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, 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 it is also 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).


  • Alain Charbit  
    Référent scientifique  
  • Chiara Guerrera  01 72 60 63 31 
    Responsable de plateforme  


    The PPN is equipped with:

    • Nano-RSLC coupled to a Q Exactive Plus Orbitrap (Thermoscientifics)
    • 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)
    • Janus automate (PerkinElmer)
    • ImagePREP (Bruker)



    The PPN has access to:

    • Nano-RSLC coupled to a Q Exactive Orbitrap (Thermoscientifics) (on 3P5, site Cochin)
    • Nano-RSLC coupled to a LTQ Orbitrap Velos (Thermoscientifics) (on 3P5, site Cochin)



    Site Broussais Site Necker

    Bureau L-162 (1er étage), Bâtiment Leriche, Porte 9

    Labo MS L-114 (RDCB), Bâtiment Leriche, Porte 9

    Bureau Batiment Hamburger  (RDC)

    Labo MS, Biochimie B, tours Lavoisier (4éme étage)

    14 Rue Maria Helena Vieira Da Silva
    CS61431, 75993 Paris cedex 14
    156 rue du Vaugirard,
    75015 Paris
    Tél. : 01 72 60 63 31 Tél. : 01 44 49 47 81


    Expertise and service provided:

    • 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 approaches)
    • Protein absolute quantification (using MRM and PRM approaches)
    • Statistical and bioinformatics data analysis (using mainly Mascot, Skyline, MaxQuant, Perseus software)
    • System biology analysis through proteins network graph (using mainly 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
    1. Nevo N, Thomas L, Chhoun C, Andrzejewska Z, Lipecka J, Guillonneau F, Bailleux A, Edelman A, Antignac, Guerrera IC. Impact of cystinosin mutations on protein stability by differential dynamic SILAC.  Molecular and Cellular Proteomics, 2017 In press
    2. Chhuon C, Pranke, Borot F, Tondelier D, Lipecka J, Fritsch J, Chanson M, Edelman A, Ollero* M, Guerrera* IC.  Changes in lipid raft proteome upon TNF-α stimulation of cystic fibrosis cells. J. Proteomics. 2016 Aug 11;145:246-53.
    3. Chhuon C, Pranke, Borot F, Tondelier D, Lipecka J, Fritsch J, Chanson M, Edelman A, Ollero* M, Guerrera* IC. Dataset of differential lipid raft and global proteomes of SILAC-labeled cystic fibrosis cells upon TNF -α stimulation.  Data Brief. 2016 Aug 20;9:51-6
    4. Lipecka J, Chhuon C, Bourderioux M, Bessard MA, van Endert P, Edelman A, Guerrera IC. Sensitivity of mass spectrometry analysis depends on the shape of the filtration unit used for filter aided sample preparation (FASP). Proteomics. 2016 Jul;16(13):1852-7
    5. Andrzejewska Z, Nevo N, Thomas L, Chhuon C, Bailleux A, Chauvet V, Courtoy PJ, Chol M, Guerrera IC, Antignac C. Cystinosin is a Component of the Vacuolar H+-ATPase-Ragulator-Rag Complex Controlling Mammalian Target of Rapamycin Complex 1 Signaling. J Am Soc Nephrol. 2016 Jun;27(6):1678-88
    6. Aoufouchi S, De Smet A, Delbos F, Gelot C, Guerrera IC, Weill JC, Reynaud CA. 129-Derived Mouse Strains Express an Unstable but Catalytically Active DNA Polymerase Iota Variant. Mol Cell Biol. 2015 Sep 1;35(17):3059-70.
    7. Ramond E, Gesbert G, Guerrera IC, Chhuon C, Dupuis M, Rigard M, Henry T, Barel M, Charbit A. Importance of host cell arginine uptake in Francisella phagosomal escape and ribosomal protein amounts. Mol Cell Proteomics. 2015 Jan 23
    8. Bourderioux M, Nguyen-Khoa T, Chhuon C, Jeanson L, Tondelier D, Walczak M, Ollero M, Bekri S, Knebelmann B, Escudier E, Escudier B, Edelman A, Guerrera IC.  A New Workflow for Proteomic Analysis of Urinary Exosomes and Assessment in Cystinuria Patients. J Proteome Res. 2014 Nov 12
    9. Guerrera IC, Jeanson L, Papon JF, Chhuon C, Zadigue P, Prulière-Escabasse V,Amselem S, Escudier E, Coste A, Edelman A. Proteomic analysis of nasal epithelial cells from cystic fibrosis patients. PLoS One. 2014 Sep 30;9(9):e108671.
    10. Guerrera IC, Quetier I, Fetouchi R, Moreau F, Vauloup-Fellous C, Lekbaby B, Rousselot C, Chhuon C, Edelman A, Lefevre M, Nicolas JC, Kremsdorf D, Lacau Saint Guily J, Soussan P. (2014) Regulation of interleukin-6 in head and neck squamous cell carcinoma is related to papillomavirus infection. J Proteome Res. Feb 7;13(2):1002-11.
