Project description:Metabolomics data collected for high biomass fecal and saliva samples on quadrupole-Orbitrap mass spectrometer to validate a standardized method for sample accession, DNA and metabolite extraction using single tubes (Matrix tubes).
Project description:Metabolomics data collected for low biomass skin and environment samples on quadrupole-Orbitrap mass spectrometer to validate a standardized method for sample accession, DNA and metabolite extraction using single tubes (Matrix tubes).
Project description:Metabolomics data collected for high biomass fecal and saliva samples on quadrupole-Orbitrap mass spectrometer to validate a standardized method for sample accession, DNA and metabolite extraction using single tubes (Matrix tubes).
Project description:Metabolomics provides a direct functional readout of a tumor’s physiology. Yet, it is lagging behind other omics technologies in facilitating disease monitoring and prognostication. This stems partly from the scarcity of large-scale metabolomic studies, but also the analytical complexities of detecting diverse metabolites with varying physicochemical properties and concentrations. To address this, we developed a machine learning framework using both tumor tissue and cell line samples across multiple cancer types that allows prediction of metabolomics from gene expression data. Two different model types were selected and trained for tissues and cell lines with their generalization capacity validated on independent cohorts, accurately predicting as high as 70-80% of tested metabolites. This work offers a scalable and efficient machine learning pipeline to determine metabolic from transcriptomic signatures, opening avenues to reconstruct and study the metabolic landscape of samples across novel and existing datasets lacking direct metabolomics measurements.
Project description:Western blotting (WB) is widely used to test antibody specificity, but the assay has low throughput and precision. Here we show that an inverted version of WB allows parallel readout with antibody arrays, shotgun mass spectrometry (MS) and immunoprecipitation followed by MS (IP-MS). The pipeline provides means for large-scale implementation of concepts proposed by an international working group on antibody validation (IWGAV).