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Proteome databases | Sequence analysis

A number of websites provide host services for massive proteomic data sets. These repositories are excellent resources for accessing raw data and quick experimental summaries.

PRIDE
Dataset

PRIDE PRoteomics IDEntifications database

A centralized, standards compliant, public data repository for proteomics data,…

A centralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post-translational modifications and supporting spectral evidence. PRIDE…

EBI
Dataset

EBI EMBL-EBI - The European Bioinformatics Institute

Supplies an access to several biological data resources. EBI is a database that…

Supplies an access to several biological data resources. EBI is a database that covers the entire range of biological sciences: raw DNA sequences to curated proteins, chemicals, structures, systems,…

The Medicago…
Dataset

The Medicago Proteome Atlas

An atlas of protein expression of Medicago truncatula in association with…

An atlas of protein expression of Medicago truncatula in association with Sinorhizobium meliloti. The Medicago Proteome Atlas provides evidence for more than 23013 protein groups (19679 from the…

Escherichia…
Dataset

Escherichia coli Multi-omics Database

Provides a database of E. coli. Escherichia coli Multi-omics Database offers a…

Provides a database of E. coli. Escherichia coli Multi-omics Database offers a comprehensive knowledge of the quantitative information regarding the inner molecular components of cells.

neXtProt
Dataset

neXtProt

Offers a seamless integration of and navigation through protein-related data.…

Offers a seamless integration of and navigation through protein-related data. NeXtProt contains proteomics data for over 85% of human proteins. Moreover, this tool includes over 8000 phenotypic…

ProteomicsDB
Dataset

ProteomicsDB

Enables navigation of proteomes, provides biological insight and fosters the…

Enables navigation of proteomes, provides biological insight and fosters the development of proteomic technology. ProteomicsDB is a mass-spectrometry-based draft of the human proteome and a public,…

ProteomeTools
Dataset

ProteomeTools

Translates the human proteome into molecular and digital tools for drug…

Translates the human proteome into molecular and digital tools for drug discovery, personalized medicine and life science research. The ProteomeTools project is a joint effort of the Technical…

HipSci
Dataset

HipSci human induced pluripotent Stem cells initiative

Generates human induced pluripotent stem cells (iPSCs) from hundreds of healthy…

Generates human induced pluripotent stem cells (iPSCs) from hundreds of healthy individuals as well as patients diagnosed with selected diseases. HipSci is a powerful resource to evaluate and…

ParameciumDB
Dataset

ParameciumDB

Provides data about the model organism Paramecium tetraurelia. ParameciumDB was…

Provides data about the model organism Paramecium tetraurelia. ParameciumDB was created by using components of the Generic Model Organism Database (GMOD). It offers data about gene expression data…

FlyDev
Dataset

FlyDev

Helps to study molecular or phenotypic effects of yet uncharacterized proteins.…

Helps to study molecular or phenotypic effects of yet uncharacterized proteins. FlyDev is a database and a visualization tool that provides high resolution proteomes of Drosophila melanogaster.…

Phosphomouse
Dataset

Phosphomouse

A web-based resource to aid analysis of existing biological data and inspire…

A web-based resource to aid analysis of existing biological data and inspire future biological investigations. Phosphomouse presents experimental data about tissue-specific protein abundance and…

HumanPSD
Dataset

HumanPSD Human Proteome Survey Database

Compiles properties of more than 53 000 characterized mammalian proteins.…

Compiles properties of more than 53 000 characterized mammalian proteins. HumanPSD provides association of human proteins with diseases and their potential utilization as biomarkers. It reports drugs…

PPDB
Dataset

PPDB Plant Proteomics DataBase

Provides an integrated resource for experimentally identified proteins in…

Provides an integrated resource for experimentally identified proteins in Arabidopsis and maize (Zea mays).

PPD
Dataset

PPD Plasma Proteome Database

Hosts qualitative and quantitative information on proteins (including those…

Hosts qualitative and quantitative information on proteins (including those from MRM-based assays) reported in plasma and serum and hence serves as reference platform for biomarker discovery.

