logo umr
Génétique Quantitative et Évolution - Le Moulon

PAPPSO - Proteomics analysis facility in the south-west of Paris

The PAPPSO facility carries out proteomics analyses within the framework of services and collaborations.

Proteomics

PAPPSO is composed of two sites:

  • at Gif-sur-Yvette in the UMR Génétique Quantitative et Évolution – Le Moulon, the team is specialized in plant biologyy ;
  • at Jouy-en-Josas in the UMR Micalis the team is specialized in prokariotes.

PAPPSO performs identification and quantification of protein amounts and of post-translational modifications. PAPPSO has developed an expertise in the performance of large experiments (several hundred samples) as well as in peptidomics and metaproteomics. For example, at present, a GWAS experiment on maize proteome involves more than a thousand samples, and a metaproteomics analysis of the intestinal microbiota involves several hundred samples.

Bioinformatics

In parallel with developments in mass spectrometry, PAPPSO is developing proteomic analysis tools adapted to large numbers and highly complex samples. These tools enable control of the entire processing chain from peptide identification to protein quantification and statistical analysis of their variation. The platform is equipped with an IT infrastructure that allows it to manage this very large amount of data. PAPPSO disseminates the tools it develops in open source, organizes training and supports users in the exploitation of their results, in particular up to their bioinformatics and statistical analysis.

Main bioinformatics tools developed by PAPPSO PAPPSO :

Equipment

PAPPSO is equipped with different mass spectrometers adapted to different levels of complexity of the protein mixture: an LTQ, an LTQ-Orbitrap, a Q-Exactive plus, an Orbitrap Fusion Lumos and a timsTOF.

Labels and certification

PAPPSO has been labelled by IBiSA since 2009. It has been regularly labelled by INRA’s CNOC as INRA Strategic Platform (2009-2013), National Strategic Platform (2013-2018) and finally ISC (2018). PAPPSO has been ISO9001 certified since 2017.


PAPPSO is attached to the LabEx SPS, Sciences des Plantes de Saclay.

Members

Former members

Thomas Renne Bioinformatics trainee (2019-2021), Benoît Valot Engineer (2006-2014)

