3.1 Global proteomic profiling of glioma samples reveals differentially regulated proteins and glycoproteins
We have performed comprehensive proteomic analysis of glioma samples using high resolution LC-MS/MS followed by MRM based validation(Figure 1) . The global proteomic analysis resulted in identification of 1024 unique proteins in at least 70% of the samples.Figure 2A represents a heatmap of top 25 differentially expressed proteins in HGG and LGG. The principal component analysis (PCA) plot showed two separate clusters for HGG and LGG with a score of 33% for PC1, 13.3% for PC2 and 10.1% for PC3 (Figure 2B).The statistical test provided 140 significant proteins (FDR q value <0.05, absolute Fold change >1.5), of which 72 proteins were downregulated and 68 proteins were upregulated in HGG when compared the protein abundance (Figure 2C) . Proteins, namely, Fibronectin (FN1), Collagen alpha-3(VI) chain (COL6A3), Collagen alpha-2(VI) chain (COL6A2), Fibrinogen beta chain (FGB), Plasminogen (PLG), Inter-alpha-trypsin inhibitor heavy chain H2 (ITIH2), Kininogen-1 (KNG1) were found to be significantly upregulated in HGG, whereas proteins like Contactin-1 (CNTN1), Tenascin-R (TNR), Neurofascin (NFASC), Ankyrin-2 (ANK2) and Neurogranin (NRGN) were found downregulated in HGG. A list of key candidate proteins and glycoproteins identified via label-free quantitative proteomics in high grade glioma tumor samples is given in Table 2.