Membranome
Dataset

Membranome Membrane Proteome

Gathers information about bitopic proteins from six complete genomes (Homo…

Gathers information about bitopic proteins from six complete genomes (Homo sapiens, Arabidopsis thaliana, Dictyostelium discoideum, Saccharomyces cerevisiae, Escherichia coli and Methanocaldococcus…

Colorectal…
Dataset

Colorectal cancer atlas

An integrated web-based resource that catalogues the genomic and proteomic…

An integrated web-based resource that catalogues the genomic and proteomic annotations identified in colorectal cancer (CRC) tissues and cell lines. The data catalogued to-date include sequence…

EchoBASE
Dataset

EchoBASE

Contains some information from post-genomic experiments that use the model…

Contains some information from post-genomic experiments that use the model bacterium Escherichia coli K12. EchoBASE allows consultation of protein–protein interaction (PPI) data, structural data and…

P3DB
Dataset

P3DB Plant Protein Phosphorylation DataBase

Provides a resource of protein phosphorylation data from multiple plants. With…

Provides a resource of protein phosphorylation data from multiple plants. With the large-scale phosphorylation data and associated web-based tools, P3DB will be a valuable resource for both plant and…

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PlaMoM
Dataset

PlaMoM Plant Mobile Macromolecules

Provides convenient and interactive search tools allowing users to retrieve, to…

Provides convenient and interactive search tools allowing users to retrieve, to analyze and also to predict mobile RNAs/proteins. Each entry in the PlaMoM database contains detailed information such…

PNU
Dataset

PNU Protein Naming Utility

Stores and applies customizable sets of naming rules to correct and standardize…

Stores and applies customizable sets of naming rules to correct and standardize gene and protein names within an annotated genome or metagenome. PNU is a web-based database that allows users to…

NPD
Dataset

NPD Nuclear Protein Database

Provides an overview of the diversity of many sub-nuclear compartments. The NPD…

Provides an overview of the diversity of many sub-nuclear compartments. The NPD is a curated database and all information is supported by links to published material. This tool provides a resource…

CSF-PR
Dataset

CSF-PR CSF Proteome Resource

An interactive literature guide to quantitative cerebrospinal fluid mass…

An interactive literature guide to quantitative cerebrospinal fluid mass spectrometry data from neurodegenerative disorders. CSF-PR includes novel approaches for filtering, visualizing and comparing…

Soybean…
Dataset

Soybean Proteome Database

Compiles information about soybean functional analysis. Soybean Proteome…

Compiles information about soybean functional analysis. Soybean Proteome Database gathers proteome data collected from plants in flooding stress conditions. It provides information about proteins…

SynDB
Dataset

SynDB

An online resource of proteins known or predicted to be related to the synapse…

An online resource of proteins known or predicted to be related to the synapse or synaptic activity.

AtNoPDB
Dataset

AtNoPDB Arabidopsis Nucleolar Protein DataBase

Provides information on 217 proteins identified in a proteomic analysis of…

Provides information on 217 proteins identified in a proteomic analysis of nucleoli isolated from Arabidopsis cell culture.

ROUGE
Dataset

ROUGE Rodent Unidentified Gene-Encoded Large Proteins

Provides access to the results of computer-assisted sequence analysis of mouse…

Provides access to the results of computer-assisted sequence analysis of mouse homologues of KIAA cDNA (mKIAA cDNA) that were isolated. ROUGE is a subsidiary database of the Human Unidentied…

CharProtDB
Dataset

CharProtDB Characterized Protein Database

Concerns biochemically characterized proteins data. CharProtDB provides a…

Concerns biochemically characterized proteins data. CharProtDB provides a source of transitive assignments of function which allow to make annotation pipelines. This annotation contains (1) gene…

LMPD
Dataset

LMPD Lipid Maps Proteome Database

Provides access to lipid-associated protein sequences and annotations. LMPD is…

Provides access to lipid-associated protein sequences and annotations. LMPD is a database that stores more than 8.000 genes and 12.000 proteins from several species, including human. Users can browse…

PlantPReS
Dataset

PlantPReS Plant Proteome Response to Stress database

Contains protein information from manually curated articles data. PlantPReS…

Contains protein information from manually curated articles data. PlantPReS currently comprises more than 20413 entries from 456 manually curated articles, and contains 10600 unique stress responsive…

MCDRP
Dataset

MCDRP Manually Curated Database of Rice Proteins

A literature based manually curated protein centric database of rice proteins.…

A literature based manually curated protein centric database of rice proteins. MCDRP provides experimental data embedded in published articles in a computer searchable format. The database has data…

HPSF
Dataset

HPSF Human Proteome Structure and Function

Provides a repository of structure and function annotations on the…

Provides a repository of structure and function annotations on the 'missing proteins' of the human proteome. HPSF hosts missing proteins that have not been validated at protein level which…

UNcleProt
Dataset

UNcleProt Universal Nuclear Protein database of barley

Provides information about the barley nuclear proteins. UNcleProt is a database…

Provides information about the barley nuclear proteins. UNcleProt is a database containing plant nuclear proteins identified in nuclei during different stages of the cell cycle. It contributes to the…

