Mass Spectrometry Unit (MSU)

Over the past decade, mass spectrometry (MS)-based proteomics has emerged as the technology of choice for large-scale protein analysis, enabling the investigation of biological processes and disease states. The Mass Spectrometry Unit (MSU) maintains a state-of-the-art MS technological platform to support both the investigators at the Department of Experimental Oncology (DEO) and clinical research at IEO. Through collaborative projects with internal groups, the Unit provides standard MS-proteomic analyses, including protein identification, differential quantitative proteomic studies (SILAC and label-free), and protein-protein interaction analysis (IP, PD, and proximity labeling experiments).

The Unit is equipped with state-of-the-art Orbitrap-hybrid mass spectrometers, operating in bottom-up workflows (DDA, DIA), and coupled to various nano-flow chromatography systems (nLC-1200, Neo Vanquish, and Evosep-one). Additionally, the Unit utilizes a 1680 HPLC (Agilent) for offline peptide fractionation (RP-HpH, SCX). The Unit has also implemented Quantitative Proteomics Made Simple (QProMS), an R-based algorithm, search engine-independent data analysis, and visualization tool.

Furthermore, the Unit is dedicated to implementing innovative MS-based strategies to facilitate in-depth proteomic profiling of clinical patient samples, including both solid tissues (frozen and FFPE) and liquid biopsies.