Critical Proteomics Databases to Know for Proteomics

Critical proteomics databases are essential for understanding proteins and their functions. They provide valuable resources for storing, sharing, and analyzing proteomics data, helping researchers uncover insights into protein interactions, expressions, and roles in health and disease.

1. UniProt (Universal Protein Resource)

   • Comprehensive protein sequence and functional information database.
   • Provides curated data on protein sequences, structures, functions, and interactions.
   • Offers tools for protein analysis, including BLAST and sequence alignment.

2. PRIDE (PRoteomics IDEntifications Database)

   • Specialized database for storing and sharing proteomics data, particularly mass spectrometry results.
   • Facilitates the submission and retrieval of proteomics experiments and their associated metadata.
   • Supports the validation and re-analysis of proteomics data through standardized formats.

3. PeptideAtlas

   • A resource that compiles and organizes peptide and protein identifications from various proteomics studies.
   • Provides a comprehensive view of the human proteome based on experimental data.
   • Offers tools for searching and visualizing peptide and protein data.

4. ProteomicsDB

   • A database that integrates proteomics data from multiple sources, focusing on human proteins.
   • Allows users to explore protein expression levels, modifications, and interactions.
   • Provides a user-friendly interface for data visualization and analysis.

5. SWISS-MODEL Repository

   • A database for protein structure models generated through homology modeling.
   • Offers access to 3D models of proteins, which can aid in understanding protein function and interactions.
   • Provides tools for model evaluation and comparison.

6. Human Protein Atlas

   • A comprehensive resource that maps the expression and localization of proteins in human tissues and cells.
   • Integrates data from various omics technologies, including transcriptomics and proteomics.
   • Aims to provide insights into the role of proteins in health and disease.

7. Global Proteome Machine Database (GPMDB)

   • A database that focuses on the analysis and storage of mass spectrometry-based proteomics data.
   • Provides tools for searching and analyzing large-scale proteomics datasets.
   • Supports the sharing of experimental data and results among researchers.

8. MassIVE (Mass Spectrometry Interactive Virtual Environment)

   • An open-access repository for mass spectrometry data, facilitating data sharing and collaboration.
   • Provides tools for data visualization, analysis, and re-analysis of mass spectrometry experiments.
   • Supports the submission of raw data and processed results for public access.

9. ProteomeXchange

   • A consortium that facilitates the exchange of proteomics data across multiple databases.
   • Provides a standardized framework for data submission and sharing, enhancing data accessibility.
   • Aims to promote transparency and reproducibility in proteomics research.

10. neXtProt

    • A knowledge platform that provides detailed information on human proteins, including functions, interactions, and disease associations.
    • Integrates data from various sources, including literature, databases, and experimental results.
    • Offers tools for searching and exploring protein-related information in a user-friendly manner.