What is new in PPDB:
- June 2021 The latest predicted protein models for maize cultivar B73 (RefGen_v5 aka APGv5 from MaizeGDB) are uploaded into PPDB. Stable BLAST alignment between proteins in APGv5, APGv3 (v3.21) and APGv1 (v4a53), rice Nipponbare (MSU rice v7) and Arabidopsis (Araport11) are provided at every protein report page. PPDB also includes 111 plastid-encoded and 163 mito-encoded proteins from NCBI Refseq.
- April 2021 A new link between PPDB and Arabidopsis PeptideAtlas http://www.peptideatlas.org/builds/arabidopsis/ is provided at every protein report page for Araport11 predicted proteins. This allows rapid access to results from uniformly reprocessed mass spectrometry proteomics datasets obtained through ProteomeXchange. The current Arabidopsis PeptideAtlas build is based on 40 million MSMS spectra (out of ~143 million) matched to Araport11 – see the bioRxiv preprint.
- March 2021 Protein coding genes from Araport11 are incorporated in PPDB and include calculated or predicted values for molecular weight, GRAVY index, isoelectric point (pI), predicted transmembrane domains, predicted subcellular localization using TargetP. Protein names, functions using the internally modified MapMan Bin system and subcellular curated locations are listed.
- New experimental MSMS-based (QExactive) proteomics data, including N-terminomes by TAILS, and updated protein annotations for Arabidopsis chloroplast stroma from wild-type (Col-0) and mutants in stromal glutamyl aminopeptidase (CGEP) are available from our study Bhuiyan et al 2020 Plant Physiology.
- New experimental MSMS-based proteomics data and updated protein annotations from affinity enrichment using transgenic wild-type and WalkerB mutant ClpC1 chaperones are available from our study Montandon et al (2019) J. Proteome Research.
- Sept 2017. Improved proteostasis functions. The functional bin annotation system was expanded to include assignment of (candidate) peptidases to MEROPS families and clans in a hierarchical manner. All (candidate) peptidases and peptidase inhibitors, as well as known auxiliary components of peptidase (systems) such as the CLP chaperones and 26S lid and base, are assigned to be within bin 29.5 ‘protein.degradation’. Nearly 700 Arabidopsis proteins have a primary functional assignment to this bin 29.5. More information can be found in Majsec et al (2017) The Plant Cell. The Plastid and Mitochondrial Peptidase Network in Arabidopsis thaliana: A Foundation for Testing Genetic Interactions and Functions in Organellar Proteostasis.
- August 2017. Updated protein subcellular annotation for Arabidopsis. Following manual curation, a total of 3598 Arabidopsis proteins (counting just one protein model per gene) now have an assignment location to one or more subcellular locations. For instance, plastids - 1718 proteins; mitochondria – 429 proteins; peroxisome - 156 proteins; cytosol – 503 proteins; plasma membrane – 298 proteins.
- 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.
- New experimental proteomics data and updated protein annotations for Arabidopsis seedlings and chloroplast stroma from wild-type (Col-0), single and double null mutants in CLPS1 and ClpC1, as well as CLPP3 are available from our studies (Nishimura et al, 2013, Plant Cell 25, 2276-301 and Kim et al (2013) Plant Physiology 162, 157-79)
- New experimental proteomics data and updated protein annotations for Arabidopsis seedlings and chloroplast plastoglobules (PGs) from wild-type (Col-0), double null mutants in ABC1K1 and ABC1K3 are available from our study (Lundquist et al, 2013, Plant Cell 25(5), 1818-39
- Updated annotation of >1550 plastid proteins available for maize and Arabidopsis (from Huang et al 2013, J. Proteomics Res. 4, 491-504)
- Curated Arabidopsis proteomics publications are added to PPDB (totaling 158 studies)
- 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/)
- 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).
- 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.
- 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).
The name of PPDB is changed to Plant Proteome Database
We have captured data from 58 proteomics publications (Arabidopsis and
). 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.
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
Arabidopsis: TAIR v8.0
Maize: AZM v4.0 & ZmGI v16.0 (from TIGR)