Biology Reference
In-Depth Information
database are deleted afterwards in several months or a couple of
years. The report demonstrated that UniProtKB was more stable
than IPI and NCBI gi numbers. In recent years, the data deposited
in publicly available proteomic databases have been increasing.
There has been concern that automatic curation of repository data
is dependent on analyses that could cause misannotation. Both
database developers and users should be aware of these potential
issues.
A posteriori
detection of such data encountered in typical
proteomics datasets was also studied [
59
].
4
Conclusion
In recent years, a large amount of proteomic information including
data related to biological functions has been created through pro-
teomic research interlocked with genomic research. The proteomic
databases we have introduced here have made such information
publicly available. In plants, only a few species have complete
genomic information but proteomic techniques can also be applied
to species without genomic information. Proteomics techniques
are useful to clarify the biological mechanisms underlying important
plant traits, and proteomic databases will contribute to the estab-
lishment of technology to regulate and enhance such biological
mechanisms and improve plant productivity.
References
1. Komatsu S, Konishi H, Shen S et al (2003) Rice
proteomics: a step toward functional analysis of
the rice genome. Mol Cell Proteomics 2:2-10
2. Komatsu S, Yano H (2006) Update and chal-
lenges on proteomics in rice. Proteomics
6:4057-4068
3. Salekdeh GH, Komatsu S (2007) Crop pro-
teomics: aim at sustainable agriculture of
tomorrow. Proteomics 7:2976-2996
4. Komatsu S, Ahsan N (2009) Soybean pro-
teomics and its application to functional analy-
sis. J Proteomics 72:325-336
5. Plant genomes central: genome projects in
progress.
http://www.ncbi.nlm.nih.gov/
genomes/PLANTS/PlantList.html
.
Accessed
10 Feb 2012
6. The Angiosperm Phylogeny Group (2009) An
update of the Angiosperm Phylogeny Group
classifi cation for the orders and families of
fl owering plants: APG III. Bot J Linn Soc
161:105-121
7. Baerenfaller K, Grossmann J, Grobei MA et al
(2008) Genome-scale proteomics reveals
Arabidopsis thaliana
gene models and pro-
teome dynamics. Science 320:938-941
8. Hummel J, Niemann M, Wienkoop S et al
(2007) ProMEX: a mass spectral reference
database for proteins and protein phosphoryla-
tion sites. BMC Bioinformatics 8:216
9. Heazlewood JL, Verboom RE, Tonti-Filippini
J et al (2006) SUBA: the
Arabidopsis
subcellular
database. Nucleic Acids Res 35:D213-D218
10. Komatsu S, Kojima K, Suzuki K et al (2004)
Rice Proteome Database based on two-
dimensional polyacrylamide gel electrophore-
sis: its status in 2003. Nucleic Acids Res
32:D388-D392
11. Helmy M, Tomita M, Ishihama Y (2011)
OryzaPG-DB: rice proteome database based
on shotgun proteogenomics. BMC Plant Biol
11:63
12. Friso G, Giacomelli L, Ytterberg AJ et al
(2004) In-depth analysis of the thylakoid
membrane proteome of
Arabidopsis thaliana
chloroplasts: new proteins, new functions, and
a plastid proteome database. Plant Cell
16:478-499
13. Sun Q, Zybailov B, Majeran W et al (2008)
PPDB, the plant proteomics database at
Cornell. Nucleic Acids Res 37:D969-D974
