Bioinformatics on Proteomics

Hsueh-Fen Juan

April 24, 2003

NTNU

Bioinformatics

?

Outline Introduction Primary Structure Analysis Protein Sequence Searching Protein Sequence Alignment Proteomics Tools Protein Identification Useful Bio-websites

Introduction

Primary Structure Analysis

Protein Sequence Searching Protein Sequence Alignment

Proteomics Tools

Protein Identification

Useful Bio-websites

Introduction ExPaSy: Expert Protein Analysis System SWISS-PROT: Protein knowledgebase TrEMBL: Computer-annotated supplement

to Swiss-Prot

Proteomics

Introduction

Primary Structure Analysis

Protein Sequence Searching Protein Sequence Alignment

Proteomics Tools

Useful Bio-websites

Primary Structure Analysis Object:

To compute the characters of proteins.

-Amino acid composition

-Atomic composition

-pI

-Molecular weight

Amino Acid & Atomic Composition

ProtParam

http://www.expasy.ch/tools/protparam.html

Amino Acid Composition

Atomic Composition

Computing pI and MW

MWpI

Introduction

Primary Structure Analysis

Protein Sequence Searching

Protein Sequence Alignment

Proteomics Tools

Protein Identification

Useful Bio-websites

P02571

Introduction

Primary Structure Analysis

Protein Sequence Searching Protein Sequence Alignment

Proteomics Tools

Protein Identification

Useful Bio-websites

Similarity is very low

No similarity

Introduction

Primary Structure Analysis

Protein Sequence Searching Protein Sequence Alignment

Proteomics Tools

Protein Identification

Useful Bio-websites

The Information Stored in Genes Is Expressed by a Multistage Process

Eur J Nucl Med 2002, 29, 115-32

http://www.expasy.ch/tools/

DNA Protein

Nature 2000, 405, 837-846

3.5 1010

42

6070

150

kDa

pH

Increase of 50%

Decrease of 50%

Unmatched spots

Matched spots

http://www.expasy.ch/melanie/

Standard Proteome Analysis by 2DE-MS

Current Opinion in Chemical Biology 2000, 4:489–494

Mass Fingerprint Searching in http://www.expasych/tools/peptident.html

Introduction

Primary Structure Analysis

Protein Sequence Searching Protein Sequence Alignment

Proteomics Tools

Protein Identification

Useful Bio-websites

Control Treated sample

Gel

+

-gel

membrane

Transfer proteins from gel to PVDF membrane

Sequencing (Very time-Consuming)

900 1000 1100 1200 1300 1400 1500 1600 1700 1800 1900 2000 2100 2200 2300 2400 2500 2600 2700 2800 2900m/z0

100

%

kcw1212-1 14 (1.129) Cn (Cen,4, 50.00, Ht); Sm (SG, 1x2.00); Sb (15,10.00 ); Cm (6:15) 1: TOF LD+ 7.95e31132.917

965.893

966.895

1022.925

1023.925

1791.532

1133.923

1517.239

1134.9241500.215

1189.9631349.2351190.965

1248.008 1350.239

1351.239

1518.245

1519.244

1574.283

1774.5311576.280

1792.532

1793.535

1794.537

2216.8611848.5772168.845

1850.563

1851.577 2126.732

2217.8702218.857

2810.3872344.987

2552.1152732.213 2866.446

Mass spectrometry

For peptide mass fingerprint data

Species

pI and MW

Introduction

Primary Structure Analysis

Protein Sequence Searching Protein Sequence Alignment

Proteomics Tools

Protein Identification

Useful Bio-websites

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/

PROSITE is a database of protein families and domains.

http://tw.expasy.org/prosite/

http://tw.expasy.org/alinks.html

http://tw.expasy.org/alinks.html#PTM

http://www.cbs.dtu.dk/databases/PhosphoBase/