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 2006, PPN mission is to enable academic teams to succeed in their proteomics projects. The platform is open to all research institutes (in France as abroad), clinical departments and the private sector.

PPN is part of SFR Necker, and it is also one of two constitutive laboratories of Paris Descartes University proteomics platform (3P5), now University of Paris.

The main focus of the platform is the development of innovative translational proteomics approaches to study human disease. The instrumental park of PPN includes one mass spectrometer dedicated to high throughput analysis and quantification of proteins and a Biolayer interferometry instrument.

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 search for diagnostic/prognostic biomarkers in body fluids by MS (translational and targeted proteomics).

 

Alain CHARBIT  01 40 61 54 06 
Référent scientifique  
Cerina CHHUON  01 40 61 54 68 
-  
Chiara GUERRERA  01 40 61 54 67 
Responsable de plateforme  
Vincent JUNG  01 40 61 54 69 
-  
Joanna LIPECKA  01 40 61 54 68 
-  

 

 
   

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)
  • 1D and 2D PAGE equipment (Biorad)
  • OFFgel Fractionator (Agilent)
  • Janus automate (PerkinElmer)
  • ImagePREP (Bruker)

                         

 

 

 

Necker
Faculté de Médecine Paris Descartes, 1st floor
160 rue du Vaugirard,
75015 Paris

Tél. : 01 40 61 54 67

proteomique.sfrnecker@inserm.fr

 

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)
  • Proteomic analysis of body fluids and extracellular vesicles (urine, BAL, sweat, plasma, amniotic fluid, CSF)
  • Statistical and bioinformatics data analysis (using mainly Mascot, Skyline, MaxQuant, Perseus software)
  • System biology analysis through proteins network graph (using mainly Ingenuity, AmiGO software, GOrilla)

  Proposed applications:

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

Publications 2015-2019

(full list : https://www.ncbi.nlm.nih.gov/pubmed?term=(guerrera%20ic)%20OR%20guerrera%20ci )