Publications

  • Balliau T. , Duruflé H., Blanchet N., Blein-Nicolas M. , Langlade NB., Zivy M. . (2021) Proteomic data from leaves of twenty-four sunflower genotypes under water deficit. OCL, (28) 12
  • Bassignani A., Plancade S., Berland M., Blein-Nicolas M. , Guillot A., Chevret D., Moritz C., Huet S., Rizkalla S., Clément K., Doré J., Langella O. , Juste C.. (2021) Benefits of Iterative Searches of Large Databases to Interpret Large Human Gut Metaproteomic Data Sets. J. Proteome Res.,
  • Bossche TVD., Kunath BJ., Schallert K., Schäpe SS., Abraham PE., Armengaud J., Arntzen M., Bassignani A., Benndorf D., Fuchs S., Giannone RJ., Griffin TJ., Hagen LH., Halder R., Henry C., Hettich RL., Heyer R., Jagtap P., Jehmlich N., Jensen M., Juste C., Kleiner M., Langella O. , Lehmann T., Leith E., May P., Mesuere B., Miotello G., Peters SL., Pible O., Reichl U., Renard BY., Schiebenhoefer H., Scryba A., Tanca A., Trappe K., Trezzi JP., Uzzau S., Verschaffelt P., Bergen M., Wilmes P., Wolf M., Martens L., Muth T.. (2021) Critical Assessment of Metaproteome Investigation (CAMPI): A Multi-Lab Comparison of Established Workflows. bioRxiv, 2021.03.05.433915
  • Cui J., Davanture M. , Lamade E., Zivy M. , Tcherkez G.. (2021) Plant low-K responses are partly due to Ca prevalence and the low-K biomarker putrescine does not protect from Ca side effects but acts as a metabolic regulator. Plant Cell Environ, 5 (44) 1565-1579
  • Douché T., Valot B., Balliau T. , San Clemente H., Zivy M. , Jamet E.. (2021) Cell wall proteomic datasets of stems and leaves of Brachypodium distachyon. Data in Brief, (35) 106818
  • Henriet C., Balliau T. , Aimé D., Le Signor C., Kreplak J., Zivy M. , Gallardo K., Vernoud V.. (2021) Proteomics of developing pea seeds reveals a complex antioxidant network underlying the response to sulfur deficiency and water stress. Journal of Experimental Botany, eraa571
  • Langella O. , Rusconi F. . (2021) mineXpert2: Full-Depth Visualization and Exploration of MS n Mass Spectrometry Data. J Am Soc Mass Spectrom,
  • Plancade S., Berland M., Blein-Nicolas M. , Langella O. , Bassignani A., Juste C.. (2021) A combined test for feature selection on sparse metaproteomics data - alternative to missing value imputation. bioRxiv, 2021.06.22.449387
  • Recorbet G., Calabrese S., Balliau T. , Zivy M. , Wipf D., Boller T., Courty PE.. (2021) Proteome adaptations under contrasting soil phosphate regimes of Rhizophagus irregularis engaged in a common mycorrhizal network. Fungal Genetics and Biology, (147) 103517
  • Rusconi F. . (2021) Free Open Source Software for Protein and Peptide Mass Spectrometry-based Science. Curr Protein Pept Sci,
  • Urrutia M., Blein-Nicolas M. , Prigent S., Bernillon S., Deborde C., Balliau T. , Maucourt M., Jacob D., Ballias P., Bénard C., Sellier H., Gibon Y., Giauffret C., Zivy M. , Moing A.. (2021) Maize metabolome and proteome responses to controlled cold stress partly mimic early-sowing effects in the field and differ from those of Arabidopsis. Plant Cell Environ,
  • Blein-Nicolas M. , Negro SS., Balliau T. , Welcker C., Cabrera-Bosquet L., Nicolas SD., Charcosset A., Zivy M. . (2020) A systems genetics approach reveals environment-dependent associations between SNPs, protein coexpression, and drought-related traits in maize. Genome Res., 11 (30) 1593-1604
  • Kilani J., Davanture M. , Simon A., Zivy M. , Fillinger S.. (2020) Comparative quantitative proteomics of osmotic signal transduction mutants in Botrytis cinerea explain mutant phenotypes and highlight interaction with cAMP and Ca2+ signalling pathways. Journal of Proteomics, (212) 103580
  • Luo J., Havé M., Clément G., Tellier F., Balliau T. , Launay-Avon A., Guérard F., Zivy M. , Masclaux-Daubresse C.. (2020) Integrating multiple omics to dissect the common and specific molecular changes occurring in Arabidopsis thaliana (L.) under nitrate and sulfate chronic limitations. Journal of Experimental Botany, eraa337
  • Tcherkez G., Carroll A., Abadie C., Mainguet S., Davanture M. , Zivy M. . (2020) Protein synthesis increases with photosynthesis via the stimulation of translation initiation. Plant Science, (291) 110352
  • Bancel E., Bonnot T., Davanture M. , Alvarez D., Zivy M. , Martre P., Déjean S., Ravel C.. (2019) Proteomic Data Integration Highlights Central Actors Involved in Einkorn (Triticum monococcum ssp. monococcum) Grain Filling in Relation to Grain Storage Protein Composition. Front. Plant Sci., (10) 832
