Mass spectrometry-based proteomics at the Amsterdam UMC is enabled by nano-liquid chromatography on-line coupled to high resolution benchtop orbitrap platforms. These platforms can measure global protein abundance levels, protein splice variants, isoforms, mutant variants, and post-translational modifications such as phosphorylation. We employ label-free profiling for comparative analysis of disease states to determine pathway activation and to identify and validate candidate biomarkers and drug targets

We have ample expertise in large scale clinical proteomics of a variety of sample types (tissues, biofluids such as cerebrospinal fluid, urinary extracellular vesicles, blood platelets, stool, sputum, FFPE and RNABee left-over samples) and dedicated statistics. Moreover, to study cellular signaling, we offer an automated phosphoproteomics workflow coupled to dedicated analysis via the INKA pipeline (www.inkascore.org) that we developed to reduce complex MS/MS-based phosphoproteomics data to a simple ranking of kinase activity and visualization of kinase-substrate networks in a single biological sample.

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