Objective: Pancreatic cancer is an asymptomatic disease and, based on statistical studies, it is the fourth leading cause of cancer-related death. Pancreatic ductal adenocarcinoma (PDAC), which accounts for over 95% of pancreatic cancers, is typically detectable at advanced stages. Standard diagnostic methods include bloodbased tests and imaging. Standard diagnostic methods include blood-based tests and imaging. Biomarkers play a key role as indicators in blood tests, offering valuable insights into disease detection and monitoring. Mesothelin, a cell-surface glycoprotein, and vimentin, an intermediate filament protein, are promising biomarker candidates. Methods: In this study, these biomarkers were conjugated with magnetic nanoparticles (MNPs) and utilized for cellular tracking through magnetic particle spectroscopy (MPS). Capan-1 (a pancreatic cancer cell line) and bone marrow stem cells (BMSC) were treated with the targeted MNPs. Subsequently, MNP-labelled cells were evaluated with imaging modalities such as MPS and confocal microscopy. Results: In the case of the MPS modality, a home-made MPS device with a detection limit of 1 ng of MNPs was used. The results showed that MPS can quantitatively trace MNPs signals and differentiate between various treatments. Conclusions: Detection of labelled cells via MPS is a novel method with features such as sensitivity, non-invasiveness, and no background noise. This new technology can pave the way for imaging quantification of pancreatic cancer in its primary stages and for tracking cancer cell populations.