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.

Web app
ProteINSIDE ProteINSIDE

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…

Atlas of Maize… Atlas of Maize Proteotypes

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.…

Plant Proteome… Plant Proteome Response to Stress database

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…

Collection of Yeast… Collection of Yeast Cells Localization Patterns

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…

Colorectal cancer… Colorectal cancer atlas

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…

Manually Curated… Manually Curated Database of Rice Proteins

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…

neXtProt neXtProt

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…

PRoteomics… PRoteomics IDEntifications database

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…

Web app
Structural Difficulty… Structural Difficulty Index

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…

Web app
Chromosome-Centric… Chromosome-Centric Human Proteome Project

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…

Nutritious Rice for… Nutritious Rice for the World

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…

Expert Protein… Expert Protein Analysis System

ExPASy Expert Protein Analysis System

A federated portal for accessing to resources for proteomics. ExPASy provides a…

A federated portal for accessing to resources for proteomics. ExPASy provides a comprehensive list of high-quality resources provided by the Swiss Institute of Bioinformatics (SIB) and several…

Phosphomouse Phosphomouse

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…

Medicago… Medicago PhosphoProtein Database

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…

The Medicago Proteome… The Medicago Proteome Atlas

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…

Membrane Proteome Membrane Proteome

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…

Cyanobacterial… Cyanobacterial KnowledgeBase

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…

A A A OPTIMAS Data Warehouse OPTIMAS Data Warehouse

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…

IntegromeDB IntegromeDB

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,…

ProPepper ProPepper

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…

WallProtDB WallProtDB

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…

Cell Surface Protein… Cell Surface Protein Atlas

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…

database of… database of Differentially Expressed Proteins in…

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…

LepChorionDB LepChorionDB

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…

ShrimpGPAT ShrimpGPAT

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…

iProX iProX

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…

UniProt proteomes UniProt proteomes

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)…

MASCP gator MASCP gator

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.

Genome Medicine… Genome Medicine Database of Japan Proteomics
MAPU MAPU

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…

Plasma Proteome… Plasma Proteome Database

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.

Human papillomavirus… Human papillomavirus Proteome DataBase

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…

OryzaPG-DB OryzaPG-DB

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.

Arabidopsis Nucleolar… Arabidopsis Nucleolar Protein DataBase

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.

Plant Proteomics… Plant Proteomics DataBase

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).

Plant Protein… Plant Protein Phosphorylation DataBase

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…

SynDB SynDB

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.

FlyMine FlyMine

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…

ProteomeXchange ProteomeXchange

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.

MfunGD Deprecated MfunGD

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.

Sys-BodyFluid Sys-BodyFluid

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…

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