ProteomicsDB

ProteomicsDB is a database that enables researchers to explore large collections of quantitative mass spectrometry-based proteomics data in a protein-centric in-memory database. With a standardized analysis pipeline, ProteomicsDB allows for comparisons between hundreds of tissues, body fluids, and cell lines, making it an essential resource for modern science.

The authors have extended the data model to include the storage and integrated visualization of other quantitative omics data from sources such as NCBI GEO, protein-protein interactions from STRING, functional annotations from KEGG, drug-sensitivity/selectivity data from several public sources, and reference mass spectra from ProteomeTools. This extended functionality transforms ProteomicsDB into a multi-purpose resource connecting quantification and meta-data for each protein.

The rich user interface of ProteomicsDB allows researchers to navigate all data sources easily, either in a protein-centric or multi-protein-centric manner. Additionally, several options are available to download data manually, while the application programming interface enables accessing quantitative data systematically.