Mass Spectrometry (MS)

The unit is equipped with an LTQ XL Ion Trap mass spectrometer from ThermoFisher with an additional ETD (Electron Transfer Dissociation) fragmentation¹⁾.

This instrument, in-line with a nano-capillary chromatograph, allows the separation of peptide mixtures with different complexity degree and the subsequent identification of the constituent proteins through dedicated software (LC-MS / MS analysis). This instrumentation is of great support in the biomedical research projects that require the identification and/or characterization of proteins and their level of expression. The samples to be analyzed can be multiple: synthetic proteins, semi-purified proteins, immuno-precipitation, sub-proteomes, total proteomes. Generally, the LC-MS / MS analysis is preceded by electrophoresis (PAGE) for a qualitative and quantitative estimate of the sample followed by protein in-gel digestion.

In case of very poor samples or for methodological needs, the digestion can be carried out in solution and followed by off-line chromatography before the LC-MS /MS analysis²⁾. In comparative studies, relative quantitative determination is possible through isotopic labeling techniques³⁾⁴⁾ or label-free⁵⁾. The unit relies particularly on extensive experience in the following areas:

• preparation and characterization, also by means of quantitative comparative analysis, of sub-proteomes extracted from cultured cells, fluids and other biological tissues;
• analysis of membrane microdomains (rafts) and extra-cellular vesicles (exosomes and microparticles);
• protein characterization: protein sequence analysis by combining different enzymes, post-translational modifications, N-termini and neo-N-termini determination by chemical derivatization, analysis of protein adducts with 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: Marta Ponzi
☎ +39 06 4990 3134
Where we are: building 30, floor A, room 11

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