Mass Spectrometry Facility
The Facility provides state-of-the-art instrumentation and expertise for a variety of Mass Spec-based proteomic applications, such as:
- Shotgun bottom-up proteomics
- Pulsed SILAC labeling
- Secretomics
- Exosomal proteomics
- MHC immunopeptidomics
- IP analysis
- Sulfhydryl redox state analysis
The Facility provides standard sample preparation pipelines but is also available to adapt or implement new procedures for the specific needs of a user. For this, the facility works in close contact with multiple research groups at IRB, IOR , EOC and with external collaboration partners, in order to design the most appropriate pipeline for every project. The Facility follows the regulations of a BSL2 laboratory.
The Facility is also engaged in their own research to develop new techniques and tools to keep increasing their skillset and offer.
This Facility is managed by the Institute for Research in Biomedicine (IRB): https://irb.usi.ch/facilities/mass-spectrometry/
Equipment
Mass Spectrometry platform
- Thermo Scientific Q Exactive HF LC-MS/MS System, combining an Advanced Quadrupole mass filter for high isolation efficiency and an ultra-high-field Orbitrap mass analyzer for fast scans at high resolution, allowing for elevated acquisition speed with exceptional analytical performance
- The platform is completed by a Thermo Scientific EASY-nLC 1200 HPLC system for nanoflow reverse phase chromatographic separation, coupled online to the mass spectrometer for streamlined electrospray ionization during peptide elution.
Data analysis
- Raw data processing is performed on a 44-core Windows workstation with 5 TB of hard disk space and 64 GB of RAM.
- The facility provides state-of-the-art raw data analysis with the quantitative proteomics freeware package MaxQuant. Additionally, it can offer data analysis with Skyline (targeted MS) or Spectronaut (DIA MS).
- Depending on the user’s needs, the facility can provide annotated matrices of quantified proteins. It also offer data interpretation and statistical analysis with the freeware Perseus platform or with custom-designed R pipelines.
