Download Introduction Primary Structure Analysis Protein Sequence Searching

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
MW
pI
Introduction
Primary
Structure Analysis
Protein
Sequence Searching
Protein
Sequence Alignment
Proteomics
Protein
Useful
Tools
Identification
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
kDa
150
Increase
of 50%
70
60
Decrease
of 50%
42
Unmatched
spots
Matched
spots
10
pH
3.5
10
http://www.expasy.ch/melanie/
Standard Proteome Analysis by
2DE-MS
Mass Fingerprint
Searching in
http://www.expas
ych/tools/peptide
nt.html
Current Opinion in
Chemical Biology 2000,
4:489–494

Introduction

Primary Structure Analysis


Protein Sequence Searching
Protein Sequence Alignment

Proteomics Tools

Protein Identification

Useful Bio-websites
Gel
Control
Treated sample
gel
membrane
+
Transfer proteins from gel to PVDF membrane
Sequencing
(Very time-Consuming)
Mass spectrometry
kcw1212-1 14 (1.129) Cn (Cen,4, 50.00, Ht); Sm (SG, 1x2.00); Sb (15,10.00 ); Cm (6:15)
1132.917
100
1: TOF LD+
7.95e3
1791.532
1792.532
1133.923
%
1517.239
1793.535
1518.245
965.893
1134.924
1500.215
966.895
1519.244
1022.925
1794.537
1189.963
1190.965 1349.235
1248.008 1350.239
1351.239
1023.925
2216.861
1848.577
1574.283
1576.280 1774.531
2168.845
1850.563
1851.577
0
900
2217.870
2218.857
2126.732
2344.987
2552.115
2732.213
2810.387 2866.446
m/z
1000
1100
1200
1300
1400
1500
1600
1700
1800
1900
2000
2100
2200
2300
2400
2500
2600
2700
2800
2900
For peptide
mass
fingerprint
data
pI and MW
Species

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/