Biology Reference
In-Depth Information
Lycopersicon esculentum
,
Solanum tuberosum
,
Nicotiana tabacum
,
Sinorhizobium meliloti
,
Glycine max
, and
Zea mays
. Furthermore a
search algorithm is implemented which allows to search single
spectra and mzXML-LC-MS/MS runs against the database.
Protein data are linked to “omes” such as metabolites, pathways,
and transcripts. Peptide identifi cation was based on peptide mass
fi ngerprinting [
50
].
This database stores reference maps of soybean (
Glycine max
cv.
Maverick) proteins based on 2-DE. The samples were collected
during seed fi lling in the plant and analyzed at 2, 3, 4, 5, and 6
weeks after fl owering. It contains expression profi les for 679 pro-
tein spots, from which 422 proteins representing 216 nonredun-
dant proteins were identifi ed [
14
].
2.3.8 Proteomics
of Oilseeds
This Web site provides information both on quantitative seed pro-
teomic data and on seed-related protocols. As a proteomic data-
base, it gives access to 475 different
Arabidopsis
seed proteins
annotated from 2-DE maps, including quantitative data according
to the accumulation profi le of each protein during the germination
process. The Web site also provides protocols that the authors have
routinely used for
Arabidopsis
seed proteome studies, such as pro-
cedures for sample preparation, electrophoresis coupled with gel
analysis in 2-D electrophoresis, and protein identifi cation by mass
spectrometry [
51
].
2.3.9 Seed Proteome
Web Portal
The current version of this database contains 23 reference maps of
soybean (
G
.
max
cv. Enrei) proteins based on 2-DE [
15
]. The
samples were collected from several organs, tissues, and organelles.
The reference maps include 8,262 detected proteins and 672 iden-
tifi ed proteins, or proteins for which a sequence or a peptide peak
has been determined. An omics aspect is also included as a table
linked to temporal expression profi les that reveals relationships
among 106 mRNAs, 51 proteins, and 89 metabolites that vary
over time under fl ooding stress (Fig.
1
). The Web interface is
representative of proteome databases based on 2-DE, and was
developed using the Make2DDB II environment [
52
], which
serves a standardized search function for the stored protein spots
based on the accession number, description of the protein, and
isoelectric point/molecular weight range. The database focuses on
the seedling stage in soybean, 0-7 days after seedling emergence,
and in this it differs from the Proteomics of Oilseeds [
14
].
2.3.10 Soybean
Proteome Database
SoyKB abbreviates Soybean Knowledge Base and stores multiple
“omes” including temporal profi les of proteins detected from
soybean (
G
.
max
cv. Williams 82) [
20
]. The proteomic data are
available for seeds, roots, and root hairs and for multiple conditions.
2.3.11 SoyKB
