State Of The Art Infrastructure

A total infrastructure of over 80 state-of-the-art mass spectrometers are available in eleven transnational access sites.

Over 30 Orbitrap’s, more than 10 Q – TOF’s, and  5 Triple Quad’s. The platform also houses a series of MALDI-TOF/TOF’s and FT-ICR high resolution instruments. Different access sites will host projects with different requirements (e.g. PTM analysis, membrane protein analysis, Bio-imaging, native structure analysis, native MS).

Utrecht University (UU) The Netherlands

A total of twenty four  high resolution mass spectrometers are housed at this facility.

12 (Q)-orbi trap based instruments (with some instruments having additional fragmentation features)

9 (Q)-TOF based instruments (1 system containing an IM cell)

3  Triple Quadrupole Instruments

Nine  of these mass spectrometers are permanently coupled to nano LC chromatrography systems.

Dissociation technique technologies such as Collission Induced dissociation (CID) including higher-energy collisional dissociation (HCD), electron transfer dissociation (ETD), and a combination of electron transfer and Higher-energy C-trap dissociation (EThcD), Ultraviolet photodissociation (UVPD), ion mobility separation (IMS), cross linking MS and H/D exchange MS technologies are common practices at this access site.

Vlaams Instituut voor Biotechnologie (VIB), Ghent, Belgium

This facility houses eight mass spectrometers, all coupled to sensitive nano-LC chromatography systems.

The instrumentation includes several high-resolution Orbitrap mass spectrometers, a triple quadrupole mass spectrometer for targeted proteomics and a MALDI-MS/MS instrument.

In combination with PSD, CID, HCD and ETD peptide fragmentation possibilities, these instruments enable high-throughput analysis of complex proteome samples as well as intact protein measurements. In addition, workflows for targeted MS-based approaches, including selected/parallel reaction monitoring (SRM/PRM) and data independent acquisition (DIA) are in place.

University of Copenhagen (UCPH), Denmark

This institution has eleven high-resolution mass spectrometers all equipped for analysis of high-throughput nanoLC-MSMS proteomics experiments.

For online LC-MS/MS experiments, the proteomics platform also has 12 Easy nLC1200, 2 Easy nLC1000 and 3 EvoSep One LCs.

The instruments include 10 of the latest generation of Q Exactive HF-X mass spectrometers exhibiting improved speed and sensitivity, and one Orbitrap Fusion Lumos mass spectrometer providing complementary fragmentation techniques and scanning techniques, such as ETD and MS3 acquisition.


Fuctional Genomics Centre Zurich (FGCZ)/ ETH Zurich, Switzerland

This facility houses nine mass spectrometers, which are equipped for nanoLC-MS/MS proteomics-type experiments.

The instruments include state-of-the-art technologies like high-resolution Orbitrap mass spectrometry, CID, HCD, electron transfer dissociation (ETD), and combinations thereof (EThcD), and cross-linking MS.

Collectively, the analytical technologies provide a full-spectrum infrastructure for high throughput and in-depth proteome analysis. Based on the broad fundament of methodological expertise and know-how, also targeted MS-based approaches, including selected reaction monitoring (SRM) and parallel reaction monitoring (PRM), as well as data independent acquisition (DIA)

Centre For Genomic Regulation (CRG)/Pompeu Fabra University (UPF), Spain

This joint facility houses five high-end mass spectrometers, including an Orbitrap Fusion Lumos, a LTQ-Orbitrap XL, a LTQ-Orbitrap Velos, a QTRAP 5500, and a QTOF 5600.

All mass spectrometers are equipped with nanoLC chromatographic systems for quantitative proteomics experiments, and they cover a wide range of mass analysers (orbitrap, TOF, quadrupoles, ion traps), fragmentation types (CID, HCD, ETD, and their combinations), and acquisition workflows (e.g. DDA, SRM, PRM, and DIA).

Spanish National Cancer Research Centre (CNIO), Spain

This facility houses five mass spectrometers (Q Exactive HF-X, Q Exactive Plus, LTQ Orbitrap Velos, Impact QqTOF and Qtrap 5500).

Technical University of Munich (TUM), Germany

This facility houses eleven mass spectrometers for the analysis of proteomic and metabolomic experiments. The infrastructure boasts the latest hardware for proteomics including three Orbitrap Fusion Lumos instruments (equipped with electron-transfer dissociation, ETD or ultra-violet photo-dissociation, UVPD) and three Orbitrap Q-Exactive HF-X instruments.

