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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…

ProteINSIDE
Web

ProteINSIDE

Provides an overview of the biological information stored in public databases…

Provides an overview of the biological information stored in public databases or provided by annotations according to the Gene Ontology, (II) predicts proteins that are secreted to search for…

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…

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 the human proteins. Moreover, this tool includes over 8000 phenotypic…

C-HPP
Web

C-HPP Chromosome-Centric Human Proteome Project

Maps the human protein subset or parts list coded by genes on each chromosome.…

Maps the human protein subset or parts list coded by genes on each chromosome. C-HPP aims to define the full set of proteins encoded in each chromosome through development of a standardized approach…

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,…

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…

FlyMine
Dataset

FlyMine

A data warehouse that addresses one of the important challenges of modern…

A data warehouse that addresses one of the important challenges of modern biology: how to integrate and make use of the diversity and volume of current biological data. Its main focus is genomic 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.

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…

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…

Membranome
Dataset

Membranome Membrane Proteome

A database for proteome-wide analysis of single-pass membrane proteins.…

A database for proteome-wide analysis of single-pass membrane proteins. Membranome currently collects data on >6000 bitopic proteins from Homo sapiens, Arabidopsis thaliana, Dictyostelium…

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…

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.

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…

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…

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…

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…

NucDiff
Desktop

NucDiff

Aligns sequences and outputs information about aligned sequence regions.…

Aligns sequences and outputs information about aligned sequence regions. NucDiff is a computational package that uses the NUCmer, delta-filter and show-snps programs from MUMmer for sequence…

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…

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…

UniProt…
Dataset

UniProt proteomes

UniProt provides 'proteome' sets of proteins thought to be expressed…

UniProt provides 'proteome' sets of proteins thought to be expressed by organisms whose genomes have been completely sequenced. It may include both manually reviewed (UniProtKB/Swiss-Prot)…

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.

AOD
Dataset

AOD AntiOxidant protein Database

Consists of a manually curated database of 710 experimentally validated…

Consists of a manually curated database of 710 experimentally validated antioxidant proteins. Information including taxonomy, source organism, subcellular location, gene ontology, catalytic activity…

SalmoBase
Dataset

SalmoBase

Provides an informational resource about Salmonid species. SalmoBase contains…

Provides an informational resource about Salmonid species. SalmoBase contains atlantic salmon genome reference, annotation and gene expression data. It offers a genome browser that allows users to…

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OmicsDI
Dataset

OmicsDI Omics Discovery Index

Permits to access, discover and disseminate omics data sets. OmicsDI is an…

Permits to access, discover and disseminate omics data sets. OmicsDI is an open-source platform that can integrate proteomics, genomics, metabolomics and transcriptomics data sets. This platform…

Listeriomics
Dataset

Listeriomics

Integrates different tools for omics data analyses. Listeriomics integrates all…

Integrates different tools for omics data analyses. Listeriomics integrates all the complete Listeria species genomes, transcriptomes, and proteomes published to date. It allows navigation among all…

CYCLoPs
Dataset

CYCLoPs Collection of Yeast Cells Localization Patterns

Provides a central platform for housing and analyzing our yeast proteome…

Provides a central platform for housing and analyzing our yeast proteome dynamics datasets at the single cell level. CYCLoPs differs from existing databases in a number of ways: (1) whereas other…

SDIndex
Web

SDIndex Structural Difficulty Index

Reflects the capability of predicting accurate structures and helps to assess…

Reflects the capability of predicting accurate structures and helps to assess the potential for developing proteome level structural databases for various organisms with some of the best…

ProteomeXchange
Dataset

ProteomeXchange

Aims to fully represent all relevant aspects of a proteomics experiment and to…

Aims to fully represent all relevant aspects of a proteomics experiment and to make them easily accessible to the user.

IPI
Dataset

IPI International Protein Index

Offers complete nonredundant data sets representing the human, mouse and rat…

Offers complete nonredundant data sets representing the human, mouse and rat proteomes, built from the Swiss-Prot, TrEMBL, Ensembl and RefSeq databases. IPI is a nonredundant human proteome set that…

HCVDB
Dataset

HCVDB

Provides key data about the hepatitis C virus sequences and ensures consistency…

Provides key data about the hepatitis C virus sequences and ensures consistency of the annotations, which enables reliable keyword queries.

WallProtDB
Dataset

WallProtDB

Aims at collecting cell wall proteomic experimental data. WallProtDB contains…

Aims at collecting cell wall proteomic experimental data. WallProtDB contains 2,170 proteins and ESTs identified experimentally in 36 cell wall proteomics studies performed on 11 different plant…

CKB
Dataset

CKB Cyanobacterial KnowledgeBase

A free access database that contains the genomic and proteomic information of…

A free access database that contains the genomic and proteomic information of 74 fully sequenced cyanobacterial genomes belonging to seven orders. CKB also contains tools for sequence analysis. The…

CSPA
Dataset

CSPA Cell Surface Protein Atlas

Provides cellular surfaceome snapshots at high resolution. The CSPA is…

Provides cellular surfaceome snapshots at high resolution. The CSPA is presented in form of an easy-to-navigate interactive database, a downloadable data matrix and with tools for targeted surfaceome…

Nutritious…
Dataset

Nutritious Rice for the World

A large dataset of models encompassing more than 60,000 small proteins and…

A large dataset of models encompassing more than 60,000 small proteins and protein domains for the rice. For each protein sequence, 5 top structures were chosen using a novel clustering methodology…

Medicago…
Dataset

Medicago PhosphoProtein Database

A repository built to house phosphoprotein, phosphopeptide, and phosphosite…

A repository built to house phosphoprotein, phosphopeptide, and phosphosite data specific to Medicago. Medicago PhosphoProtein Database holds 3457 unique phosphopeptides that contain 3404…

