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.