FIGURE 2 System-wide analysis of clinical samples. AHeatmap describing samples collected from 29 patients, including gliomas from WHO grade II to IV with or without IDH1 mutations as well as BrMs from lung cancer (L.C), breast cancer (B.C), ovarian cancer (O.C), and colorectal cancer (CC). In addition, 27 samples were utilized for later analysis with more than 50% overlap of identified proteins in each sample. B Contrast-enhanced magnetic resonance imaging (MRI) of BrMs and gliomas. Patients with BrMs from L.C, O.C and B.C as well as gliomas of WHO grade III with IDH1 mutation (III-Mut), IV with IDH1 mutation (IV-Mut), and gliosarcoma (IV-GSM) are shown.C Number of quantified proteins segregated by binned average protein intensities in four commercial HeLa digests for mass spectrometry quality control (QC). D Distribution of peptide intensities in parallel HeLa (H) treatments (n = 3) for experimental quality control.E Number of protein group, peptide and propensity score matching (PSM) identifications for BrMs (n = 14) and gliomas (n = 13). Values above columns indicate average numbers of identification. Error bars indicate standard error of mean based on biological replicates.