Proteomics

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Proteomics
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Proteomics

• 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.

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1. SWISS-2DPAGE database

• SWISS-2DPAGE is an annotated two-dimensional
  polyacrylamide gel electrophoresis (2-D PAGE)
  database established in 1993.
• 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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SWISS-2DPAGE Search Page
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• View entry in original SWISS-2DPAGE format
• Entry name VSP2_ARATH
• Primary accession number82122
• 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
• TaxonomyEukaryota Viridiplantae Streptophyta
  Embryophyta Tracheophyta Spermatophyta
  Magnoliophyta eudicotyledons core eudicots
  Rosidae eurosids II Brassicales Brassicaceae
  Arabidopsis.
• References1  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/MwHow to interpret a protein map
• Arabidopsis thaliana MAP LOCATIONS SPOT
  2D-001KKV pI6.47, Mw29849 the clicked spot
  
• MAPPING MASS SPECTROMETRY 1.

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Mass spectrometry (MS)
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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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3. Mascot

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

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• 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/20020713/FATeiic.dat)
• P82691 Mass 1011 Total score 25
  Peptides matched 1 Pyrokinin-1 (Pea-PK-1)
  (FXPRL-amide)
• P82041 Mass 1736 Total score 24 Peptides
  matched 1 Uperin 3.4 1. 3.
• P36396 Mass 2069 Total score 23
  Peptides matched 1 Sex-determining region Y
  protein (Testis-determining factor) (Fragment)

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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).

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Post-translational modifications Mass values used
in FindMod

• Modifications Abbreviation Monoisotopic Average
  __
• Acetylation ACET 42.0106 42.0373
• Amidation AMID -0.9840 -0.9847
• Beta-methylthiolation BMTH 45.9877118 46.08688
• Biotin BIOT 226.0776 226.2934
• Carbamylation CAM 43.00581 43.02502
• Citrullination CITR 0.9840276 0.98476
• C-Mannosylation CMAN 162.052823 162.1424
• Deamidation DEAM 0.9840 0.9847
• N-acyl diglyceride
• cysteine (tripalmitate) DIAC 788.7258 789.3202
• Dimethylation DIMETH 28.0314 28.0538
• FAD FAD 783.1415 783.542
• Farnesylation FARN 204.1878 204.3556
• Formylation FORM 27.9949 28.0104
• Geranyl-geranyl GERA 272.2504 272.4741
• Gamma-carboxyglutamic acid GGLU 43.98983 44.0098
• O-GlcNAc GLCN 203.0794 203.1950

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Biochemical Pathway Databases

• Linking the biochemical pathways together and
  integration with the genomic data are the great
  tasks of biochemical pathway databases.

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Metabolomics From Genes to Pathways
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Where do we go?

• Deconstruction of biological processes into
  their molecular components.

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DNA (Genomics)
RNA (Transcriptomics)
Protein (Proteomics)
Metabolites (Metabolomics)
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From Gene, genome, cell, organism, population,
toward System Biology
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What are we going to do?
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Fact Individual research units would not work
any more!

• Recommendation
• Team up!
• Go beyond your own, your institute, and your
  country boundaries.

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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.

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Fact A mass of data is available freely!

• Recommendation
• Learn how to use!
• Make use of them to develop technologies.

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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.

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Thanks for Your Attention
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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.