    11. Nikolov IGJoki N, Galmiche A, Nguyen-Khoa T, Guerrera IC, Guillonneau F, Ivanovski O, Phan O, Maizel J, Marçon F, Benchitrit J, Lucas A, Edelman A, Lacour B, Drüeke TB, Massy ZA.(2013) Farnesyltransferase inhibitor R115777 protects against vascular disease in uremic mice. Atherosclerosis. 2013 Jul;229(1):42-51
    12. Dieppedale J, Gesbert GRamond EChhuon CDubail IGuerrera IC,  Charbit A. (2012) A link between oxidative stress defense and tricarboxylic acid cycle in Francisella tularensis pathogenesis. Mol Cell Proteomics. 2013 Aug;12(8):2278-92
    13. Jeanson, L., Kelly, M., Coste, A., Guerrera, I.C., Fritsch, J., Nguyen-Khoa, T., Baudouin-Legros, M., Papon, J.-F., Zadigue, P., Prulière-Escabasse, V., et al. (2012). Oxidative stress induces unfolding protein response and inflammation in nasal polyposis. Allergy 67, 403–412.
    14. Colas, J., Faure, G., Saussereau, E., Trudel, S., Rabeh, W.M., Bitam, S., Guerrera, I.C., Fritsch, J., Sermet-Gaudelus, I., Davezac, N., et al. (2012). Disruption of cytokeratin-8 interaction with F508del-CFTR corrects its functional defect. Hum. Mol. Genet. 21, 623–634.
    15. Nikolov, I.G., Joki, N., Nguyen-Khoa, T., Guerrera, I.C., Maizel, J., Benchitrit, J., Machado dos Reis, L., Edelman, A., Lacour, B., Jorgetti, V., et al. (2012). Lanthanum carbonate, like sevelamer-HCl, retards the progression of vascular calcification and atherosclerosis in uremic apolipoprotein E-deficient mice. Nephrol. Dial. Transplant. 27, 505–513.
    16. Guerrera, I.C., Ollero, M., Vieu, D.-L., and Edelman, A. (2011). Quantitative differential proteomics of cystic fibrosis cell models by SILAC (stable isotope labelling in cell culture). Methods Mol. Biol. 742, 213–225.
    17. Bouchoux, J., Beilstein, F., Pauquai, T., Guerrera, I.C., Chateau, D., Ly, N., Alqub, M., Klein, C., Chambaz, J., Rousset, M., et al. (2011). The proteome of cytosolic lipid droplets isolated from differentiated Caco-2/TC7 enterocytes reveals cell-specific characteristics. Biol. Cell 103, 499–517.
    18. Ollero, M., Astarita, G., Guerrera, I.C., Sermet-Gaudelus, I., Trudel, S., Piomelli, D., and Edelman, A. (2011a). Plasma lipidomics reveals potential prognostic signatures within a cohort of cystic fibrosis patients. J. Lipid Res. 52, 1011–1022.
    19. Ollero, M., Guerrera, I.C., Astarita, G., Piomelli, D., and Edelman, A. (2011b). New lipidomic approaches in cystic fibrosis. Methods Mol. Biol. 742, 265–278.
    20. Blouin, C.M., Le Lay, S., Eberl, A., Köfeler, H.C., Guerrera, I.C., Klein, C., Le Liepvre, X., Lasnier, F., Bourron, O., Gautier, J.-F., et al. (2010). Lipid droplet analysis in caveolin-deficient adipocytes: alterations in surface phospholipid composition and maturation defects. J. Lipid Res. 51, 945–956.
    21. Moriceau, S., Kantari, C., Mocek, J., Davezac, N., Gabillet, J., Guerrera, I.C., Brouillard, F., Tondelier, D., Sermet-Gaudelus, I., Danel, C., et al. (2009). Coronin-1 is associated with neutrophil survival and is cleaved during apoptosis: potential implication in neutrophils from cystic fibrosis patients. J. Immunol. 182, 7254–7263.
    22. Guerrera, I.C., Astarita, G., Jais, J.-P., Sands, D., Nowakowska, A., Colas, J., Sermet-Gaudelus, I., Schuerenberg, M., Piomelli, D., Edelman, A., et al. (2009). A novel lipidomic strategy reveals plasma phospholipid signatures associated with respiratory disease severity in cystic fibrosis patients. PLoS ONE 4, e7735.
    23. Guerrera, I.C., Keep, N.H., and Godovac-Zimmermann, J. (2007). Proteomics study reveals cross-talk between Rho guanidine nucleotide dissociation inhibitor 1 post-translational modifications in epidermal growth factor stimulated fibroblasts. J. Proteome Res. 6, 2623–2630.
    24. Bensalem, N., Masscheleyn, S., Mozo, J., Vallée, B., Brouillard, F., Trudel, S., Ricquier, D., Edelman, A., Guerrera, I.C., Miroux, B. (2007). High sensitivity identification of membrane proteins by MALDI TOF-MASS spectrometry using polystyrene beads. J. Proteome Res. 6, 1595–1602.
    25. Guerrera, I.C., Predic-Atkinson, J., Kleiner, O., Soskic, V., and Godovac-Zimmermann, J. (2005). Enrichment of phosphoproteins for proteomic analysis using immobilized Fe(III)-affinity adsorption chromatography. J. Proteome Res. 4, 1545–1553.
    26. Guerrera, I.C., and Kleiner, O. (2005). Application of mass spectrometry in proteomics. Biosci. Rep. 25, 71–93.