What is new in PPDB:

2014

  • The latest maize genome high confidence gene set (39,475 genes and 63241 gene models; version (Plant Ensembl v3.21; FTP site ftp://ftp.ensemblgenomes.org/pub/release-21/plants/fasta/zea_mays/pep/) incorporated into PPDB. Bi-directional BLAST search results to Arabidopsis thaliana (TAIRv7), rice (v7), PFAM domains, subcellular localization predictions (TargetP) and protein transmembrane predictions (TMHMM) are available.
  • The latest rice genome assembly from Orysa sativa, spp Japonica (cv Nipponbare) (56143 gene and 66495 gene models; FTP site ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/all.dir/) (Kawahara et al 2013 Rice 7) is incorporated into PPDB. Bi-directional BLAST search results to Arabidopsis thaliana (TAIRv7), maize (4a.53 and 3.21), PFAM domains, subcellular localization predictions (TargetP) and protein transmembrane predictions (TMHMM) are available.

2013

2012

2011

  • The Arabidopsis database is updated to TAIR v10 (27416 genes and 35386 gene models; FTP site ftp://ftp.arabidopsis.org/home/tair/Sequences/blast_datasets/TAIR10_blastsets/)

2010

  • Experimental data are available underlying the study" Reconstruction of metabolic pathways, protein expression and homeostasis machineries across maize bundle sheath and mesophyll chloroplasts; large scale quantitative proteomics using the first maize genome assembly" (Friso et al 2010, Plant Physiology).

2009

  • Gene annotation of maize genome sequence release 4a53 is loaded into PPDB. Reciprocal BLAST results between maize, rice and arabidopsis is available.
  • Subcellular localization predictions, PFAM domains and physiical-chemical properties are listed for each 4a53 maize protein.

2008

  • New NAR paper describe PPDB database and software. (PMID:18832363
  • Gene annotation of maize genome sequence release 2b5 is loaded into PPDB. Reciprocal BLAST results between maize, rice and arabidopsis is available.
  • TAIR provides links to PPDB for each Arabidopsis gene locus.
  • curated assignment of plasma membrane proteins (Ath).
  • switch the database to Arabidopsis genome annotation v8 - MS/MS data used for the PLOSONE paper are all researched against v8
  • incorporation of a large scale chloroplast proteome analysis of Arabidopsis - this includes subcellular location and post-translational modification analysis (published in PLOSONE, Zybailov et al.)
  • experimental data on the comparative analysis of maize bundle sheath and mesophyll membrane proteomes available - published in (Majeran et al., 2008).

2007

  • The name of PPDB is changed to Plant Proteome Database

2006

  • We have captured data from 58 proteomics publications (Arabidopsis and Brassica ). The data set have been deposited into PPDB.
  • newly curated location based on experimental evidence for hundreds of plastid proteins, including nucleoids, ribosomes, and plastoglobules.
  • new experimental output parameters: experimental sequence coverage from internal MS data, subcellular localization based on GFP/YFP for >1000 proteins - from the SUBA database. 
  •  experimental protein sequence coverage display by internally mass spectrometry data (via 'pop-up' windows on each protein page report). - experimental MS/MS data on the peripheral and lumenal proteome of A. thaliana - published in (Giacomelli et al., 2006).
  • experimental data on the plastoglobule proteome of A. thaliana available - published in (Ytterberg et al., 2006).
  • Arabidopsis gene models are updated to TAIR v6.0. All MS/MS-based proteins identifications published since summer 2004 are reanalyzed against v6.0.
2005
  • experimental data on the oligomeric stromal proteome of A. thaliana available- published in (Peltier et al., 2006).
  • experimental data on the comparative analysis of maize bundle sheath and mesophyll chloroplast proteome available - with unique display of comparative quantitative information on each protein report page - published in (Majeran et al., 2005).
Current version:
  • Arabidopsis: TAIR v8.0
  • Maize: AZM v4.0 & ZmGI v16.0 (from TIGR)