What is proteomics? 1 Defined as the analysis of the entire protein complement in a given cell, tissue, or organism.” ■ Proteomics“ also assesses activities modifications, localization and interactions of proteins in complexes a Proteomes of organisms share intrinsic differences across species and growth conditions 0/27/2005 Chaoqun Wu, Fudan University
10/27/2005 Chaoqun Wu, Fudan University Chaoqun Wu, Fudan University 16 What is Proteomics? What is Proteomics? Defined as Defined as “the analysis of the entire protein the analysis of the entire protein complement in a given cell, tissue, or complement in a given cell, tissue, or organism. organism.” Proteomics Proteomics “also assesses activities, also assesses activities, modifications, localization, and interactions modifications, localization, and interactions of proteins in complexes. of proteins in complexes.” Proteomes of organisms share intrinsic Proteomes of organisms share intrinsic differences across species and growth differences across species and growth conditions. conditions
The role of proteomics The existence of an ore does not imply the existence of a functional gene Limitations of comparative genomics mRNa levels may not correlate with protein levels Protein modifications> post-transcriptional modifications, isoforms, post-translational modifications, mutants Issues of proteolysis, sequestration, etc relevant only at the protein level Protein complex composition, protein-protein Interactions, structures 0/27/2005 Chaoqun Wu, Fudan University
10/27/2005 Chaoqun Wu, Fudan University Chaoqun Wu, Fudan University 17 The Role of Proteomics ¾ The existence of an ORF does not imply the existence of a functional gene. ¾ Limitations of comparative genomics. ¾ mRNA levels may not correlate with protein levels. ¾ Protein modifications Æ post-transcriptional modifications, isoforms, post-translational modifications, mutants. ¾ Issues of proteolysis, sequestration, etc. relevant only at the protein level. ¾ Protein complex composition, protein-protein interactions, structures
Proteins classes for Analysis ■ Membrane a Soluble proteins ■ Nuclear a Chromosome-associated ■ Phosphorylated a Glycosylated ■ Complexes 0/27/2005 Chaoqun Wu, Fudan University
10/27/2005 Chaoqun Wu, Fudan University Chaoqun Wu, Fudan University 18 Proteins classes for Analysis Proteins classes for Analysis Membrane Membrane Soluble proteins Soluble proteins Nuclear Nuclear Chromosome Chromosome-associated associated Phosphorylated Phosphorylated Glycosylated Glycosylated Complexes Complexes
Proteomics A functional understanding of the cell Definition. a proteome is the entire protein complement expressed by a given biological system in given conditions” Wilkins et al., Bio Technology 14, 61-65 (1996) 0/27/2005 Chaoqun Wu, Fudan University
10/27/2005 Chaoqun Wu, Fudan University Chaoqun Wu, Fudan University 19 Proteomics Proteomics A functional understanding of the cell A functional understanding of the cell Definition: “A proteome is the entire protein A proteome is the entire protein complement expressed by a given complement expressed by a given biological system in given biological system in given conditions conditions ” Wilkins Wilkins et al., BioTechnology BioTechnology 14,61-65 (1996) 65 (1996)
Classification EXpression proteomics up and down-regulation of protein level e.g. normal and tumor cell, rest and drug- induced cell, mature and inmature cell malignant, metastatic cancer cells etc Functional proteomics characterization of cellular compartments multiprotein complexes, protein interaction net and signaling pathway, etc 0/27/2005 Chaoqun Wu, Fudan University
10/27/2005 Chaoqun Wu, Fudan University Chaoqun Wu, Fudan University 20 • Expression proteomics: up and down-regulation of protein level, e.g. normal and tumor cell, rest and druginduced cell, mature and inmature cell, malignant, metastatic cancer cells etc. • Functional proteomics: characterization of cellular compartments, multiprotein complexes, protein interaction net and signaling pathway,etc. Classification