The Q-Exactive mass spectrometer (Thermo Fisher Scientific) is equipped with a nano-electrospray ionization source which is interfaced to the nanoUPLC Easy LC 1000 from Proxeon Biosystems. The MS/MS acquisition is downstream to a HCD (high energy collision dissociation) fragmentation.

The high resolution mass spectrometer is able to carry out quantitative proteomics analyses, both label-free and SILAC/iTRAQ/TMT approaches. PTM characterization can be easily performed. Moreover, thanks to the quadrupole, PRM analyses are also feasible in order to quantify proteins that are in low abundance in cells and tissues.

Mascot 2.6 is used for the identification of proteins.  Freely downloadable Max Quant/Perseus software, together with MeV software is used for identification, quantification and statistical validation of the proteomic data.