复旦大学生命科学学院：《蛋白质组学》Defining proteomics

Proteome c 蛋白质組 复旦大学生命科学学院 吴超群 0/27/2005 Chaoqun Wu, Fudan University

10/27/2005 Chaoqun Wu, Fudan University Chaoqun Wu, Fudan University 1 Proteomic 复旦大学生命科学学院 吴超群

Defining Proteomics Branch of discovery science focusing on proteins a In 1994 defined as the complete set of proteins that is expressed and modified following expression by the entire genome in the lifetime of a cell. If we look at an organism it means that we are looking at the proteome of 3 trillion of cells and -1000 different cell types with different protein profiles a Can be more specific such as the complement of proteins expressed by a cell at any one time 1 Today proteomics is a scientific discipline that will bridge the gap between our understanding of genome sequences and cellular behavior 0/27/2005 Chaoqun Wu, Fudan University

10/27/2005 Chaoqun Wu, Fudan University Chaoqun Wu, Fudan University 2 Defining Proteomics Defining Proteomics Branch of discovery science focusing on proteins Branch of discovery science focusing on proteins In 1994 defined as In 1994 defined as “the complete set of proteins that is the complete set of proteins that is expressed and modified following expression by the expressed and modified following expression by the entire genome in the lifetime of a cell entire genome in the lifetime of a cell”. If we look at an . If we look at an organism it means that we are looking at the proteome of organism it means that we are looking at the proteome of 3 trillion of cells and ~1000 different cell types with 3 trillion of cells and ~1000 different cell types with different protein profiles. different protein profiles. Can be more specific such as the complement of Can be more specific such as the complement of proteins expressed by a cell at any one time. proteins expressed by a cell at any one time. Today proteomics is a scientifi Today proteomics is a scientific discipline that will bridge c discipline that will bridge the gap between our understanding of genome the gap between our understanding of genome sequences and cellular behavior. sequences and cellular behavior

Genomics and proteomics a new field with a new vocabulary Omics DNA Genome means area of research RNA Transcriptome proteins Proteome Metabolome Metabolites Protein-protein, Protein-DNA Interactome Protein-RNA interactions 10/27/2005 Chaoqun Wu, Fudan University

10/27/2005 Chaoqun Wu, Fudan University Chaoqun Wu, Fudan University 3 Genomics and Proteomics a new Genomics and Proteomics a new field with a new vocabulary field with a new vocabulary -Omics: means area means area of research of research DNA RNA proteins Metabolites Protein-protein, Protein-DNA, Protein-RNA interactions Genome Transcriptome Proteome Metabolome Interactome

The omics" nomenclature Genomics DNA ( Gene) Transcription Transcriptomics →RNA Functional Translation Genomics Proteomics PROTEIN Enzymatic reaction Metabolomics METABOLITE 0/27/2005 Chaoqun Wu, Fudan University

10/27/2005 Chaoqun Wu, Fudan University Chaoqun Wu, Fudan University 4 The “omics” nomenclature nomenclature… Genomics DNA (Gene) Functional Genomics Transcriptomics RNA Proteomics PROTEIN Metabolomics METABOLITE Transcription Translation Enzymatic reaction

Why study protein expression? Nucleus Cytosol Inactive mrNA RNA Degradation control Primary DNA RNA mRNA mRNA transcript Translation control RNA pr otein Modifier RNA ransport Transcriptional Processing control proteIn contro control Post-translational control 0/27/2005 Chaoqun Wu, Fudan University

10/27/2005 Chaoqun Wu, Fudan University Chaoqun Wu, Fudan University 5 Why study protein expression? Why study protein expression? Nucleus Cytosol Inactive mRNA RNA Degradation control RNA Transport control Translation control Post-translational control Primary RNA transcript Transcriptional control RNA Processing control DNA mRNA mRNA Modified protein protein

■ The proteome Protein complement of a genome vAriable In different cell and tissue types in same organism In different growth and developmental stages of organism I Dynamic Depends on response of genome to environmental factors Disease state m Drug challenge Growth conditions a Stress 0/27/2005 Chaoqun Wu, Fudan University

10/27/2005 Chaoqun Wu, Fudan University Chaoqun Wu, Fudan University 6 The proteome The proteome – – Protein complement of a gen in complement of a genome Variable Variable – – In different cell and tissue types in same organism In different cell and tissue types in same organism – – In different growth and developmental stages of In different growth and developmental stages of organism organism Dynamic Dynamic – – Depends on response of genome to environmental Depends on response of genome to environmental factors factors Disease state Disease state Drug challenge Drug challenge Growth conditions Growth conditions Stress

人类了解自己的历史 整体水平→器官水平细胞水平□→分子水平 系统生物学 0/27/2005 Chaoqun Wu, Fudan University

10/27/2005 Chaoqun Wu, Fudan University Chaoqun Wu, Fudan University 7

Content L. Introduction l. Proteomics and genomics ll. dentification and Quantification of proteins V Structural proteomics V. Identification of protein post- translational modifications VI. Protease degradomics Vll. Platforms for proteomics Vl. Mass Spectrometry IX. Post-MS Analysis X. Bioinformatics for proteomics 0/27/2005 Chaoqun Wu, Fudan University

10/27/2005 Chaoqun Wu, Fudan University Chaoqun Wu, Fudan University 8 Content I. Introduction II. Proteomics and Genomics III. Identification and Quantification of Proteins IV. Structural Proteomics V. Identification of Protein Post￾translational Modifications VI. Protease degradomics: VII. Platforms for proteomics VIII. Mass Spectrometry IX. Post-MS Analysis X. Bioinformatics for Proteomics

Part Introduction 0/27/2005 Chaoqun Wu, Fudan University

10/27/2005 Chaoqun Wu, Fudan University Chaoqun Wu, Fudan University 9 Part I. Introduction

二十世纪中期以来,随着DNA双 螺旋结构的提出和蛋白质空间结构的 X射线解析,开始了分子生物学时代, 对遗传信息载体DNA和生命功能的主 要体现者蛋白质的研究,成为生命科 学研究的主要内容。 0/27/2005 Chaoqun Wu, Fudan University

10/27/2005 Chaoqun Wu, Fudan University Chaoqun Wu, Fudan University 10 二十世纪中期以来，随着DNA双 螺旋结构的提出和蛋白质空间结构的 X射线解析，开始了分子生物学时代， 对遗传信息载体DNA和生命功能的主 要体现者蛋白质的研究，成为生命科 学研究的主要内容。 二十世纪中期以来，随着DNA双 螺旋结构的提出和蛋白质空间结构的 X射线解析，开始了分子生物学时代， 对遗传信息载体DNA和生命功能的主 要体现者蛋白质的研究，成为生命科 学研究的主要内容