Serial surface mass spectrometry metabolomics on sample-limited tissue archives reveals signatures for predicting pediatric brain tumor relapse

We present here a novel surface mass spectrometry strategy to perform untargeted metabolite profiling of formalin-fixed paraffin-embedded (FFPE) pediatric ependymoma archives. Sequential Orbitrap secondary ion mass spectrometry (3D OrbiSIMS) and liquid extraction surface analysis-tandem MS (LESA-MS/MS) permitted the detection of 887 metabolites (163 chemical classes) from pediatric ependymoma tumor tissue microarrays (diameter <1 mm; thickness: 4 m). From these 163 classes, 60 classes were detected with both techniques, whilst LESA-MS/MS and 3D OrbiSIMS individually allowed the detection of another 83 and 20 unique metabolite classes, respectively. Through data fusion and multivariate analysis, we were able to identify key metabolites and corresponding pathways predictive of tumor relapse which were retrospectively confirmed using gene expression analysis with publicly available data. Altogether, this sequential mass spectrometry strategy has shown to be a versatile tool to perform high throughput metabolite profiling on sample-limited tissue archives. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=91 SRC="FIGDIR/small/182071v3_ufig1.gif" ALT="Figure 1"> View larger version (11K): org.highwire.dtl.DTLVardef@1f9c850org.highwire.dtl.DTLVardef@1ce0568org.highwire.dtl.DTLVardef@c5023borg.highwire.dtl.DTLVardef@15ad6e_HPS_FORMAT_FIGEXP M_FIG For Table of Contents Only C_FIG