ShrimpGPAT
Dataset

ShrimpGPAT

A free and easily accessed service for the shrimp research community that…

A free and easily accessed service for the shrimp research community that provides a comprehensive and up-to-date database of quality-filtered decapod gene and protein sequences together with…

Atlas of Maize…
Dataset

Atlas of Maize Proteotypes

Quantifies protein abundance and phosphorylation levels across developmental…

Quantifies protein abundance and phosphorylation levels across developmental time. The Atlas of Maize Proteotypes comprises 14165 proteins and 18405 phosphopeptides, quantified across eight tissues.…

ProPepper
Dataset

ProPepper

A database of cereal prolamin epitopes, peptides and proteins for expert users…

A database of cereal prolamin epitopes, peptides and proteins for expert users that are dealing with protein chemistry, proteomics and mass spectrometry, method developments and related applications…

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The L.…
Dataset

The L. monocytogenes 10403S BioCyc database

A resource for researchers studying Listeria and related organisms. The L.…

A resource for researchers studying Listeria and related organisms. The L. monocytogenes 10403S BioCyc database allows users to (i) have a comprehensive view of all reactions and pathways predicted…

FR database
Dataset

FR database

A database using manual curation from 38 423 articles published before 1 April…

A database using manual curation from 38 423 articles published before 1 April 2014, and integrating protein interactomes and several transcriptome datasets. FR database provides detailed information…

CyanOmics
Dataset

CyanOmics

A database based on the results of Synechococcus sp. PCC 7002 omics studies.…

A database based on the results of Synechococcus sp. PCC 7002 omics studies. CyanOmics comprises one genomic dataset, 29 transcriptomic datasets and one proteomic dataset and should prove useful for…

MouseMine
Dataset

MouseMine

Supports powerful query, reporting, and analysis capabilities over a…

Supports powerful query, reporting, and analysis capabilities over a significant portion of the MGI database. The main source of MouseMine data is the Mouse Genome Informatics, which includes a…

SPGDB
Dataset

SPGDB Streptococcus pneumoniae Genome Database

Integrates and analyzes the completely sequenced and available S. pneumoniae…

Integrates and analyzes the completely sequenced and available S. pneumoniae genome sequences. Further, links to several tools are provided to compare the pool of gene and protein sequences, and…

hpvPDB
Dataset

hpvPDB Human papillomavirus Proteome DataBase

Domiciles proteomic and genomic information on 150 HPV strains sequenced to…

Domiciles proteomic and genomic information on 150 HPV strains sequenced to date. Retreival of such vast information from different resources with a provision of prediction and validation of proteins…

MASCP gator
Dataset

MASCP gator

An aggregation portal for Arabidopsis proteomic data currently being produced…

An aggregation portal for Arabidopsis proteomic data currently being produced by the community and unites a large collection of specialized resources to a single portal.

WheatGenome.inf…
Dataset

WheatGenome.info

An integrated database resource which includes multiple web-based applications.…

An integrated database resource which includes multiple web-based applications. These include a GBrowse2-based wheat genome viewer with BLAST search portal, TAGdb for searching wheat…

SWICZ
Dataset

SWICZ

Hosts a proteomics database for Streptomyces, Caulobacter and Neisseria. SWICZ…

Hosts a proteomics database for Streptomyces, Caulobacter and Neisseria. SWICZ contains knowledge based data of time series of protein expression for various stages of development of the given…

IntegromeDB
Dataset

IntegromeDB

A biological web search engine based on the Semantic Web technologies. The…

A biological web search engine based on the Semantic Web technologies. The IntegromeDB search engine allows scanning data on gene regulation, gene expression, protein-protein interactions, pathways,…

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Optimas-DW
Dataset

Optimas-DW OPTIMAS Data Warehouse

A comprehensive data collection for maize. Optimas-DW integrates data from…

A comprehensive data collection for maize. Optimas-DW integrates data from different data domains such as transcriptomics, metabolomics, ionomics, proteomics and phenomics. A web interface allows…

OpenfluDB
Dataset

OpenfluDB OpenFlu database

An algorithm was developed to act as the interface between EMPRES-i disease…

An algorithm was developed to act as the interface between EMPRES-i disease event data and publicly available influenza virus sequences in OpenfluDB.

CloneCollection
Dataset

CloneCollection

Contains a collection of statistics concerning: kinases, cell death, membrane…

Contains a collection of statistics concerning: kinases, cell death, membrane proteins, nuclear proteins, metabolism, signal transduction, secreted proteins, and transcription factors.…

LepChorionDB
Dataset

LepChorionDB

A relational database, containing all Lepidoptera chorion proteins identified…

A relational database, containing all Lepidoptera chorion proteins identified to date. Lepidoptera chorion proteins can be classified in two major protein families, A and B. This classification was…

iProX
Dataset

iProX

An integrated Proteome resources center in China. Currently, iProX is composed…

An integrated Proteome resources center in China. Currently, iProX is composed of a proteomics database and an experiment data submission system. iProX encourages and welcomes direct user submissions…

Sys-BodyFluid
Dataset

Sys-BodyFluid

It contains eleven kinds of body fluid proteomes, including plasma/serum,…

It contains eleven kinds of body fluid proteomes, including plasma/serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, seminal…

dbDEPC
Dataset

dbDEPC database of Differentially Expressed Proteins in Human Cancer

A database with the goal of collecting curated cancer proteomics data. dbDEPC…

A database with the goal of collecting curated cancer proteomics data. dbDEPC provides a resource for information on protein-level expression changes. It explores protein profile differences among…

MfunGD
Dataset

MfunGD

Provides a resource for annotated mouse proteins and their occurrence in…

Provides a resource for annotated mouse proteins and their occurrence in protein networks.

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