Mass Spectrometry (MS)

Two Tribrid Orbitrap Fusion high resolution mass spectrometers are present in the MS Unit. The Tribrid architecture combines three mass analyzers: a quadrupole, an ion trap and an Orbitrap. Multiple fragmentation techniques are adopted: CID (Collision Induced Dissociation), HCD (Higher-energy Collisional Dissociation) and ETD (Electron transfer dissociation)¹⁾.

A FAIMS interface (field asymmetric-waveform ion-mobility spectrometry) is also available. The spectrometers, on line with nano-capillary chromatographs, allow the separation of more or less complex peptide mixtures and the subsequent identification of the constituent proteins, through dedicated software. This instrumentation is of great support in those biomedical research projects in which one is interested in the identification and/or characterization of proteins and their level of expression. The samples to analyze can be many: synthetic proteins, semi-purified proteins, immuno-precipitations, sub-proteomes, total proteomes. Generally, the LC-MS/MS analysis is preceded by protein mixture in solution digestion²⁾ or protein separation by electrophoresis (PAGE) followed by in-gel digestion, in order to carry out a qualitative and quantitative estimation of the sample.

In comparative studies it is possible to determine the relative quantity using isotope labeling³⁾⁴⁾ or label-free⁵⁾ techniques. In particular, the unit draws on extensive experience in the following areas:

• preparation and characterization, also through quantitative comparative analysis, of sub-proteomes extracted from cultured cells, fluids and other biological tissues;
• analysis of membrane microdomains (rafts) and extracellular vesicles (exosomes and microparticles);
• characterization of proteins: analysis of the protein sequence by combining different enzymes, study of post-translational modifications, determination of the N-terminus and neo-N-termini by chemical derivatization, formation of adducts between proteins and small molecules and/or drugs;
• interactomics by analysis of immunoprecipitates;
• quantitative analysis of specific peptides in mixture.

Several bioinformatic analysis approaches are available for the analysis of results.

1. preliminary contact the MS unit staff;
2. fill out the online form 'Service Request' briefly illustrating the scientific problem, type and number of samples etc.;
3. plan a meeting with the unit staff to discuss methods of analysis, costs, timing etc.

We recommend that you follow the advices in the 'Guidelines' section during sample preparation.

Contact: Serena Camerini
☎ +39 06 4990 3164
Fax +39 06 4990 2040
Where we are: building 30, floor A, room 11