Simple SummaryPancreatic cancer is a significant problem worldwide. Most cancers are diagnosed at an advanced stage. Limited knowledge of the pathogenesis of pancreatic tumors results in limited diagnostic and therapeutic possibilities. Using metabolome analysis, we identified unique metabolite profiles specific not only for pancreatic ductal adenocarcinoma (PDAC) but also for neuroendocrine pancreatic tumor (PNET), which may be helpful to understand the pathogenesis of pancreatic diseases. Additionally, we discovered that disturbed metabolites, mainly acetylcarnitine C2, serotonin, and glycerophospholipid PC aa C34:1, have potential to be used as biomarkers for diagnosing and monitoring the progression of pancreatic tumors. Serum-circulating metabolites can be easily monitored without invasive procedures; they show the current condition of clinical patients and therefore help with pharmacological treatments or dietary strategies.AbstractBackground: Pancreatic cancer is the most common pancreatic solid malignancy with an aggressive clinical course and low survival rate. There are a limited number of reliable prognostic biomarkers and a need to understand the pathogenesis of pancreatic tumors; neuroendocrine (PNET) and pancreatic ductal adenocarcinomas (PDAC) encouraged us to analyze the serum metabolome of pancreatic tumors and disturbances in the metabolism of PDAC and PNET. Methods: Using the AbsoluteIDQ®p180 kit (Biocrates Life Sciences AG, Innsbruck, Austria) with liquid chromatography–mass spectrometry (LC-MS), we identified changes in metabolite profiles and disrupted metabolic pathways serum of NET and PDAC patients. Results: The concentration of six metabolites showed statistically significant differences between the control group and PDAC patients (p.adj< 0.05). Glutamine (Gln), acetylcarnitine (C2), and citrulline (Cit) presented a lower concentration in the serum of PDAC patients, while phosphatidylcholine aa C32:0 (PC aa C32:0), sphingomyelin C26:1 (SM C26:1), and glutamic acid (Glu) achieved higher concentrations compared to serum samples from healthy individuals. Five of the tested metabolites: C2 (FC = 8.67), and serotonin (FC = 2.68) reached higher concentration values in the PNET serum samples compared to PDAC, while phosphatidylcholine aa C34:1 (PC aa C34:1) (FC = −1.46 (0.68)) had a higher concentration in the PDAC samples. The area under the curves (AUC) of the receiver operating characteristic (ROC) curves presented diagnostic power to discriminate pancreatic tumor patients, which were highest for acylcarnitines: C2 with AUC = 0.93, serotonin with AUC = 0.85, and PC aa C34:1 with AUC = 0.86. Conclusions: The observations presented provide better insight into the metabolism of pancreatic tumors, and improve the diagnosis and classification of tumors. Serum-circulating metabolites can be easily monitored without invasive procedures and show the present clinical patients’ condition, helping with pharmacological treatment or dietary strategies.