analyzer The Detector; Tandem Mass Spectrometry; Mass Spectrometry inßtheßContext ofßHIV-1 Proteomics; Chromatography Considerations; Mass Spectrometry Acquisition: Qualitative VersusßQuantitative Methods; Data-Dependent Analysis; Label-Free Quantitative Approaches: Spectral Counting andßData-ƯIndependent Analysis; Labeling Approaches; Isobaric Tagging; Stably Incorporated Labeled Amino Acids; Informatics; Targeted HIV-1 Proteomics andßtheßPath toßClinical Applications; Selective Reaction Monitoring; Quick Start Guide forßSRM.
Thinking Back toßOur Experiments andßMotivations Alternative Approaches; Affinity Pulldown Approaches; Antigen Presentation; Protein Arrays; Conclusions; References; Chapter 5: HIV-1 Sequencing; Introduction; Reasons Why Understanding HIV/SIV Variation Is Important fromßaßBiological andßProteomics Perspective; The Evolution ofßHIV/SIV Sequencing Technologies; HIV/SIV Deep Sequencing Methodologies; Pre-experimental Questions; Sequencing Methodology; Sequence Analysis; Trimming, Merging, andßMapping FASTQ Reads; Quantify theßFrequency ofßIndividual SNPs AcrossßtheßVirus Genome.
Nucleocapsid, NC, p7NC p6Gag; GagPol (http://www.uniprot.org/uniprot/P12497); p6Pol, Preprotease, Transframe Protein; PR, Protease; RT, Reverse Transcriptase; IN, Integrase; Env (http://www.uniprot.org/uniprot/P03377); Accessory Proteins; Vpr (http://www.uniprot.org/uniprot/P12520); Nef (http://www.uniprot.org/uniprot/P03406); Regulatory Proteins; Incorporation ofßCellular Proteins intoßHIV-1: Bystanders, Partners, Captives, andßAssassins; The Purity Problem; HIV-1 Proteome Summary; References; Chapter 3: 25 Years ofßHIV-1 Biochemistry; Aspects ofßHIV-1 Particle Biochemistry.
HIV-1 Proteomics Before There WasßProteomics Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis; Immunoblotting/Western Blotting; Reversed-Phase High-Pressure Chromatography; Automated N-Terminal (Edman Degradation) Protein Sequencing; Amino Acid Analysis; References; Part 2: Modern HIV-1 Proteomics; Chapter 4: Proteomic Studies ofßHIV-1; Introduction; Proteomic Studies ofßHIV-1; Proteomics: "A Three-Legged Stool"; Sample Preparation; Protein andßPeptide Quantitation; Sample Cleanup: Beware ofßTraditional Detergents; Mass Spectrometry: TheßBasics; Vacuum System andßSource.
The Mass Analyzer The Detector; Tandem Mass Spectrometry; Mass Spectrometry inßtheßContext ofßHIV-1 Proteomics; Chromatography Considerations; Mass Spectrometry Acquisition: Qualitative VersusßQuantitative Methods; Data-Dependent Analysis; Label-Free Quantitative Approaches: Spectral Counting andßData-ƯIndependent Analysis; Labeling Approaches; Isobaric Tagging; Stably Incorporated Labeled Amino Acids; Informatics; Targeted HIV-1 Proteomics andßtheßPath toßClinical Applications; Selective Reaction Monitoring; Quick Start Guide forßSRM.
Thinking Back toßOur Experiments andßMotivations Alternative Approaches; Affinity Pulldown Approaches; Antigen Presentation; Protein Arrays; Conclusions; References; Chapter 5: HIV-1 Sequencing; Introduction; Reasons Why Understanding HIV/SIV Variation Is Important fromßaßBiological andßProteomics Perspective; The Evolution ofßHIV/SIV Sequencing Technologies; HIV/SIV Deep Sequencing Methodologies; Pre-experimental Questions; Sequencing Methodology; Sequence Analysis; Trimming, Merging, andßMapping FASTQ Reads; Quantify theßFrequency ofßIndividual SNPs AcrossßtheßVirus Genome.