*** publication 1er ou dernier auteur par les ingenieurs de la plateforme

  1. ***Critical role of a sheath phosphorylation site on the assembly and function of an atypical type VI secretion system. Ziveri J, Chhuon C, Jamet A, Rytter H, Prigent G, Tros F, Barel M, Coureuil M, Lays C, Henry T, Keep NH, *Guerrera IC, *Charbit A. Mol Cell Proteomics. 2019 Oct 2.
  2. STK38 kinase acts as XPO1 gatekeeper regulating the nuclear export of autophagy proteins and other cargoes.  Martin AP, Jacquemyn M, Lipecka J, Chhuon C, Aushev VN, Meunier B, Singh MK, Carpi N, Piel M, Codogno P, Hergovich A, Parrini MC, Zalcman G, Guerrera IC, Daelemans D, Camonis JH. EMBO Rep. 2019 Nov 5;20(11):e48150. doi: 10.15252/embr.201948150.
  3. Defects in t6A tRNA modification due to GON7 and YRDC mutations lead to Galloway-Mowat syndrome.  Arrondel, Missoury, Snoek, Patat, Menara, Collinet, Liger, Durand, Gribouval, Boyer, Buscara, Martin, Machuca, Nevo, Lescop, Braun, Boschat, Sanquer, Guerrera IC, Revy, Parisot, Masson, BODDAERT, Charbit, Decramer, Novo, Macher, Ranchin, Bacchetta, Laurent, Collardeau-Frachon, Albertien van Eerde, Hildebrandt, Magen, Antignac, van Tilbeurgh, and Mollet.  Nature communications (Accepted).
  4. Intracellular offsprings released from SFB filaments are flagellated. Nkamba I, Mulet C, Dubey GP, Gorgette O, Couesnon A, Salles A, Moya-Nilges M, Jung V, Gaboriau-Routhiau V, Guerrera IC, Shima T, Umesaki Y, Nigro G, Krijnse-Locker J, Berard M, Cerf-Bensussan1 N, Sansonetti PJ, Schnupf P., Nature Microbiology 2019 (accepted).
  5. CMIP is a negative regulator of T cell signaling. Oniszczuk J, Sendeyo K, Chhuon C, Savas B, Cogné E, Vachin P, Henique C, Guerrera IC, Astarita G, Frontera V, Pawlak A, Audard V, Sahali D, Ollero M. Cell Mol Immunol. 2019 Aug 8. doi: 10.1038/s41423-019-0266-5. [Epub ahead of print] PubMed PMID: 31395948.
  6. Essential role of GEXP15, a specific Protein Phosphatase type 1 partner, in Plasmodium berghei in asexual erythrocytic proliferation and transmission. Hollin T, De Witte C, Fréville A, Guerrera IC, Chhuon C, Saliou JM, Herbert F, Pierrot C, Khalife J. PLoS Pathogens 2019 Jul 26;15(7):e1007973. doi:10.1371/journal.ppat.1007973. PMID: 31348803
  7. Plasmodium pseudo-Tyrosine Kinase-like binds PP1 and SERA5 and is exported to host erythrocytes Gnangnon B, Fréville A, Cailliau K, Leroy C, De Witte C, Tulasne D, Martoriarti A, Jung V, Guerrera IC, Marion S, Khalife J, Pierrot C. Sci Rep. 2019 May 31;9(1):8120. doi: 10.1038/s41598-019-44542-3. PubMed PMID: 31148576;
  8. Human IFT52 mutations uncover a novel role for the protein in microtubule dynamics and centrosome cohesion. Dupont MA, Humbert C, Huber C, Siour Q, Guerrera IC, Jung V, Christensen A, Pouliet A, Garfa-Traore M, Nitschké P, Injeyan M, Millar K, Chitayat D, Shannon P, Girisha KM, Shukla A, Mechler C, Lorentzen E, Benmerah A, Cormier-Daire V, Jeanpierre C, Saunier S, Delous M. Hum Mol Genet. 2019 May 1. pii: ddz091. doi: 10.1093/hmg/ddz091.
  9. Interaction between galectin-3 and cystinosin uncovers a pathogenic role of inflammation in kidney involvement of cystinosis. Lobry T, Miller R, Nevo N, Rocca CJ, Zhang J, Catz SD, Moore F, Thomas L, Pouly D, Bailleux A, Guerrera IC, Gubler MC, Cheung WW, Mak RH, Montier T, Antignac C, Cherqui S. Kidney Int. 2019 Mar 6. pii: S0085-2538(19)30172-3. doi: 10.1016/j.kint.2019.01.029.
  10. Chronic Staphylococcus aureus lung infection correlates with proteogenomic and metabolic adaptations leading to an increased intracellular persistence. Tan X, Coureuil M, Ramond E, Euphrasie D, Dupuis M, Tros F, Meyer J, Nemazanyy I, Chhuon C, Guerrera IC, Ferroni A, Sermet-Gaudelus I, Nassif X, Charbit A, Jamet A. Clin Infect Dis. 2019 Feb 7. doi: 10.1093/cid/ciz106.
