The Mass Spectrometry (MS) Core Facility provides internal and external researchers with modern chromatographic and mass spectrometric tools for the identification and characterization of a broad range of biological species. It provides consultancy services and analytical method development for specific applications, as well as mass spectra data processing. Samples are analyzed either directly by the service or by researchers (previously trained by facility members), who can use mass spectrometers through an open-access system. Protein identification and quantitation by classical proteomic approaches are performed in collaboration with the PCB’s Proteomics Platform.

The services offered include MS, MS/MS and MSn analysis using atmospheric pressure ionisation techniques (electrospray and APcI) coupled to LC, nanoLC or infusion inlets. IM-MS (ion mobility mass spectrometry) and HDX-MS (hydrogen deuterium exchange coupled to MS) are also used for structural characterization of proteins.

Lines of expertise

• Intact protein analysis. Top-down. Middle-down.
• Native MS: Structural characterization by IM-MS and HDX-MS. Non-covalent complexes analysis.
• Peptide enzymatic digests analysis (MS, MS/MS) for protein identification and post- translational modifications (PTMs) determination. Bottom-up MS-based proteomics (in coordination with the PCB's Proteomic Platform).
• Small molecule analysis for exact mass determination.

Equipment and specialised applications

1. LTQ FT Ultra (Thermo Scientific). Hybrid Mass Spectrometer consisting of a linear Ion Trap, combined with a Fourier Transform Ion Cyclotron Cell. It is also provided with ECD and IRMPD for complementary protein fragmentation in the mass spectrometer. This instrument is used to perform Top-down MS protein analysis and Bottom-up applications. In its normal configuration, this instrument works coupled to an LC device (Surveyor LC -Thermo-) and a chip-based nanoESI interface (Advion Triversa Nanomate).
2. Synapt High Definition MS System (Waters-Micromass). Hybrid QTOF instrument with an incorporated Triwave Cell. This instrument allows tandem MS to be combined with ion mobility, thus permitting the analysis of samples differentiated not only by their mass to charge ratio, but also by their shape and size. The instrument is used to analyse the macromolecular structure and conformation of intact proteins and to study non-covalent interactions. When working in its normal configuration, it is attached to a chip-based nanoESI interface (Advion Triversa Nanomate), thus combining the analysis of samples by infusion mode and by nanoLC coupling (NanoAcquity UPLC, Waters; purchased in 2009).
3. LCT-Premier XE (Waters-Micromass). Orthogonal acceleration time-of-fight mass spectrometer ideal for the analysis of high molecular weight compounds. This instrument has been modified to achieve inert conditions inside the ionisation source, in order to allow amide H/D exchange experiments for the study of the dynamic and structural properties of proteins and their complexes. In another set-up configuration, it is used to analyse small molecules for their structural characterisation and provides accuracies of less than 3ppm. For LC-purifications, it is normally attached to an LC device (UPLC Acquity, Waters).