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Proteomics

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Proteomics directly

detects expression ofproteins.

Proteome research permits thediscovery of new protein markers

for diagnostic purposes and ofnovel molecular targets for drugdiscovery.

Proteomics

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1. SWISS-2DPAGE database

SWISS-2DPAGE is an annotated two-dimensional polyacrylamide gelelectrophoresis (2-D PAGE) databaseestablished in 1993.

The SWISS-2DPAGE database is maintainedby the Swiss Institute of Bioinformatics, in

collaboration with the Central ClinicalChemistry Laboratory of the GenevaUniversity 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 number:82122

Entered in SWISS-2DPAGE inRelease 13, December 2000Last modified inRelease 14, October 2001

Name and origin of the protein :DescriptionVegetative storage protein 2.

Gene name(s)VSP2 OR AT5G24770FromArabidopsis thaliana (Mouse-earcress). [TaxID: 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., SanchezJ.-C., Hochstrasser D.F., Thiellement H.;Submitted (OCT-2000) to the SWISS-2DPAGE database.

2D PAGE maps for identified proteinsCompute the theoretical pI/Mw

How to interpret a protein mapArabidopsis thaliana

MAP LOCATIONS: SPOT 2D-001KKV: pI=6.47, Mw=29849 *** the clickedspot ***

MAPPING: MASS SPECTROMETRY [1].

http://www.expasy.ch/cgi-bin/get-ch2d-entry?O82122http://www.ebi.ac.uk/newt/framedisplay.jsp?search=3702&from=wwwhttp://www.expasy.ch/cgi-bin/pi_tool?O82122http://www.expasy.ch/ch2d/expl-gifs.htmlhttp://www.expasy.ch/cgi-bin/ch2d-compute-map?ARABIDOPSIS,O82122,2D-001KKVhttp://www.expasy.ch/cgi-bin/map3/http://www.expasy.ch/cgi-bin/map3/http://www.expasy.ch/cgi-bin/map3/http://www.expasy.ch/cgi-bin/map3/http://www.expasy.ch/cgi-bin/ch2d-compute-map?ARABIDOPSIS,O82122,2D-001KKVhttp://www.expasy.ch/cgi-bin/ch2d-compute-map?ARABIDOPSIS,O82122,2D-001KKVhttp://www.expasy.ch/cgi-bin/ch2d-compute-map?ARABIDOPSIS,O82122,2D-001KKVhttp://www.expasy.ch/cgi-bin/ch2d-compute-map?ARABIDOPSIS,O82122,2D-001KKVhttp://www.expasy.ch/cgi-bin/ch2d-compute-map?ARABIDOPSIS,O82122,2D-001KKVhttp://www.expasy.ch/ch2d/expl-gifs.htmlhttp://www.expasy.ch/cgi-bin/pi_tool?O82122http://www.ebi.ac.uk/newt/framedisplay.jsp?search=3702&from=wwwhttp://www.expasy.ch/cgi-bin/get-ch2d-entry?O82122http://www.expasy.ch/cgi-bin/get-ch2d-entry?O82122http://www.expasy.ch/cgi-bin/get-ch2d-entry?O82122http://www.expasy.ch/cgi-bin/get-ch2d-entry?O82122

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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-specifiedpeptide masses are compared with the

theoretical peptides calculated for all

proteins in the SWISS-PROT/TrEMBLdatabases.

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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)

http://www.matrixscience.com/cgi/master_results.pl?file=../data/20020713/protein_view.pl?file=../data/20020713/FATeiic.dat&hit=1http://www.matrixscience.com/cgi/master_results.pl?file=../data/20020713/protein_view.pl?file=../data/20020713/FATeiic.dat&hit=1http://www.matrixscience.com/cgi/master_results.pl?file=../data/20020713/protein_view.pl?file=../data/20020713/FATeiic.dat&hit=2http://www.matrixscience.com/cgi/master_results.pl?file=../data/20020713/protein_view.pl?file=../data/20020713/FATeiic.dat&hit=3http://www.matrixscience.com/cgi/master_results.pl?file=../data/20020713/protein_view.pl?file=../data/20020713/FATeiic.dat&hit=3http://www.matrixscience.com/cgi/master_results.pl?file=../data/20020713/protein_view.pl?file=../data/20020713/FATeiic.dat&hit=3http://www.matrixscience.com/cgi/master_results.pl?file=../data/20020713/protein_view.pl?file=../data/20020713/FATeiic.dat&hit=2http://www.matrixscience.com/cgi/master_results.pl?file=../data/20020713/protein_view.pl?file=../data/20020713/FATeiic.dat&hit=2http://www.matrixscience.com/cgi/master_results.pl?file=../data/20020713/protein_view.pl?file=../data/20020713/FATeiic.dat&hit=1http://www.matrixscience.com/cgi/master_results.pl?file=../data/20020713/protein_view.pl?file=../data/20020713/FATeiic.dat&hit=1http://www.matrixscience.com/cgi/master_results.pl?file=../data/20020713/protein_view.pl?file=../data/20020713/FATeiic.dat&hit=1http://www.matrixscience.com/cgi/master_results.pl?file=../data/20020713/protein_view.pl?file=../data/20020713/FATeiic.dat&hit=1

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4. FindMod

This tool examines peptide mass

fingerprinting data for mass differences

between empirical and theoretical

peptides. Where mass differencescorrespond to a post-translational

modification (PTM).