  11. LC-MS/MS-based quantification of efflux transporter proteins at the BBB. Gomez-Zepeda D, Taghi M, Smirnova M, Sergent P, Liu WQ, Chhuon C, Vidal M, Picard M, Thioulouse E, Broutin I, Guerrera IC, Scherrmann JM, Parmentier Y, Decleves X, Menet MC. J Pharm Biomed Anal. 2019 Feb 5;164:496-508. doi: 10.1016/j.jpba.2018.11.013. Epub 2018 Nov 8.
  12. ***High N-glycan multiplicity is critical for neuronal adhesion and sensitizes the developing cerebellum to N-glycosylation defect. Medina-Cano D, Ucuncu E, Nguyen LS, Nicouleau M, Lipecka J, Bizot JC, Thiel C, Foulquier F, Lefort N, Faivre-Sarrailh C, Colleaux L, Guerrera IC, Cantagrel V. Elife. 2018 Oct 12;7. pii: e38309. doi: 10.7554/eLife.38309.
  13. ***Comparative proteomics of respiratory exosomes in cystic fibrosis, primary ciliary dyskinesia and asthma. Rollet-Cohen V, Bourderioux M, Lipecka J, Chhuon C, Jung V, Mesbahi M, Nguyen-Khoa T, Guérin-Pfyffer S, Schmitt A, Edelman A, Sermet-Gaudelus I, Guerrera IC. J Proteomics. 2018 Aug 15;185:1-7. doi: 10.1016/j.jprot.2018.07.001. Epub 2018 Jul 3.PMID: 30032860
  14. M’baya-Moutoulaa, E, Louveta, L, Moliniéb R, Guerrera IC, Cerutti C, Fourdinier O, Nourrye V, Gutierrez L, Morlière P, Mesnard F, Ziad A.M., Metzinger-le Meutha V. , and Metzinger L (2018). A multi-omics analysis of the regulatory changes induced by miR-223 in a monocyte/macrophage cell line. BBA Molecular Basis of Disease, in press
  15. ***Rollet-Cohen, V., Bourderioux, M., Lipecka, J; Chhuon, C., Mesbahi M, Nguyen-Khoa, T; Guérin-Pfyffer, S.; Schmitt, A; Edelman, A; Sermet-Gaudelus, I, Guerrera, IC. (2018) Comparative proteomics of respiratory exosomes in Cystic Fibrosis, Primary Ciliary Dyskinesia and Asthma. Journal of Proteomics, in press
  16. Braun, D. A., Rao, J., Mollet, G., Schapiro, D., Daugeron, M.-C., Tan, W., Gribouval, O., Boyer, O., Revy, P., Jobst-Schwan, T., Schmidt, J. M., Lawson, J. A., Schanze, D., Ashraf, S., Ullmann, J. F. P., Hoogstraten, C. A., Boddaert, N., Collinet, B., Martin, G., Liger, D., Lovric, S., Furlano, M., Guerrera, I. C., Sanchez-Ferras, O., Hu, J. F., Boschat, A.-C., Sanquer, S., Menten, B., Vergult, S., De Rocker, N., Airik, M., Hermle, T., Shril, S., Widmeier, E., Gee, H. Y., Choi, W.-I., Sadowski, C. E., Pabst, W. L., Warejko, J. K., Daga, A., Basta, T., Matejas, V., Scharmann, K., Kienast, S. D., Behnam, B., Beeson, B., Begtrup, A., Bruce, M., Ch’ng, G.-S., Lin, S.-P., Chang, J.-H., Chen, C.-H., Cho, M. T., Gaffney, P. M., Gipson, P. E., Hsu, C.-H., Kari, J. A., Ke, Y.-Y., Kiraly-Borri, C., Lai, W.-M., Lemyre, E., Littlejohn, R. O., Masri, A., Moghtaderi, M., Nakamura, K., Ozaltin, F., Praet, M., Prasad, C., Prytula, A., Roeder, E. R., Rump, P., Schnur, R. E., Shiihara, T., Sinha, M. D., Soliman, N. A., Soulami, K., Sweetser, D. A., Tsai, W.-H., Tsai, J.-D., Topaloglu, R., Vester, U., Viskochil, D. H., Vatanavicharn, N., Waxler, J. L., Wierenga, K. J., Wolf, M. T. F., Wong, S.-N., Leidel, S. A., Truglio, G., Dedon, P. C., Poduri, A., Mane, S., Lifton, R. P., Bouchard, M., Kannu, P., Chitayat, D., Magen, D., Callewaert, B., van Tilbeurgh, H., Zenker, M., Antignac, C., and Hildebrandt, F. (2017) Mutations in KEOPS-complex genes cause nephrotic syndrome with primary microcephaly. Nat. Genet. 49, 1529–1538
  17. Duriez, M., Mandouri, Y., Lekbaby, B., Wang, H., Schnuriger, A., Redelsperger, F., Guerrera, C. I., Lefevre, M., Fauveau, V., Ahodantin, J., Quetier, I., Chhuon, C., Gourari, S., Boissonnas, A., Gill, U., Kennedy, P., Debzi, N., Sitterlin, D., Maini, M. K., Kremsdorf, D., and Soussan, P. (2017) Alternative splicing of hepatitis B virus: A novel virus/host interaction altering liver immunity. J. Hepatol. 67, 687–699