  • Belouah I., Nazaret C., Pétriacq P., Prigent S., Bénard C., Mengin V., Blein-Nicolas M. , Denton AK., Balliau T. , Augé S., Bouchez O., Mazat JP., Stitt M., Usadel B., Zivy M. , Beauvoit B., Gibon Y., Colombié S.. (2019) Modeling Protein Destiny in Developing Fruit. Plant Physiology, 3 (180) 1709-1724
  • Belouah I., Blein-Nicolas M. , Balliau T. , Gibon Y., Zivy M. , Colombié S.. (2019) Peptide filtering differently affects the performances of XIC-based quantification methods. J Proteomics, (193) 131-141
  • Bienvenut W. V. , 2 décembre 2019, Des débuts de la protéomique à l'acétylation N-terminale des protéines chez les plantes
  • Chauffour F., Bailly M., Perreau F., Cueff G., Suzuki H., Collet B., Frey A., Clément G., Soubigou-Taconnat L., Balliau T. , Krieger-Liszkay A., Rajjou L., Marion-Poll A.. (2019) Multi-omics Analysis Reveals Sequential Roles for ABA during Seed Maturation. Plant Physiol., 2 (180) 1198-1218
  • Cui J., Davanture M. , Zivy M. , Lamade E., Tcherkez G.. (2019) Metabolic responses to potassium availability and waterlogging reshape respiration and carbon use efficiency in oil palm. New Phytologist, 1 (223) 310-322
  • Duruflé H., Ranocha P., Balliau T. , Dunand C., Jamet E.. (2019) Transcriptomic and cell wall proteomic datasets of rosettes and floral stems from five Arabidopsis thaliana ecotypes grown at optimal or sub-optimal temperature. Data in Brief, (27) 104581
  • Havé M., Luo J., Tellier F., Balliau T. , Cueff G., Chardon F., Zivy M. , Rajjou L., Cacas JL., Masclaux‐Daubresse C.. (2019) Proteomic and lipidomic analyses of the Arabidopsis atg5 autophagy mutant reveal major changes in ER and peroxisome metabolisms and in lipid composition. New Phytol, 3 (223) 1461-1477
  • Henry C., Haller L., Blein-Nicolas M. , Zivy M. , Canette A., Verbrugghe M., Mézange C., Boulay M., Gardan R., Samson S., Martin V., André-Leroux G., Monnet V.. (2019) Identification of Hanks-Type Kinase PknB-Specific Targets in the Streptococcus thermophilus Phosphoproteome. Front. Microbiol., (10) 1329
  • Rusconi F. . (2019) mineXpert: Biological Mass Spectrometry Data Visualization and Mining with Full JavaScript Ability. J. Proteome Res., 5 (18) 2254-2259
  • Aloui A., Recorbet G., Lemaître-Guillier C., Mounier A., Balliau T. , Zivy M. , Wipf D., Dumas-Gaudot E.. (2018) The plasma membrane proteome of Medicago truncatula roots as modified by arbuscular mycorrhizal symbiosis. Mycorrhiza, 1 (28) 1-16
  • Balliau T. , Blein-Nicolas M. , Zivy M. . (2018) Evaluation of Optimized Tube-Gel Methods of Sample Preparation for Large-Scale Plant Proteomics. Proteomes, 1 (6) 6
  • Berrabah F., Balliau T. , Ait-Salem EH., George J., Zivy M. , Ratet P., Gourion B.. (2018) Control of the ethylene signaling pathway prevents plant defenses during intracellular accommodation of the rhizobia. The New phytologist, 1 (219) 310-323
  • Bichang'a G., Da Lage JL., Capdevielle-Dulac C., Zivy M. , Balliau T. , Sambai K., Le Ru B., Kaiser L., Juma G., Maina ENM., Calatayud PA.. (2018) alpha-Amylase Mediates Host Acceptance in the Braconid Parasitoid Cotesia flavipes. J Chem Ecol, 11 (44) 1030-1039
  • Havé M., Balliau T. , Cottyn-Boitte B., Dérond E., Cueff G., Soulay F., Lornac A., Reichman P., Dissmeyer N., Avice JC., Gallois P., Rajjou L., Zivy M. , Masclaux-Daubresse C.. (2018) Increases in activity of proteasome and papain-like cysteine protease in Arabidopsis autophagy mutants: back-up compensatory effect or cell-death promoting effect?. J Exp Bot, 6 (69) 1369-1385
  • Bonnot T., Bancel E., Alvarez D., Davanture M. , Boudet J., Pailloux M., Zivy M. , Ravel C., Martre P.. (2017) Grain subproteome responses to nitrogen and sulfur supply in diploid wheat Triticum monococcum ssp. monococcum. The Plant Journal, 5 (91) 894-910
  • Duruflé H., Hervé V., Ranocha P., Balliau T. , Zivy M. , Chourré J., San Clemente H., Burlat V., Albenne C., Déjean S., Jamet E., Dunand C.. (2017) Cell wall modifications of two Arabidopsis thaliana ecotypes, Col and Sha, in response to sub-optimal growth conditions: An integrative study. Plant Science, (263) 183-193
  • Duruflé H., Clemente HS., Balliau T. , Zivy M. , Dunand C., Jamet E.. (2017) Cell wall proteome analysis of Arabidopsis thaliana mature stems. PROTEOMICS, 8 (17) 1600449
