Panorama is a freely-available, open-source repository server application for targeted mass spectrometry assays that integrates into a Skyline mass spec workflow.
PeptideAtlas is a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments.
Joint Genome Institute
Genomes of microbes, fungi algae and plants
Ensembl is a genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation.
"iProX is an integrated proteome resources center in China, which is built to accelerate the worldwide data sharing in proteomics. iProX is composed of a data submission system and a proteome database. The submission system is established under the guidance of the data-sharing policy made by ProteomeXchange consortium."
The ProteomeXchange Consortium was established to provide globally coordinated standard data submission and dissemination pipelines involving the main proteomics repositories, and to encourage open data policies in the field
NCBI Reference Sequence Database: "A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein."
A proteomic database named jPOST (Japan ProteOme STandard Repository/Database) to integrate proteome datasets generated from multiple projects and institutions.
MassIVE is a community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data. MassIVE datasets can be assigned ProteomeXchange accessions to satisfy publication requirements.
Uniprot proteomes contains protein sequences from organisms that have had their genomes sequences. Some of these protein sequences may be manually curated while other automatically annotated.