Here we performed a systematic quantitative proteome profiling of GIST from 13 patients classified into low, intermediate and high risk subgroups. An extended cohort of GIST (n = 131) was used for immunohistochemical validation of proteins of interest. 9510 proteins were quantified, covering nearly 60% of the GIT transcriptome from The Human Protein Altas. 630 proteins were simultaneously up- or down-regulated in GIST tumorous tissues independent of risk rating, while 384 proteins showed differentially expressed patterns among GIST subgroups with statistical significance