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Proteomics.  Proteomics directly detects expression of proteins.  Proteome research permits the discovery of new protein markers for diagnostic purposes.

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Presentation on theme: "Proteomics.  Proteomics directly detects expression of proteins.  Proteome research permits the discovery of new protein markers for diagnostic purposes."— Presentation transcript:

1 Proteomics

2  Proteomics directly detects expression of proteins.  Proteome research permits the discovery of new protein markers for diagnostic purposes and of novel molecular targets for drug discovery. Proteomics

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4 1. SWISS-2DPAGE database SWISS-2DPAGE is an annotated two- dimensional polyacrylamide gel electrophoresis (2-D PAGE) database established in The SWISS-2DPAGE database is maintained by the Swiss Institute of Bioinformatics, in collaboration with the Central Clinical Chemistry Laboratory of the Geneva University Hospital.

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6 SWISS-2DPAGE Search Page

7 View entry in original SWISS-2DPAGE format Entry name: VSP2_ARATH Primary accession number:82122 Entered in SWISS-2DPAGE inRelease 13, December 2000 Last modified in Release 14, October 2001 Name and origin of the protein: DescriptionVegetative storage protein 2. Gene name(s)VSP2 OR AT5G24770 From Arabidopsis thaliana (Mouse-ear cress). [TaxID: 3702]3702 TaxonomyEukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids II; Brassicales; Brassicaceae; Arabidopsis. References[1] MAPPING ON GEL. Sarazin B., Tonella L., Marques K., Paesano S., Chane-Favre L., Sanchez J.-C., Hochstrasser D.F., Thiellement H.; Submitted (OCT-2000) to the SWISS-2DPAGE database. 2D PAGE maps for identified proteins Compute the theoretical pI/Mw How to interpret a protein mapCompute the theoretical pI/Mw How to interpret a protein map Arabidopsis thaliana MAP LOCATIONS: SPOT 2D-001KKV: pI=6.47, Mw=29849 *** the clicked spot ***2D-001KKV MAPPING: MASS SPECTROMETRY [1].[1]

8 Mass spectrometry (MS)

9 2. PeptIdent PeptIdent is a tool that allows the identification of proteins using pI, MW and peptide mass fingerprinting data. Experimentally measured, user-specified peptide masses are compared with the theoretical peptides calculated for all proteins in the SWISS-PROT/TrEMBL databases.

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11 3. Mascot Mascot is a powerful search engine that uses mass spectrometry data to identify proteins from primary sequence databases.

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13 Concise Protein Summary Report Switch to full Protein Summary Report To create a bookmark for this report, right click this link: Concise Summary Report (../data/ /FATeiic.dat) P82691 Mass: 1011 Total score: 25 Peptides matched: 1 Pyrokinin-1 (Pea-PK-1) (FXPRL-amide)P82691 P82041 Mass: 1736 Total score: 24 Peptides matched: 1 Uperin P82041 P36396 Mass: 2069 Total score: 23 Peptides matched: 1 Sex- determining region Y protein (Testis-determining factor) (Fragment)P36396

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15 4. FindMod This tool examines peptide mass fingerprinting data for mass differences between empirical and theoretical peptides. Where mass differences correspond to a post-translational modification (PTM).

16 Post- translational modification s Mass values used in FindMod ModificationsAbbreviationMonoisotopic Average __ AcetylationACET Acetylation AmidationAMID Amidation Beta-methylthiolationBMTH Beta-methylthiolation BiotinBIOT Biotin CarbamylationCAM Carbamylation CitrullinationCITR Citrullination C-MannosylationCMAN C-Mannosylation DeamidationDEAM Deamidation N-acyl diglyceride cysteine (tripalmitate)DIAC DimethylationDIMETH Dimethylation FADFAD FAD FarnesylationFARN Farnesylation FormylationFORM Formylation Geranyl-geranylGERA Geranyl-geranyl Gamma-carboxyglutamic acidGGLU Gamma-carboxyglutamic acid O-GlcNAcGLCN O-GlcNAc Glucosylation (Glycation)GLUC Glucosylation (Glycation) HydroxylationHYDR Hydroxylation LipoylLIPY Lipoyl MethylationMETH Methylation MyristoylationMYRI Myristoylation PalmitoylationPALM Palmitoylation PhosphorylationPHOS Phosphorylation Pyridoxal phosphatePLP Pyridoxal phosphate PhosphopantetheinePPAN Phosphopantetheine Pyrrolidone carboxylic acidPYRR Pyrrolidone carboxylic acid SulfationSULF Sulfation TrimethylationTRIMETH Trimethylation

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19 Biochemical Pathway Databases Linking the biochemical pathways together and integration with the genomic data are the great tasks of biochemical pathway databases.

20 Metabolomics: From Genes to Pathways:

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26 Where do we go? “Deconstruction of biological processes into their molecular components”.

27 DNA (Genomics) RNA (Transcriptomics) Protein (Proteomics) Metabolites (Metabolomics)

28 From: Gene, genome, cell, organism, population,… toward System Biology

29 What are we going to do?

30 Fact: Individual research units would not work any more! Recommendation: Team up! Go beyond your own, your institute, and your country boundaries.

31 Fact: Genomic data are suppose to reduce time and efforts for preparation of reagents, resources and information. Recommendation: Think big! Search and use data intelligently. Turn attention to complex biology from various angles, i.e. have all needed specialty in your team.

32 Fact: A mass of data is available freely! Recommendation: Learn how to use! Make use of them to develop technologies.

33 Fact: Biology world is rapidly changing! Recommendation: Keep up with changes! Re-establish systems with more flexibility and more freedom. Loose regulations for funding, employment, etc. Re-design your research project.

34 Thanks for Your Attention

35 Cautions: One protein with different roles: Alpha-enolase in liver T-crystallin in eye lens One structure in proteins with diverse functions: TIM barrels in isomerases, oxidoreductase and hydrolases. 30% error in automated annotations.


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