All six Orbitrap instruments are furnished with ultra-high performance nano-liquid chromatography systems. This outstanding equipment base enables proteomic projects at any scale and ranging from high-throughput discovery (data-dependent acquisition, DDA), targeted (parallel reaction monitoring, PRM) and data-independent (DIA) experiments.

Institute of Microbiology of the CAS, v. v. i. (IMIC) /Masaryk University (MU), Czech Republic

These facilities jointly house two FT-ICR mass spectrometers (Bruker solariX Ultra-high Resolution Hybrid Qh-Fourier Transform Mass Spectrometers). Both 12 Tesla and 15 Tesla instruments are equipped with a MALDI/ESI dual source, ETD fragmentation module and ParaCell. The 15 T instrument is equipped with an infrared laser for infrared multiphoton dissociation. Nano RSLC 3000 (ThermoFisher Scientific) and Agilent 1200 (Agilent Technologies) HPLC systems and PAL autosampler/robot (CTC analytics), MALDI-TOF/TOF MS (Ultraflex III, Bruker Daltonics) and IMMS Q-TOF (Synapt G2 HD, Waters)

Central European Institute of Technology (CEITEC) / Masaryk University (MU), Czech Republic

Instruments available at these facilities include: MALDI-TOF/TOF MS (UltraflexExtreme, Bruker Daltonik). LC MS/MS experiments are provided by the coupling of  nano LC chromatographic systems to an Orbitrap Fusion Lumos and an Orbitrap Elite.

Pasteur Instituut (IP), France

The Pasteur Instituut houses six mass spectrometers, all equipped for nanoLC-MS/MS proteomics-type experiments.

The instruments include state-of-the-art technologies like CID, HCD, Surface Induced Dissociation (SID), Electron Transfer Dissociation (ETD), and combinations thereof (EThcD), Ion Mobility Separation (IMS), cross-linking MS and H/D exchange MS (with an automated HDX platform). Ultra-violet photo-dissociation (UVPD) will be available soon.

European Institute Of Oncology (IEO), Italy

This facility operates one dedicated ultra-high-pressure liquid chromatography (UHPLC) system coupled with a high field hybrid quadruple-orbitrap mass spectrometer (QExactive-HF) and has additional access to an identical instrument setup is also available at the centralized Consortium (COGENTECH) of the Campus, when additional measurement is needed.

This MS platform is integrated to an ample set of consolidated biochemical and analytical protocols for histone, protein, peptide, modified peptide and sub-proteomes purification prior to MS-analysis. Standard Data-dependent acquisition (DDA) methods are normally used, but hybrid DDA-single reaction monitoring (SIM) can also be employed to specifically target modified peptides in complex matrices.

Genomic Unit

HiSeq 2000, Miseq, NovaSeq 6000, Nanostring nCounter, Biomek FX, LabChip GX; Bioanalyzer 2100, TapeStation, 10X Genomics Chromium, Covaris S220 series, to perform WGS, WES, RNAseq, ChIP-Seq, RepliSeq, Methylation, single-cells RNA analyses.

Crystallography Unit

The Crystallography Unit offers Static Light Scattering, Isothermal Titration Calorimetry, Thermofluor, Mosquito nanodispenser, Crystal Imager for protein expression in insect cells (baculovirus), Biochemical characterization of macromolecular complexes and their affinities, Crystallogenesis, X-ray diffraction data collection and structure determination.

Imaging Unit

The Imaging Unit is equipped with Fluorescence and Confocal Microscopes (including FRAP, FRET, Photoactivation, Tissue Mosaic Reconstruction), Robotized microscopy for high content and resolution image cytometry, to offer services like Basic Image acquisition and Widefield Timelapse, Tissue and Organoids Fluorescence Imaging, Live Cell Imaging (Confocal Timelapse, FRAP, Photoactivation, FRET), Deconvolution (Widefield), in addition to Training and assistance for Users

KTH Royal Institute Of Technology Stolkhom, Sweden

Cell Profiling

The expertise of the Cell Profiling facility is in antibody based imaging to study spatial proteomics in situ. The Cell Profiling facility offers a broad range of infrastructure services within the following pillars; proteomics, bioimaging and molecular structure, single cell biology, genomics, metabolomics, chemical biology and genome engineering, bioinformatics, drug discovery and diagnostics.