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Post-

translational

modifications Mass

values used

in FindMod

Modifications Abbreviation MonoisotopicAverage __

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

Glucosylation (Glycation) GLUC 162.0528 162.1424

Hydroxylation HYDR 15.9949 15.9994

Lipoyl LIPY 188.033 188.3027

Methylation METH 14.0157 14.0269

Myristoylation MYRI 210.1984 210.3598

Palmitoylation PALM 238.2297 238.4136 Phosphorylation PHOS 79.9663 79.9799

Pyridoxal phosphate PLP 229.014 229.129

Phosphopantetheine PPAN 339.078 339.3234

Pyrrolidone carboxylic acid PYRR -17.0266 -17.0306

Sulfation SULF 79.9568 80.0642

Trimethylation TRIMETH 42.0471 42.0807

http://www.expasy.ch/tools/findmod/ACET.htmlhttp://www.expasy.ch/tools/findmod/ACET.htmlhttp://www.expasy.ch/tools/findmod/AMID.htmlhttp://www.expasy.ch/tools/findmod/AMID.htmlhttp://www.expasy.ch/tools/findmod/BMTH.htmlhttp://www.expasy.ch/tools/findmod/BMTH.htmlhttp://www.expasy.ch/tools/findmod/BIOT.htmlhttp://www.expasy.ch/tools/findmod/BIOT.htmlhttp://www.expasy.ch/tools/findmod/CAM.htmlhttp://www.expasy.ch/tools/findmod/CAM.htmlhttp://www.expasy.ch/tools/findmod/CITR.htmlhttp://www.expasy.ch/tools/findmod/CITR.htmlhttp://www.expasy.ch/tools/findmod/CMAN.htmlhttp://www.expasy.ch/tools/findmod/CMAN.htmlhttp://www.expasy.ch/tools/findmod/DEAM.htmlhttp://www.expasy.ch/tools/findmod/DEAM.htmlhttp://www.expasy.ch/tools/findmod/DIMETH.htmlhttp://www.expasy.ch/tools/findmod/DIMETH.htmlhttp://www.expasy.ch/tools/findmod/FAD.htmlhttp://www.expasy.ch/tools/findmod/FAD.htmlhttp://www.expasy.ch/tools/findmod/FARN.htmlhttp://www.expasy.ch/tools/findmod/FARN.htmlhttp://www.expasy.ch/tools/findmod/FORM.htmlhttp://www.expasy.ch/tools/findmod/FORM.htmlhttp://www.expasy.ch/tools/findmod/GERA.htmlhttp://www.expasy.ch/tools/findmod/GERA.htmlhttp://www.expasy.ch/tools/findmod/GGLU.htmlhttp://www.expasy.ch/tools/findmod/GGLU.htmlhttp://www.expasy.ch/tools/findmod/GLCN.htmlhttp://www.expasy.ch/tools/findmod/GLCN.htmlhttp://www.expasy.ch/tools/findmod/GLUC.htmlhttp://www.expasy.ch/tools/findmod/GLUC.htmlhttp://www.expasy.ch/tools/findmod/HYDR.htmlhttp://www.expasy.ch/tools/findmod/HYDR.htmlhttp://www.expasy.ch/tools/findmod/LIPY.htmlhttp://www.expasy.ch/tools/findmod/LIPY.htmlhttp://www.expasy.ch/tools/findmod/METH.htmlhttp://www.expasy.ch/tools/findmod/METH.htmlhttp://www.expasy.ch/tools/findmod/MYRI.htmlhttp://www.expasy.ch/tools/findmod/MYRI.htmlhttp://www.expasy.ch/tools/findmod/PALM.htmlhttp://www.expasy.ch/tools/findmod/PALM.htmlhttp://www.expasy.ch/tools/findmod/PHOS.htmlhttp://www.expasy.ch/tools/findmod/PHOS.htmlhttp://www.expasy.ch/tools/findmod/PLP.htmlhttp://www.expasy.ch/tools/findmod/PLP.htmlhttp://www.expasy.ch/tools/findmod/PPAN.htmlhttp://www.expasy.ch/tools/findmod/PPAN.htmlhttp://www.expasy.ch/tools/findmod/PYRR.htmlhttp://www.expasy.ch/tools/findmod/PYRR.htmlhttp://www.expasy.ch/tools/findmod/SULF.htmlhttp://www.expasy.ch/tools/findmod/SULF.htmlhttp://www.expasy.ch/tools/findmod/TRIMETH.htmlhttp://www.expasy.ch/tools/findmod/TRIMETH.htmlhttp://www.expasy.ch/tools/findmod/TRIMETH.htmlhttp://www.expasy.ch/tools/findmod/TRIMETH.htmlhttp://www.expasy.ch/tools/findmod/SULF.htmlhttp://www.expasy.ch/tools/findmod/SULF.htmlhttp://www.expasy.ch/tools/findmod/PYRR.htmlhttp://www.expasy.ch/tools/findmod/PYRR.htmlhttp://www.expasy.ch/tools/findmod/PPAN.htmlhttp://www