Main instrumentation
| Bruker timsTOF Pro Mass spectrometer with a dual-TIMS analyzer allowing parallel accumulation serial fragmentation technique (PASEF). It is interfaced to an Ultimate 3000 Nano LC system from Thermo, and is our instrument of choice for DIA MS analyses. |  |
| Thermo Scientific Exploris 480 Hybrid quadrupole-Orbitrap mass spectrometer for high-resolution analyses. It is interfaced to a Vanquish Neo LC system from Thermo, and is our instrument of choice for protein interaction analyses. |  |
| Thermo Scientific Orbitrap Fusion Mass spectrometer Orbitrap system with a “Tribrid architecture” combining quadrupole, Orbitrap and linear ion trap mass analyzers. It is installed with an ETD fragmentation system, particularly suitable for the analysis of post-translational modifications and large peptides/intact proteins. Combined with FAIMS, it is our intrument of choice for TMT-phosphoprotemics analyses. |  |
| ProteinSimple Jess This instrument performs size-based automated capillary Western blot assays, for antibody-based targeted quantitation of proteins. |  |
Other instruments
| Integra Assist Plus | Pipetting robot used for sample preparation, integrating multi-channel or single-channel pipettes. |
| FastPrep FP120 | Sample disruption instrument using ceramic (zirconium oxide) beads to quickly and efficiently homogenize, grind, and lyse biological samples. In our lab, it is mostly used for tissue samples. |
| BeatBox (PreOmics) | Cell lysis and tissue homogenizer using proprietary coated GYUTO beads for sample disruption. |
| GeSim Nano-Plotter 2.1 spotter | Non-contact printer using piezoelectric pipetting tips to dispense drops of 400 or 40 picolitres. |
| Innopsys Innoscan 710 IR | Confocal scanner equipped with 2 extremely sensitive photomultipliers to detect fluoresecence at 670 and 785 nm on microscope slides. |
Software and data analysis workflows
| Software | Analytical workflow |
| Mascot – Matrix Science | Identification, DDA |
| Scaffold – Proteome Software | Post-analysis processing (Identification, DDA) |
| MaxQuant – maxquant.org | Quantification, DDA |
| Spectronaut – Biognosys | Quantification, DIA |
| PEAKS – Bioinformatics Solutions | Identification, PTM |
| Proteome Discoverer – ThermoFisher | Identification, quantification, DDA |
| Perseus – maxquant.org | Post-analysis processing (quantification DDA & DIA), statistics |
| Compass for Simple Western – Biotechne | Simple Western data analysis |