RabDB
Dataset

RabDB

Displays Rab annotation for all genomes available as a part of Superfamily…

Displays Rab annotation for all genomes available as a part of Superfamily 1.75. RabDB a database created to explore the universe of the Rab family of small GTPases, key regulators of the Eukaryotic…

HUMA
Dataset

HUMA Human Mutation Analysis

Provides a platform for analyzing variation. The HUMA interface includes tools…

Provides a platform for analyzing variation. The HUMA interface includes tools to analyze variation in protein sequence and structures. It contains information about sequence, structure, variation…

MAPU
Dataset

MAPU

Contains several body fluid proteomes; including plasma, urine, and…

Contains several body fluid proteomes; including plasma, urine, and cerebrospinal fluid. Cell lines have been mapped to a depth of several thousand proteins and the red blood cell proteome has also…

Alga-PrAS
Dataset

Alga-PrAS Algal Protein Annotation Suite

Provides physicochemical, structural and functional annotations of algal…

Provides physicochemical, structural and functional annotations of algal proteome data. Alga-PrAS includes whole protein sequences of 31 algae, such as green algae, red algae, glaucophyte, oomycetes,…

Human normal…
Dataset

Human normal thyroid database

Provides a large dataset of proteome of thyroid with high confidence. Human…

Provides a large dataset of proteome of thyroid with high confidence. Human normal thyroid database offers a useful reference for biomarker discovery of thyroid disease and provides insights into the…

Human normal…
Dataset

Human normal pituitary database

Provides a large dataset of proteome of pituitary with high confidence. Human…

Provides a large dataset of proteome of pituitary with high confidence. Human normal pituitary database offers a useful baseline reference for pituitary biomarker discovery and provides insight into…

ARA-PEPs
Dataset

ARA-PEPs

Provides the research community with up-to-date information on putative…

Provides the research community with up-to-date information on putative peptides in A. thaliana, collected from publicly available datasets and predicted based on novel expression data. ARA-PEPs is a…

DPD
Dataset

DPD Dark Proteome Database

Provides Swiss-Prot protein information. DPD reveals the dark and non-dark…

Provides Swiss-Prot protein information. DPD reveals the dark and non-dark regions and their corresponding characterization such as disordered, transmembrane, and compositional bias. It will help…

Plant-PrAS
Dataset

Plant-PrAS Plant-Protein Annotation Suite

A database of physicochemical and structural properties, and novel functional…

A database of physicochemical and structural properties, and novel functional region in plant proteomes. Plant-PrAS database plant species are Arabidopsis, soybean, poplar, rice, moss and algae. We…

cuticleDB
Dataset

cuticleDB

A relational database containing all structural proteins of Arthropod cuticle…

A relational database containing all structural proteins of Arthropod cuticle identified to date.

GeMDBJ Proteomics
Dataset
YeastMine
Dataset

YeastMine

Allows users to query the different types of data present in the Saccharomyces…

Allows users to query the different types of data present in the Saccharomyces Genome Database (SGD) data. YeastMine is an integrated data warehouse with precomputed tables based on the InterMine…

dbTEU
Dataset

dbTEU DataBase of Trace Element Utilization

Provides a biological trace elements database. dbTEU includes all known…

Provides a biological trace elements database. dbTEU includes all known transporters and user proteins (excluding metal-binding chaperones and regulators) for five trace elements: Cu, Mo, Ni, Co and…

UniProt…
Dataset

UniProt proteomes

Provides 'proteome' sets of proteins thought to be expressed by…

Provides 'proteome' sets of proteins thought to be expressed by organisms whose genomes have been completely sequenced. UniProt proteomes is a database that gives access to “Reference…

Strepto-DB
Dataset

Strepto-DB

A database for comparative genomics of group A and group B streptococci.

A database for comparative genomics of group A and group B streptococci.

OryzaPG-DB
Dataset

OryzaPG-DB

A rice proteome database based on shotgun proteogenomics, which incorporates…

A rice proteome database based on shotgun proteogenomics, which incorporates the genomic features of experimental shotgun proteomics data.

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Radiolaria
Dataset

Radiolaria

Compiles information about dinoflagellate transcriptomes. Radiolaria is a…

Compiles information about dinoflagellate transcriptomes. Radiolaria is a dataset derived from a study containing four recently described dinoflagellates added to 57 de novo assembled transcriptomes…

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DGIL Porcine…
Dataset

DGIL Porcine Translational Research Database

Allows users to translate findings made in rodents to pigs and from those in…

Allows users to translate findings made in rodents to pigs and from those in pigs to humans. DGIL Porcine Translational Research Database is an online resource allowing identification of genes that…

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