Proteomic Databases and Resources
The primary goal of this section is to consolidate 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
pep2pro
The pep2pro resource is a further development of AtProteome and provides proteome information on Arabidopsis thaliana. The underlying proteome analysis database allowed integrating and analysing the large proteome datasets and the website shows all the information about the protein identifications with a proteogenomic mapping of the peptides onto the genome.
ProMEX
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.
GABI
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).
ARAMEMNON
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.
NASC
Find within this database a set of proteomics experiments and their related data. The experiments were made at the Cambridge Centre for Proteomics.
AtProteome (superseded by pep2pro outlined above)
AtProteome assembles proteomic data of about 13.000 proteins and provides information about identified proteotypic peptides, abundances and tissue and organelle-specific appearance.
The pep2pro resource is a further development of AtProteome and provides proteome information on Arabidopsis thaliana. The underlying proteome analysis database allowed integrating and analysing the large proteome datasets and the website shows all the information about the protein identifications with a proteogenomic mapping of the peptides onto the genome.
ProMEX
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.
GABI
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).
ARAMEMNON
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.
NASC
Find within this database a set of proteomics experiments and their related data. The experiments were made at the Cambridge Centre for Proteomics.
AtProteome (superseded by pep2pro outlined above)
AtProteome assembles proteomic data of about 13.000 proteins and provides information about identified proteotypic peptides, abundances and tissue and organelle-specific appearance.
Interaction
Arabidopsis Interactome Viewer
An interactome for Arabidopsis thaliana predicted from interacting orthologs in yeast, worm, fruit fly and human.
Arabidopsis interactome
A collection of TAIR protein-protein interaction datasets.
Arabidopsis Membrane Interactome Project
To understand the regulation of cell-environment, cell-cell, and intracellular compartment to cytosol interactions better, we plan to determine the interactions of 8,400 proteins from the reference plant Arabidopsis. This set comprises essentially integral membrane proteins (~4,300) and a large number (>1,000) of proteins predicted to be involved in signaling or protein modification.
Plant-Pathogen Immune Network
This website is intended for the interactive online exploration of the Plant-Pathogen Immune Network (PPIN-1)
An interactome for Arabidopsis thaliana predicted from interacting orthologs in yeast, worm, fruit fly and human.
Arabidopsis interactome
A collection of TAIR protein-protein interaction datasets.
Arabidopsis Membrane Interactome Project
To understand the regulation of cell-environment, cell-cell, and intracellular compartment to cytosol interactions better, we plan to determine the interactions of 8,400 proteins from the reference plant Arabidopsis. This set comprises essentially integral membrane proteins (~4,300) and a large number (>1,000) of proteins predicted to be involved in signaling or protein modification.
Plant-Pathogen Immune Network
This website is intended for the interactive online exploration of the Plant-Pathogen Immune Network (PPIN-1)
SubCellular
GelMap
Gelmap is a universal tool for visualization and identification of proteins from gel-based proteomic experiments. The Arabidopsis component currently houses extensive BN-PAGE and 2-DE from Arabidopsis mitochondrial studies and will expand to cover other aspects gel-based proteomics in Arabidopsis.
SUBA
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
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.
AT_CHLORO
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).
AraPerox
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.
AMPP
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.
AMPDB
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.
plprot
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.
AtNoPDB
The Arabidopsis Nucleolar Protein database provides information on plant proteins in comparison to human and yeast proteins and images of cellular localisations for over a third of these proteins. This data was derived from a proteomic analysis of nucleoli purified from Arabidopsis cell cultures.
Gelmap is a universal tool for visualization and identification of proteins from gel-based proteomic experiments. The Arabidopsis component currently houses extensive BN-PAGE and 2-DE from Arabidopsis mitochondrial studies and will expand to cover other aspects gel-based proteomics in Arabidopsis.
SUBA
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
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.
AT_CHLORO
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).
AraPerox
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.
AMPP
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.
AMPDB
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.
plprot
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.
AtNoPDB
The Arabidopsis Nucleolar Protein database provides information on plant proteins in comparison to human and yeast proteins and images of cellular localisations for over a third of these proteins. This data was derived from a proteomic analysis of nucleoli purified from Arabidopsis cell cultures.
Tissue
SEED-PROTEOME
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.
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
PhosPhAt
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.
PhosCalc
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).
PPDB
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.
P3DB: Plant Protein Phosphorylation Database
The P3DB: Plant Protein Phosphorylation Database contains published phosphoproteomic data from Arabidopsis and also incorporates phosphoproteomic information from other plant species including Brassica napus, rice, Medicago truncatula, Glycine max.
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.
PhosCalc
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).
PPDB
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.
P3DB: Plant Protein Phosphorylation Database
The P3DB: Plant Protein Phosphorylation Database contains published phosphoproteomic data from Arabidopsis and also incorporates phosphoproteomic information from other plant species including Brassica napus, rice, Medicago truncatula, Glycine max.
Quantitative Proteomics
MRMaid
MRMaid helps you design SRM assays by suggesting peptides and product ions to monitor based on millions of experimental spectra from the PRIDE database.
Arabidopsis Proteotypic Predictor (APP)
The Arabidopsis Proteotypic Predictor (APP) indicates the probability of whether a peptide is predicted to be proteotypic for targeted proteomics studies in Arabidopsis.
MRMaid helps you design SRM assays by suggesting peptides and product ions to monitor based on millions of experimental spectra from the PRIDE database.
Arabidopsis Proteotypic Predictor (APP)
The Arabidopsis Proteotypic Predictor (APP) indicates the probability of whether a peptide is predicted to be proteotypic for targeted proteomics studies in Arabidopsis.
Metabolite
AtMetExpress
Metabolite analysis of Arabidopsis organs with visual interface. We analyzed phytochemical accumulation during development of the model plant Arabidopsis thaliana using liquid chromatography-mass spectrometry (LC-MS) in samples covering many growth stages and organs.
Golm Metabolome Database
It facilitates the search for and dissemination of mass spectra from biologically active metabolites quantified using Gas chromatography (GC) coupled to mass spectrometry (MS).
Arabidopsis Metabolomics Consortium
This is an NSF-funded multi-institutional project that is developing metabolomics as a functional genomics tool for elucidating the functions of Arabidopsis genes.
Metabolite analysis of Arabidopsis organs with visual interface. We analyzed phytochemical accumulation during development of the model plant Arabidopsis thaliana using liquid chromatography-mass spectrometry (LC-MS) in samples covering many growth stages and organs.
Golm Metabolome Database
It facilitates the search for and dissemination of mass spectra from biologically active metabolites quantified using Gas chromatography (GC) coupled to mass spectrometry (MS).
Arabidopsis Metabolomics Consortium
This is an NSF-funded multi-institutional project that is developing metabolomics as a functional genomics tool for elucidating the functions of Arabidopsis genes.
