Databases
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Proteomic Databases and Resources
The primary goal of this section is to consolodate and coordinate proteomics resources using Arabidopsis thaliana. The MASCP subcommittee has begun to assemble a list of proteomic resources and databases from different groups.
General
AtProteome assembles proteomic data of about 13.000 proteins and provides information about identified proteotypic peptides, abundances and tissue and organelle-specific appearance.
ProMEX is a mass spectral library, consisting of tryptic peptide product ion spectra from protein samples of Arabidopsis thaliana, Medicago truncatula, Chlamydomonas reinhardtii, Tomato and Potato. The database serves as a reference and can be used for protein identification in uncharacterized samples. Protein identification by ProMEX is linked to other molecular levels of biological organization such as metabolite, pathway and transcript data. The database is further connected to annotation and classification services via BioMoby. ProMEX allows also text searches based on AGI code, metadata such as experimental information of the samples, and mass spectrometric instrument parameters.
2-DE gel images and supplementary tables to the Arabidopsis thaliana plant tissue proteome:
1. Overview of 2DE gel images of 8 different Arabidopsis thaliana tissues (inflorescence, stem, primary leaf, leaf, seed, seedling, silique, root).
2. Overview and download of 2-DE gel images and result tables from MALDI-TOF MS analysed Arabidopsis thaliana tissues (primary leaf, seedling, silique).
Find within this database a set of proteomics experiments and their related data. The experiments were made at the Cambridge Centre for Proteomics.
Protein phosphorylation and dephosphorylation are fundamental to cellular regulation. These post-translational modifications, which are catalyzed by protein kinases and phosphatases, constitute a reversible molecular switch. The breadth of cellular processes regulated by protein kinases is reflected in the genomes of plants. Currently it is estimated that nearly 1000 genes encode proteins belonging to the eukaryotic protein kinase superfamily in Arabidopsis thaliana. An additional 300 genes encode protein phosphatases. Furthermore, at least 50 members of two-component systems are predicted to be present in Arabidopsis (e.g. histidine kinases and response regulators).
Interaction
Arabidopsis Interactome Viewer
An interactome for Arabidopsis thaliana predicted from interacting orthologs in yeast, worm, fruit fly and human.
A collection of TAIR protein-protein interaction datasets.
Subcellular
The SubCellular Proteomic Database (SUBA) houses large scale proteomic and GFP localisation sets from cellular compartments of Arabidopsis. It also contains precompiled bioinformatic predictions for protein subcellular localisations from a set of 10 different prediction tools. Complex relational queries can be perform between these experimental and predicted datasets to find and collate evidence for the subcellular location of Arabidopsis proteins.
PPDB is a specialized proteome database with a focus on plant plastids.The main objective is to provide a centralized, curated, data deposit for in-house experimentally determined plastid and other proteins in Arabidopsis thaliana and maize (Zea mays), their annotated functions, as well as their experimental and predicted molecular properties and subcellular localization. Most recently, PTMs (e.g. N-terminal acetylation, deamidation, proline hydroxylation) determined by high resolution, and high accuracy mass spectrometry are also reported for Arabidopsis proteins. Mass spectrometry details for all in-house identified proteins are provided as much as possible (individual ion and Mowse protein scores, mass errors, etc.), with the objective to allow the db visitor to judge the significance of protein and PTM identifications.
The AT_CHLORO database represents a recent analysis of the Arabidopsis chloroplast proteome and its sub structures (envelope, stroma, thylakoid) with detailed proteomic information (peptides, MW, retention times, identification statistics).
This database does not only contain all Arabidopsis orthologs of known peroxisomal matrix and membrane-associated enzymes, metabolite transport proteins and the PEX proteins (peroxisome biogenesis proteins) but also a large number of novel Arabidopsis proteins that carry a putative peroxisome targeting signal type 1 (PTS1) or type 2 (PTS2) and may be targeted to plant peroxisomes. Data compilation of diverse information is intended to facilitate the identification of unknown proteins that have an important enzymatic or regulatory function in photorespiration, fatty acid b-oxidation, N and S metabolism, and in the biosynthesis or degradation of plant hormones.
An Arabidopsis thaliana mitochondrial proteome project was started for a comprehensive investigation of mitochondrial functions in plants. As a first step the proteome of mitochondria isolated from suspension cell cultures was characterized by high resolution 2D gel electrophoresis and mass spectrometry (Kruft et al. 2001, Plant Physiol.127, 1694-1710; Werhahn and Braun 2002, Electrophoresis 23, 640-646). Currently the proteomes of selected Arabidopsis knock-out mutants concerning nuclear genes of mitochondrial proteins are under investigation in our laboratory.
The Arabidopsis Mitochondrial Protein Database is a relational database containing information on the predicted and experimentally confirmed protein complement of mitochondria from the model plant Arabidopsis thaliana. The database contains a cobination of large-scale proteomic analyses conducted in-hose as well as previously published data from the scientific literature. It also cotains pre-compiled subcellular predictions for mitochondrial localisation.
ARAMEMNON is a database about all putative membrane proteins of Arabidopsis thaliana, Rice (Oryza sativa) and about some 4800 putative membrane proteins of ~270 other seed plants.
plprot - a plastid protein database-integrates data from large scale proteome analyses of different plastid types.These include etioplasts, chloroplasts, chromoplasts and the undifferentiated proplastid-like organelles of tobacco BY2 cells. This comparison allows establishing a core proteome that is common to all plastid types and provides furthermore information about plastid type-specific functions.
Tissue
We are interested in determining the biochemical and genetic mechanisms that control seed dormancy, seed longevity, and that regulate the transition from quiescence to highly active metabolism during germination and seedling establishment. To this end, we are developing a proteome analysis of the model plant Arabidopsis thaliana. This global proteomics approach would allow characterization of the accumulation pattern of key metabolic enzymes in dormant seeds, after-ripened non-dormant seeds, and germinating seeds.
Post-Translational Modification
The Arabidopsis Protein Phosphorylation Site Database contains large scale proteomic based data from both published and unpublished sources. Data is provided as either a searchable list of identified peptides or ions with annotated phosphorylation site (where available) or as a protein summary page with AGI. It also contains a pre-computed prediction of pS for the entire Arabidopsis proteome developed by an in-house prediction algorithm trained with 802 Arabidopsis serine phosphopeptides.
The phosphorylation site probability calculator carries out assessment of the relative likelihoods of phosphorylation at each potentially phosphorylated S, T or Y in an amino acid sequence, based on the intensity of peaks in a corresponding mass spectrum file. The calculator is an implementation of the method used to determine the phosphorylation score for each peptide described in papers by the Mann group (Olsen and Mann 2004; Olsen et al., 2006).
While the PPDB database has its main focus on chloroplasts (see above), recent analysis of leaf samples have produced a significant collection of mapped PTMs including deamidation, hydroxylation, propionylation, formylation, amino acid substitutions and acetylation.
Plant Phosphoproteome Database (RIPP-DB)
The Plant Phosphoproteome Database provides information on phosphopeptides which were identified from Arabidopsis and rice cells by LC-MS/MS-based shotgun phosphoproteomics approach.