Bioinformatic Tools in Crop Improvement - Crop Improvement: New Approaches and Modern Techniques - page 74

Table 2.6 Integrative databases for Proteomics and Protein (Polypeptide) analysis in plants

Database Name Plant Species/Purpose Uniform Resource Locator

(URL)

Matrix
Science—Mascot

Home page for peptide mass fin-
gerprint database, searches and
peptide identification

http://www.matrixscience.com/
search_form_select.html

Entrez Databases Entrez database and tools; a multi-

purpose proteomics site

http://www.ncbi.nlm.nih.gov/
About/tools/restable_mol.
html

Main Page—Mascp Arabidopsis proteomic multinational

sub-committee

http://www.masc-proteomics.
org/mascp/index.php/
Main_Page

World-2DPAGE
Constellation:
SWISS-2DPAGE

ExPASy Swiss protein 2D PAGE;
important web site for documen-
tation and software

http://world-2dpage.expasy.org/
swiss-2dpage/

The World-2DPAGE
Constellation

ExPASy Swiss protein 2D PAGE
site; important repository and
search engine software

http://world-2dpage.expasy.org/

Kazusa Genome
Resources

Genome and proteomic resources
from Miyakogusa.jp

http://genome.kazusa.or.jp/

Cyanobase CyanoBase; resources for

cyanobacteria

http://genome.kazusa.or.jp/
cyanobase

Rhizobase RhizoBase; resources for

rhyzobacteria

http://genome.kazusa.or.jp/
rhizobase/

MudPIT Multidimensional protein identifica-

tion technology

http://www.proteome.soton.
ac.uk/mudpit.htm

FTICR/MS
Technology

Fourier transform mass spectrom-
etry (FTMS) derived from ion
cyclotron resonance (ICR)
spectrometry

http://www.wangnmr.com/
FTICR_MS_technology.htm

DIGE Protein abundance changes using

dige multi-fluorescent dye

http://www.med.uc.edu/pro-
teomics/dige.htm

DECODON—Dif-
ferential in gel
electrophoresis
(DIGE)—image
analysis—Delta2D

Generic proteomics site for informa-
tion on methodologies

http://www.decodon.com/Solu-
tions/Delta2D/digeAnalysis.
html

Proteomics services:
2D DIGE, iTRAQ,
MS, and Phosphor-
ylation sites

Generic proteomics site for informa-
tion on methodologies

http://www.appliedbiomics.
com/

3Dye™ 2D DIGE Kits Kits and uses for 3Dye 2D DIGE http://www.lumiprobe.

com/p/2d-dige-kits

Isotope-Coded Affin-
ity Tags (ICAT)
Methodology

The ICAT methodology and its
uses—an interactive site

http://www.bio.davidson.edu/
courses/genomics/ICAT/
ICAT.html

ICAT, Quantitation,
Quantification, Iso-
tope Coded Affinity
Tag Technology

ICAT uses in relative quantitative
proteomics, especially regulation

http://www.creative-proteomics.
com/ICAT.htm