Biology Reference
In-Depth Information
increasing, now including resources such as DIPOS and PRIN for
rice [
18
,
19
]. Furthermore, several databases have been organizing
omics including transcriptome data and metabolomic pathways,
including ProMEX [
8
], the Soybean Proteome Database [
15
], and
SoyKB [
20
]. In this chapter, we also introduce the Web-based pro-
teomic tools and prediction programs GelMap [
21
], iLoc-Plant
[
22
], MRMaid [
23
], Musite [
24
], PeptideAtlas SRM Experiment
Library (PASSEL) [
25
], PredPlantPTS1 [
26
], ProteoRed MIAPE
[
27
], and a general database relating to plant proteomics,
Proteomics Identifi cations (PRIDE) database [
28
].
Based on the efforts of the Human Proteome Organization
Proteomics Standards Initiative (HUPO PSI-MI), molecular interac-
tion data have been standardized and a common query interface (PSI
Common QUery InterfaCe, PSICQUIC,
http://code.google.
com/p/psicquic/
)
was developed [
29
]. This service allows the que-
rying of nearly 30 molecular interaction databases all together.
Interfaces such as these are desirable in the fi eld of plant proteomics.
Genomic and proteomic studies have an interdependent rela-
tionship such that the development of one enhances development
of the other. In the last decade, the availability of nucleotide
sequences has accelerated the identifi cation of proteins obtained by
mass spectrometry (MS) and/or protein sequencers [
30
]. This
acceleration has been greatly enhanced by the availability of the
genomic sequences that have replaced EST sequences in recent
years. The interdependency in the reverse direction might be
referred to as proteogenomics [
31
-
34
]. It aims at improving
genome annotation by using proteomic information based on MS.
The information based on proteogenomics is also applicable to
several analyses including frameshifts of coding sequences and
posttranslational modifi cations such as N-terminal methionine
excision, signal peptides, and proteolysis [
34
,
35
]. The proteoge-
nomics approach has been applied to
A
.
thaliana
[
36
].
2
Plant Proteome Databases and Repositories
Here we summarize the representative databases and Web sites
relating to plant proteomics. Each section is presented in alpha-
betical order. The URLs are tabulated in Table
2
.
2.1 Arabidopsis
Thaliana Databases
This database was developed for chloroplast proteome data from
A
.
thaliana
. The proteome datasets were extracted from
Arabidopsis
leaves. LC-MS/MS-based analysis was used to identify ~1,300
proteins from more than 10,000 unique peptide sequences. The
partitioning of each protein in the three chloroplast compartments
was validated by using a semiquantitative proteomics approach
(spectral count). The chloroplasts were purifi ed by Percoll density
gradients and SDS-PAGE [
37
].
2.1.1 AT_CHLORO