  18. Gomez-Zepeda, D., Chaves, C., Taghi, M., Sergent, P., Liu, W.-Q., Chhuon, C., Vidal, M., Picard, M., Thioulouse, E., Broutin, I., Guerrera, I.C., Scherrmann, J.-M., Parmentier, Y., Decleves, X., and Menet, M.-C. (2017) Targeted unlabeled multiple reaction monitoring analysis of cell markers for the study of sample heterogeneity in isolated rat brain cortical microvessels. J. Neurochem. 142, 597–609
  19. Sicot, G., Servais, L., Dinca, D. M., Leroy, A., Prigogine, C., Medja, F., Braz, S. O., Huguet-Lachon, A., Chhuon, C., Nicole, A., Gueriba, N., Oliveira, R., Dan, B., Furling, D., Swanson, M. S., Guerrera, I. C., Cheron, G., Gourdon, G., and Gomes-Pereira, M. (2017) Downregulation of the Glial GLT1 Glutamate Transporter and Purkinje Cell Dysfunction in a Mouse Model of Myotonic Dystrophy. Cell Rep 19, 2718–2729
  20. ***Nevo, N., Thomas, L., Chhuon, C., Andrzejewska, Z., Lipecka, J., Guillonneau, F., Bailleux, A., Edelman, A., Antignac, C., and Guerrera, I. C. (2017) Impact of Cystinosin Glycosylation on Protein Stability by Differential Dynamic Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC). Mol. Cell Proteomics 16, 457–468
  21. Ziveri, J., Tros, F., Guerrera, I. C., Chhuon, C., Audry, M., Dupuis, M., Barel, M., Korniotis, S., Fillatreau, S., Gales, L., Cahoreau, E., and Charbit, A. (2017) The metabolic enzyme fructose-1,6-bisphosphate aldolase acts as a transcriptional regulator in pathogenic Francisella. Nat Commun 8, 85
  22. Meijer, B. M., Jang, S. M., Guerrera, I. C., Chhuon, C., Lipecka, J., Reisacher, C., Baleux, F., Sansonetti, P. J., Muchardt, C., and Arbibe, L. (2017) Threonine eliminylation by bacterial phosphothreonine lyases rapidly causes cross-linking of mitogen-activated protein kinase (MAPK) in live cells. J. Biol. Chem. 292, 7784–7794
  23. ***Chhuon, C., Pranke, I., Borot, F., Tondelier, D., Lipecka, J., Fritsch, J., Chanson, M., Edelman, A., Ollero, M., and Guerrera, I. C. (2016) Dataset of differential lipid raft and global proteomes of SILAC-labeled cystic fibrosis cells upon TNF -α stimulation. Data Brief 9, 51–56
  24. ***Chhuon, C., Pranke, I., Borot, F., Tondelier, D., Lipecka, J., Fritsch, J., Chanson, M., Edelman, A., Ollero, M., and Guerrera, I. C. (2016) Changes in lipid raft proteome upon TNF-α stimulation of cystic fibrosis cells. J Proteomics 145, 246–253
  25. ***Lipecka, J., Chhuon, C., Bourderioux, M., Bessard, M.-A., van Endert, P., Edelman, A., and Guerrera, I. C. (2016) Sensitivity of mass spectrometry analysis depends on the shape of the filtration unit used for filter aided sample preparation (FASP). Proteomics 16, 1852–1857
  26. ***Andrzejewska, Z., Nevo, N., Thomas, L., Chhuon, C., Bailleux, A., Chauvet, V., Courtoy, P. J., Chol, M., Guerrera, I. C., and Antignac, C. (2015) Cystinosin is a Component of the Vacuolar H+-ATPase-Ragulator-Rag Complex Controlling Mammalian Target of Rapamycin Complex 1 Signaling. J. Am. Soc. Nephrol.,
  27. Aoufouchi, S., De Smet, A., Delbos, F., Gelot, C., Guerrera, I. C., Weill, J.-C., and Reynaud, C.-A. (2015) 129-Derived Mouse Strains Express an Unstable but Catalytically Active DNA Polymerase Iota Variant. Mol. Cell. Biol. 35, 3059–3070
  28. Ramond, E., Gesbert, G., Guerrera, I. C., Chhuon, C., Dupuis, M., Rigard, M., Henry, T., Barel, M., and Charbit, A. (2015) Importance of host cell arginine uptake in Francisella phagosomal escape and ribosomal protein amounts. Mol. Cell Proteomics 14, 870–881