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Proteomic data sets

Proteomic software tools and databases

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.

Arabidopsis Nucleolar Protein DataBase

OMIC_03261

Arabidopsis Nucleolar Protein DataBase
AtNoPDB

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

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

Cell Surface Protein Atlas

OMIC_09675

Cell Surface Protein Atlas
CSPA

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

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 rediscovery. The cellular surfaceome snapshots of…

Colorectal cancer atlas

OMIC_10347

Colorectal cancer atlas

database of Differentially Expressed Proteins in…

OMIC_07506

database of Differentially Expressed Proteins in Human Cancer
dbDEPC

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

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 different cancers. dbDEPC is expected to be a…

FlyMine

OMIC_02691

FlyMine

A data warehouse that addresses one of the important challenges of modern biology: how to…

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 proteomics data for Drosophila and other insects.…

Genome Medicine Database of Japan Proteomics

OMIC_03917

Genome Medicine Database of Japan Proteomics
GeMDBJ Proteomics

An integrated proteome database for use in cancer research.

An integrated proteome database for use in cancer research.

Human papillomavirus Proteome DataBase

OMIC_03504

Human papillomavirus Proteome DataBase
hpvPDB

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

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 structures would help researchers in designing…

iProX

OMIC_06098

iProX

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

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 of protein and peptide identification data to be…

LepChorionDB

OMIC_06254

LepChorionDB

A relational database, containing all Lepidoptera chorion proteins identified to date.…

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 based on multiple sequence alignments of conserved…

Manually Curated Database of Rice Proteins

OMIC_04474

Manually Curated Database of Rice Proteins
MCDRP

A unique curated database of rice proteins based on published experimental data.

A unique curated database of rice proteins based on published experimental data.

MAPU

OMIC_03916

MAPU

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

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 been analyzed in depth.

MASCP gator

OMIC_05414

MASCP gator

An aggregation portal for Arabidopsis proteomic data currently being produced by the…

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.

MfunGD

OMIC_04538

MfunGD

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

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

neXtProt

OMIC_03915

neXtProt

A human protein-centric knowledge platform. Developed at the Swiss Institute of…

A human protein-centric knowledge platform. Developed at the Swiss Institute of Bioinformatics (SIB), it aims to help researchers answer questions relevant to human proteins. To achieve this goal, neXtProt is built on a corpus containing both…

OryzaPG-DB

OMIC_03281

OryzaPG-DB

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

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

Plant Protein Phosphorylation DataBase

OMIC_03237

Plant Protein Phosphorylation DataBase
P3DB

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

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 nonplant biologists in the field of protein…

Plant Proteomics DataBase

OMIC_03256

Plant Proteomics DataBase
PPDB

Provides an integrated resource for experimentally identified proteins in Arabidopsis and…

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

Plasma Proteome Database

OMIC_03918

Plasma Proteome Database
PPD

Hosts qualitative and quantitative information on proteins (including those from…

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.

ProPepper

OMIC_10207

ProPepper

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

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 in food science, agricultural breeding or medical…

ProteINSIDE

OMIC_09281

ProteINSIDE

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

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 proteins that mediate signalisation between cells or…

ProteomExchange

OMIC_02458

ProteomExchange

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

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

PRoteomics IDEntifications database

OMIC_02456

PRoteomics IDEntifications database
PRIDE

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

A centralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post-translational modifications and supporting spectral evidence. PRIDE is a core member in the ProteomeXchange (PX)…

ShrimpGPAT

OMIC_06121

ShrimpGPAT

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

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 putative functional prediction and sequence analysis…

SynDB

OMIC_02781

SynDB

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

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

Sys-BodyFluid

OMIC_03919

Sys-BodyFluid

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

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 fluid, human milk and amniotic fluid.

UniProt proteomes

OMIC_05991

UniProt proteomes

UniProt provides ‘proteome’ sets of proteins thought to be expressed by…

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) and unreviewed (UniProtKB/TrEMBL) entries.

WallProtDB

OMIC_09683

WallProtDB

Aims at collecting cell wall proteomic experimental data. WallProtDB contains 2,170…

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 species. Two criteria have to be met for entering…