Cellular membranes feature dynamic submicrometer-scale lateral domains termed lipid rafts, membrane rafts or glycosphingolipid-enriched microdomains (GEM). Numerous proteomics studies have been conducted on the lipid raft proteome, however, interpretation of individual studies is limited by potential undefined contaminant proteins. To enable integrated analyses, we previously developed RaftProt (http://lipid-raft-database.di.uq.edu.au/), a searchable database of mammalian lipid raftassociated proteins. Despite being a highly used resource, further developments in annotation and utilities were required. Here, we present RaftProt V2 (http://raftprot.org), an improved update of Raft- Prot. Besides the addition of new datasets and re-mapping of all entries to both UniProt and UniRef IDs, we have implemented a stringent annotation based on experimental evidence level to assist in identification of possible contaminant proteins. Raft- Prot V2 allows for simultaneous search of multiple proteins/experiments at the cell/tissue type and UniRef/Gene level, where correlations, interactions or overlaps can be investigated. The web-interface has been completely re-designed to enable interactive data and subset selection, correlation analysis and network visualization. Overall, RaftProt aims to advance our understanding of lipid raft function through integrative analysis of datasets collected from diverse tissue and conditions. Database URL: http://raftprot.org.