In this project we aimed to establish a proteome-based pipeline for a non-model Baikal endemic amphipod species Eulimnogammarus cyaneus (Dybowsky, 1874). We used next-generation transcriptome sequencing to create a database for protein identification and investigated the proteome of E. cyaneus with LC-MS with particular emphasis on sexual dimorphism and response to acute thermal stress. We were able to characterize ca. 1000 protein groups and found male- and female-specific proteins, as well as proteins specific for thermal stress conditions.