Plant Proteomics: From Genome Sequencing to Proteome Databases and Repositories - Plant Proteomics: Methods and Protocols - page 30

This database contains an organ-specific proteome map for
A . thaliana . The protein identifi cation information is displayed by
proteogenomic mapping of the peptides onto the genome.
Additional information on the identifi cation of proteins is linked,
such as the amino acid sequence of the fi rst splice variant of the
protein and the detected peptides sorted by their position in the
protein [ 7 ].

2.1.3 AtProteome

This database is a further development of AtProteome and pro-
vides proteome information on A . thaliana [ 40 ]. The Web site
shows the protein identifi cation information by proteogenomic
mapping of the peptides onto the genome. The TAIR9 dataset is
provided as the default dataset. The pep2pro data analysis pipeline
also handles data export to the PRIDE database [ 28 ] and data
retrieval by the MASCP Gator ( http://gator.masc-proteomics.
org/ ) .

2.1.4 pep2pro

PhosPhAt is a database of phosphorylation sites in A . thaliana .
The database contains ~1,200 defi ned tryptic peptides matching
~1,000 distinct proteins. Phosphorylation sites are marked as
“defi ned” if the precise location of the phosphorylated amino acid
has been unambiguously determined by mass spectrometric analy-
sis [ 41 , 42 ].

2.1.5 PhosPhAt

This database focuses on protein localization in A . thaliana . It
stores more than 6,700 nonredundant proteins observed in ten
distinct subcellular locations. Various experimental methods were
used for the localization, such as chimeric fl uorescent fusion pro-
teins, MS, literature references, and location prediction software
based on amino acid sequences [ 9 ].

2.1.6 SUBA

A comprehensive genome database for A . thaliana , The Arabidopsis
Information Resource (TAIR), also provides data repositories for
Arabidopsis proteomics resources: (1) primary protein sequences,
(2) protein domains, (3) protein structures including 3-D structure
images, (4) protein-protein interactions, (5) biochemical proper-
ties including enzymes and biochemical pathways [ 43 ].

2.1.7 TAIR

2.2 Rice Databases

DIPOS provides information on interacting proteins in rice ( Oryza
sativa ), where the interactions are predicted using two computa-
tional methods, interologs and domain-based methods [ 18 ]. An
interolog is a conserved interaction between a pair of proteins that
have interacting homologs in another organism [ 44 ]. The database
stores nearly 15 M pairwise interactions among 27,746 proteins.
Each interaction is assigned a confi dence score, and biological
explanations of pathways and interactions are also provided.

2.2.1 DIPOS