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Instrumentation
The proteomics facility uses mass spectrometers linked to nano-flow chromatographic chains (nano LC-MS/MS).
Q Exactive Plus
- coupled with an Easy-nanoLC1000 (ThermoScientific) :
This equipment was installed in January 2016, financed by IdEX Unistra (Medium-heavy equipment).
This ThermoScientific brand mass spectrometer is a Quadrupole-Orbitrap hybrid: it combines the quadrupole selection of precursor ions with the high resolution and mass accuracy of the Orbitrap analyzer.
The platform uses this instrument for qualitative and quantitative proteomic analyses, for all the proposed research services: “Classical protein identification”, “Interactomics” and “Differential analyses”, as well as the characterisation of post-translationnal modifications.
Triple TOF 5600
- coupled with a nanoLC-Ultra-2D-plus (Sciex) :
This equipment was acquired in December 2011 with LabEX NetRNA fundinging.
This Sciex brand mass spectrometer is a Quadrupole – Time Of Flight hybrid (Quad-TOF).
The facility uses this instrument for protein development and quality control.
Bioinformatic analyses :
The facility has a computer server installed on the university campus. This makes it possible to use a wide range of demanding software for the reprocessing of mass spectrometry data:
- Mascot and Mascot Daemon: database searches (version 2.6, MatrixScience).
- Proline : open-source software suite dedicated to qualitative and quantitative proteomic analysis (ProFI, Proteomics French Infrastructure).
- Dedicated software for Sciex data analysis: ProteinPilot, PeakView et MarkerView.
- Dedicated software for Thermo data analysis : ProteomeDiscoverer.
- ProgenesisQI : for relative quantitation from « Label-Free » data (Non Linear Dynamics).
- Skyline : open-source software dedicated to the reprocessing of targeted analysis data (SRM, MRM, PRM) and quantitative data (MS1 XIC, SWATH).
