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Bioinformatics on Proteomics Hsueh-Fen Juan April 24, 2003 NTNU
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Bioinformatics ?
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Outline Introduction Primary Structure Analysis Protein Sequence Searching Protein Sequence Alignment Proteomics Tools Protein Identification Useful Bio-websites
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Introduction Primary Structure Analysis Protein Sequence Searching Protein Sequence Alignment Proteomics Tools Protein Identification Useful Bio-websites
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Introduction ExPaSy: Expert Protein Analysis System SWISS-PROT: Protein knowledgebase TrEMBL: Computer-annotated supplement to Swiss-Prot
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Proteomics
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Introduction Primary Structure Analysis Protein Sequence Searching Protein Sequence Alignment Proteomics Tools Useful Bio-websites
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Primary Structure Analysis Object: To compute the characters of proteins. -Amino acid composition -Atomic composition -pI -Molecular weight
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Amino Acid & Atomic Composition ProtParam
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http://www.expasy.ch/tools/ protparam.html
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Amino Acid Composition Atomic Composition
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Computing pI and MW
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MW pIpI
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Introduction Primary Structure Analysis Protein Sequence Searching Protein Sequence Alignment Proteomics Tools Protein Identification Useful Bio-websites
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P02571
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Introduction Primary Structure Analysis Protein Sequence Searching Protein Sequence Alignment Proteomics Tools Protein Identification Useful Bio-websites
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Similarity is very low No similarity
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Introduction Primary Structure Analysis Protein Sequence Searching Protein Sequence Alignment Proteomics Tools Protein Identification Useful Bio-websites
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The Information Stored in Genes Is Expressed by a Multistage Process Eur J Nucl Med 2002, 29, 115-32
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http://www.expasy.ch/tools/
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DNA Protein
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Nature 2000, 405, 837-846
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3.510 42 60 70 150 kDa pH Increase of 50% Decrease of 50% Unmatched spots Matched spots
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http://www.expasy.ch/melanie/
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Standard Proteome Analysis by 2DE-MS Current Opinion in Chemical Biology 2000, 4:489–494 Mass Fingerprint Searching in http://www.expas ych/tools/peptide nt.html
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Introduction Primary Structure Analysis Protein Sequence Searching Protein Sequence Alignment Proteomics Tools Protein Identification Useful Bio-websites
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ControlTreated sample Gel
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+ - gel membrane Transfer proteins from gel to PVDF membrane Sequencing (Very time-Consuming)
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Mass spectrometry
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For peptide mass fingerprint data
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Species pI and MW
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Introduction Primary Structure Analysis Protein Sequence Searching Protein Sequence Alignment Proteomics Tools Protein Identification Useful Bio-websites
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Useful Bio Websites PROSITE http://tw.expasy.org/prosite/ Amos' WWW links page http://tw.expasy.org/alinks.html Phosphoprotein Database (PPDB) http://www-lmmb.ncifcrf.gov/phosphoDB/
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PROSITE is a database of protein families and domains. http://tw.expasy.org/prosite/
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http://tw.expasy.org/alinks.html
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http://tw.expasy.org/alinks.html#PTM
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http://www.cbs.dtu.dk/databases/PhosphoBase/
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