.expasy.ch/tools/findmod/PPAN.htmlhttp://www.expasy.ch/tools/findmod/PLP.htmlhttp://www.expasy.ch/tools/findmod/PLP.htmlhttp://www.expasy.ch/tools/findmod/PHOS.htmlhttp://www.expasy.ch/tools/findmod/PHOS.htmlhttp://www.expasy.ch/tools/findmod/PALM.htmlhttp://www.expasy.ch/tools/findmod/PALM.htmlhttp://www.expasy.ch/tools/findmod/MYRI.htmlhttp://www.expasy.ch/tools/findmod/MYRI.htmlhttp://www.expasy.ch/tools/findmod/METH.htmlhttp://www.expasy.ch/tools/findmod/METH.htmlhttp://www.expasy.ch/tools/findmod/LIPY.htmlhttp://www.expasy.ch/tools/findmod/LIPY.htmlhttp://www.expasy.ch/tools/findmod/HYDR.htmlhttp://www.expasy.ch/tools/findmod/HYDR.htmlhttp://www.expasy.ch/tools/findmod/GLUC.htmlhttp://www.expasy.ch/tools/findmod/GLUC.htmlhttp://www.expasy.ch/tools/findmod/GLCN.htmlhttp://www.expasy.ch/tools/findmod/GLCN.htmlhttp://www.expasy.ch/tools/findmod/GLCN.htmlhttp://www.expasy.ch/tools/findmod/GLCN.htmlhttp://www.expasy.ch/tools/findmod/GGLU.htmlhttp://www.expasy.ch/tools/findmod/GGLU.htmlhttp://www.expasy.ch/tools/findmod/GGLU.htmlhttp://www.expasy.ch/tools/findmod/GGLU.htmlhttp://www.expasy.ch/tools/findmod/GERA.htmlhttp://www.expasy.ch/tools/findmod/GERA.htmlhttp://www.expasy.ch/tools/findmod/GERA.htmlhttp://www.expasy.ch/tools/findmod/GERA.htmlhttp://www.expasy.ch/tools/findmod/FORM.htmlhttp://www.expasy.ch/tools/findmod/FORM.htmlhttp://www.expasy.ch/tools/findmod/FARN.htmlhttp://www.expasy.ch/tools/findmod/FARN.htmlhttp://www.expasy.ch/tools/findmod/FAD.htmlhttp://www.expasy.ch/tools/findmod/FAD.htmlhttp://www.expasy.ch/tools/findmod/DIMETH.htmlhttp://www.expasy.ch/tools/findmod/DIMETH.htmlhttp://www.expasy.ch/tools/findmod/DEAM.htmlhttp://www.expasy.ch/tools/findmod/DEAM.htmlhttp://www.expasy.ch/tools/findmod/CMAN.htmlhttp://www.expasy.ch/tools/findmod/CMAN.htmlhttp://www.expasy.ch/tools/findmod/CMAN.htmlhttp://www.expasy.ch/tools/findmod/CMAN.htmlhttp://www.expasy.ch/tools/findmod/CITR.htmlhttp://www.expasy.ch/tools/findmod/CITR.htmlhttp://www.expasy.ch/tools/findmod/CAM.htmlhttp://www.expasy.ch/tools/findmod/CAM.htmlhttp://www.expasy.ch/tools/findmod/BIOT.htmlhttp://www.expasy.ch/tools/findmod/BIOT.htmlhttp://www.expasy.ch/tools/findmod/BMTH.htmlhttp://www.expasy.ch/tools/findmod/BMTH.htmlhttp://www.expasy.ch/tools/findmod/BMTH.htmlhttp://www.expasy.ch/tools/findmod/BMTH.htmlhttp://www.expasy.ch/tools/findmod/AMID.htmlhttp://www.expasy.ch/tools/findmod/AMID.htmlhttp://www.expasy.ch/tools/findmod/ACET.htmlhttp://www.expasy.ch/tools/findmod/ACET.html

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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 toPathways:

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http://localhost/var/www/apps/conversion/tmp/scratch_9//Chromosome/Workshop%20Manual/pg06.html

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Where do we go?

Deconstruction of biologicalprocesses 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,

towardSystem Biology

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What are we going to

do?

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Fact:

Individual research units wouldnot work any more!

Recommendation:

Team up!

Go beyond your own, your institute, andyour 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 developtechnologies.

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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.