Chiara Guerrera

Proteomics approaches are essential to both clinical and basic research to study diseases at protein level and to help understand the underlying mechanisms.

Founded in 2004, Proteomic platform Necker (PPN) mission is to enable Necker teams to succeed in their proteomics projects and it is open to research institutes and clinical departments. PPN is part of SFR Necker, and one of two constitutive laboratories of Paris Descartes University proteomics platform (3P5). Since 2011, PPN is a strong partner of the mass spectrometry APHP Necker Platform for the development of innovative translational proteomics approaches. The instrumental park of PPN includes two new-generation mass spectrometers dedicated to high throughput analysis and quantification of proteins.

Through its activities of service, collaboration and research and development, the PPN offers state of the art technology and expertise to help understanding disease (PTMs, differential and interaction proteomics) and to develop diagnostic/prognostic clinical tests by MS (translational and targeted proteomics).

Available Equipment

The PPN is equipped with

• An Octet red96, installed in 2016 (funded by Ibisa and INEM)
• Nano-RSLC coupled to a Q Exactive Plus Orbitrap (Thermoscientifics): installed in 2014 and 50% co-funded by Imagine
• UPLC coupled to a TQS Xevo (Waters) (shared with MS APHP Necker Platform)
• MALDI TOF TOF Autoflex (Bruker)
• Nano-HPLC coupled to a Ion Trap HCTplus (Bruker)
• 1D and 2D PAGE equipment (Biorad)
• OFFgel Fractionator (Agilent)

The PPN has access to

• A Nano-RSLC coupled to a Q Exactive Orbitrap (Thermoscientifics) (3P5, Cochin campus)
• A Nano-RSLC coupled with an Orbitrap Fusion (Thermoscientifics) (3P5, Cochin campus) 
• A Nano-RSLC coupled to a LTQ Orbitrap Velos (Thermoscientifics) (3P5, Cochin campus)

Expertise and service provided:

The PPN provides :

• Consulting for researchers and design of tailored strategy for their project
• Protein identification for simple or complex mixtures
• Protein identification and quantification (using SILAC, ITRAQ, Labelfree methods)
• Absolute quantificationof proteins (using MRM and PRM methods)
• Statistical and bioinformatics data analysis (primarily using Mascot, Skyline, MaxQuant, Perseus software)
• System biology analysis through proteins network graph (chiefly using Ingenuity, AmiGO software)

Proposed applications

• Identification of novel protein-protein, RNA-protein, DNA-protein interactions
• Identification and quantification of PTMs, such as acetylation and phosphorylation
• Study of global differential proteome in disease vs control
• Multiplexed dosage of known proteins )
• Biomarkers discovery and validation
• Quality checks of recombinant proteins