Table 2.

Overview of platforms with application for protein analysis.

Platform	Database	What Is	Applications	URL	Reference
AureoLib/Aurewiki	Staphylococcus. aureus	AureoLib is a library to provide easy and intuitive access to protein synthesis data derived from various proteomics experiments	Aureolib provides protein synthesis data derived from various proteomic experiments (adaptation processes); Aurewiki provides functional and expression data (pangenome).	http://www.aureolib.de (accessed on 19 July 2021)	Fuchs et al. [129]
BioGrid	Multiplex	The Biological General Repository for Interaction Datasets (BioGRID) is a public database focused on specific biological processes with disease relevance.	Repository of genetic and protein interactions, chemical associations, and post-translational modifications, from model organisms and humans.	http://thebiogrid.org/ (accessed on 19 July 2021)	Oughtred et al. [130,131]
Cytoscape	Multiplex	Cytoscape is an open source software platform	Visualization of the molecular interaction networks and biological pathways, and integration of these networks with annotations, gene expression profiles and other data.	http://www.cytoscape.org/index.html (accessed on 19 July 2021)	Shannon et al. [132], Smoot ME et al. [133]
PeptideShaker	Multiplex	PeptideShaker is a search engine platform for the identification of proteins from multiple searches and de novo engines.	Protein identification with functional data.	http://compomics.github.io/projects/peptide-shaker.html (accessed on 19 July 2021)	Vaudel et al. [134]
PeptideAtlas	Multiplex	PeptideAtlas is a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem MS proteomics experiments.	Protein identification, full annotation, database, data repository, peptides sequence, mapping and storing among others	http://www.peptideatlas.org/ (accessed on 19 July 2021)	Desiere et al. [135]
REACTOME	Multiplex	REACTOME is an open-access, manually curated and peer-reviewed pathway database.	Visualization, interpretation and analysis of pathways and interactions in the human biological system.	http://www.reactome.org/ (accessed on 19 July 2021)	Fragegat et al. [136]
STRING	Multiplex	STRING is a database of well-known protein interactions, including direct (physical) and indirect (functional) associations, aggregated from other (primary) databases.	Protein–protein interaction identification, pathway analysis, network connectivity, functional prioritazation.	https://string-db.org/ (accessed on 19 July 2021)	Snel et al. [137] Szklarczyk et al. [128]