Biology Reference
In-Depth Information
3,404 nonredundant sites of phosphorylation on 829 proteins.
Through a Web-based interface, users can browse identifi ed proteins
or search for proteins of interest, and also conduct BLAST searches
of the database using peptide sequences and phosphorylation
motifs as queries [
48
].
This database stores plant protein phosphorylation site data, orga-
nizing information on 32,963 nonredundant sites collected from
23 experimental studies of six plant species. The data can be
searched for a protein of interest using an integrated BLAST module
to query similar sequences with known phosphorylation sites [
49
].
2.3.3 P3DB
The plprot is a plastid proteome database that provides informa-
tion about the proteomes of chloroplasts, etioplasts, and undiffer-
entiated plastids. The database stores more than 2,000 proteins.
The basic module integrates a homology search and comparative
information on the proteomes of different plastid types. Data from
A
.
thaliana
, tobacco, and rice are contained in the database [
16
].
2.3.4 plprot
PPDB is a Plant Proteome DataBase for
A
.
thaliana
and maize
(
Zea mays
). PPDB was developed for plant plastids and expanded
to the whole plant proteome. The name of the database was
changed accordingly, using the same abbreviation, from Plastid
PDB to Plant PDB. The current database has large-scale proteomic
data in diverse forms: (1) 5,000 identifi ed proteins both in
Arabidopsis
and maize, (2) 80 published
Arabidopsis
proteome
datasets from subcellular compartments or organs linked to each
locus, and (3) 1,500
Arabidopsis
proteins manually assigned sub-
cellular locations. Information from MS-based identifi cation and
posttranslational modification is available for each identified
protein [
12
,
13
].
2.3.5 PPDB
The PRIDE database provides standardized MS proteomics data.
It is one of the main repositories of proteomics data that have been
generated by MS approaches. Recently, it has become a database
that various journals in the fi eld are supporting and even mandat-
ing deposition of proteomics data in. Datasets are stored in PRIDE
without modifi cation or reanalysis, and the research community
can access the original results obtained by the research group [
28
].
2.3.6 PRIDE
ProMEX is a database of MS/MS reference spectra (mostly
Orbitrap precursor ion mass data) from
plants and microbes
[
8
,
42
,
60
]. The data were generated based on liquid chromatography
coupled to ion trap MS (LC-IT-MS). This current release 2.9/2012
contains 51,793 tryptic peptide product ion spectra entries of
27,886 different peptide sequence entries from
Medicago truncatula
,
Chlamydomonas reinhardtii
,
Bradyrhizobium japonicum
,
Arabidopsis
thaliana
,
Phaseolus vulgaris
,
Lotus japonicus
,
Lotus corniculatus
,
2.3.7 ProMEX
