Agilent GeneSpring and Mass Profiler Professional (MPP) software was used to perform integrated multi-omics analysis of mRNA expression, miRNA expression, protein expression, and copy number aberration (CNA) associated with glioblastoma multiforme (GBM), the most frequent and lethal of the central nervous system tumors. The genomic data was obtained from The Cancer Genome Atlas (TCGA) project. The molecular subtypes defined by TCGA for GBM were based on mRNA expression. We applied GeneSpring metadata analysis framework to explore the relationship between GBM subtypes and genomic CNA. A multi-omics correlation analysis was performed between mRNAs involved in neurogenesis and their validated miRNAs highlighting the molecular events in Proneural tumors that result in suppression of p53 signaling. Furthermore, a combined analysis of mRNA expression data from TCGA with an independent, label-free GBM proteomics study revealed core subset of 54 signature genes and proteins highlighting the integrated biology analysis power of GeneSpring/MPP software. The core genomics signature clearly differentiated the known tumor subtypes in TCGA cohort. Intriguingly, while TCGA categorization of the proteomics samples were not experimentally determined, the core proteomics signature separated this cohort in 2 or 3 groups, suggesting that different TCGA subtypes may be present.