FIGURE 1 Schematic diagram of the workflow. Proteomic samples were prepared and analyzed by mass spectrometry. The protein profiles of the two types of brain tumors were discussed separately, followed by comparative analysis to find potential biomarkers that could distinguish between the two tumors of different origin.
During the MS acquisition, four commercial HeLa digests (200 ng each) were uniformly inserted for monitoring MS for instrumental quality control (QC), which showed a constant stability across the entire process of sample analysis (Figure 2C, Figure S1A and B). In addition, three HeLa samples (H) were treated in parallel with tumor tissues from sample preparation to data analysis. Two types of tumors were analyzed alternately at random, and the HeLa sample was inserted every 10 samples for quality control, resulting in an average of approximately 5200 identified proteins and 4499 co-quantified proteins in HeLa cells ( Figure S1C and D). Furthermore, a similar distribution of peptide intensities, low coefficient of variation (CV), and high correlation (0.99) of LFQ proteins were observed in the three HeLa samples (Figure 2D, Figure S1E-G). Overall, we performed robust proteomic analysis for two types of brain tumors using rigorous experiment controls. As a result, 27 of the 29 cohort samples successfully passed the quality control filters with more than 50% overlap of identified proteins in each sample. In total, 8,370 protein groups and 116,526 peptides were identified across all samples, and averages of 4,200 proteins and 33,000 peptides were recovered per sample (Figure 2E). In addition, the missed cleavage rate was as low as 10% on average ( Figure S1H), indicating a well-controlled sample preparation.