  • Duruflé H., Hervé V., Balliau T. , Zivy M. , Dunand C., Jamet E.. (2017) Proline Hydroxylation in Cell Wall Proteins: Is It Yet Possible to Define Rules?. Front. Plant Sci., (8)
  • Galland M., He D., Lounifi I., Arc E., Clément G., Balzergue S., Huguet S., Cueff G., Godin B., Collet B., Granier F., Morin H., Tran J., Valot B., Rajjou L.. (2017) An Integrated “Multi-Omics” Comparison of Embryo and Endosperm Tissue-Specific Features and Their Impact on Rice Seed Quality. Front Plant Sci, (8)
  • Jean N., Dumont E., Herzi F., Balliau T. , Laabir M., Masseret E., Mounier S.. (2017) Modifications of the soluble proteome of a mediterranean strain of the invasive neurotoxic dinoflagellate Alexandrium catenella under metal stress conditions. Aquatic Toxicology, (188) 80-91
  • Langella O. , Valot B., Balliau T. , Blein-Nicolas M. , Bonhomme L., Zivy M. . (2017) X!TandemPipeline: A Tool to Manage Sequence Redundancy for Protein Inference and Phosphosite Identification. J. Proteome Res., 2 (16) 494-503
  • Millan-Oropeza A., Henry C., Blein-Nicolas M. , Aubert-Frambourg A., Moussa F., Bleton J., Virolle MJ.. (2017) Quantitative Proteomics Analysis Confirmed Oxidative Metabolism Predominates in Streptomyces coelicolor versus Glycolytic Metabolism in Streptomyces lividans. J. Proteome Res., 7 (16) 2597-2613
  • Negroni L., Zivy M. , Lemaire C., Lacapere JJ.. (2017) Mass Spectrometry of Mitochondrial Membrane Protein Complexes. , 233-246
  • Regente M., Pinedo M., San Clemente H., Balliau T. , Jamet E., de la Canal L.. (2017) Plant extracellular vesicles are incorporated by a fungal pathogen and inhibit its growth. J Exp Bot, 20 (68) 5485-5495
  • Renvoisé M., Bonhomme L., Davanture M. , Zivy M. , Lemaire C., Tan AC., Huang PH.. (2017) Phosphoproteomic Analysis of Isolated Mitochondria in Yeast. , 283-299
  • Rouzet A., Reboux G., Dalphin JC., Gondouin A., De Vuyst P., Balliau T. , Millon L., Valot B., Roussel S.. (2017) An immunoproteomic approach revealed antigenic proteins enhancing serodiagnosis performance of bird fancier's lung. Journal of Immunological Methods, (450) 58-65
  • Villegente M., Marmey P., Job C., Galland M., Cueff G., Godin B., Rajjou L., Balliau T. , Zivy M. , Fogliani B., Sarramegna-Burtet V., Job D.. (2017) A Combination of Histological, Physiological, and Proteomic Approaches Shed Light on Seed Desiccation Tolerance of the Basal Angiosperm Amborella trichopoda. Proteomes, 3 (5)
  • Blein-Nicolas M. , Zivy M. . (2016) Thousand and one ways to quantify and compare protein abundances in label-free bottom-up proteomics. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 8 (1864) 883-895
  • Dobrenel T., Mancera-Martínez E., Forzani C., Azzopardi M., Davanture M. , Moreau M., Schepetilnikov M., Chicher J., Langella O. , Zivy M. , Robaglia C., Ryabova LA., Hanson J., Meyer C.. (2016) The Arabidopsis TOR Kinase Specifically Regulates the Expression of Nuclear Genes Coding for Plastidic Ribosomal Proteins and the Phosphorylation of the Cytosolic Ribosomal Protein S6. Front Plant Sci, (7)
  • Herve V., Durufle H., San Clemente H., Albenne C., Balliau T. , Zivy M. , Dunand C., Jamet E.. (2016) An enlarged cell wall proteome of Arabidopsis thaliana rosettes. Proteomics, 24 (16) 3183-3187
  • Sabarly V., Aubron C., Glodt J., Balliau T. , Langella O. , Chevret D., Rigal O., Bourgais A., Picard B., de Vienne D., Denamur E., Bouvet O., Dillmann C.. (2016) Interactions between genotype and environment drive the metabolic phenotype within Escherichia coli isolates. Environmental microbiology, 1 (18) 100-17
  • Blein-Nicolas M. , Albertin W., da Silva T., Valot B., Balliau T. , Masneuf-Pomarède I., Bely M., Marullo P., Sicard D., Dillmann C., de Vienne D., Zivy M. . (2015) A Systems Approach to Elucidate Heterosis of Protein Abundances in Yeast. Mol. Cell Proteomics, 8 (14) 2056-2071
  • Albertin W., Marullo P., Bely M., Aigle M., Bourgais A., Langella O. , Balliau T. , Chevret D., Valot B., da Silva T., Dillmann C., de Vienne D., Sicard D.. (2013) Linking post-translational modifications and variation of phenotypic traits. Molecular & cellular proteomics : MCP, 3 (12) 720-35
  • Blein-Nicolas M. , Albertin W., Valot B., Marullo P., Sicard D., Giraud C., Huet S., Bourgais A., Dillmann C., de Vienne D., Zivy M. . (2013) Yeast proteome variations reveal different adaptive responses to grape must fermentation. Molecular biology and evolution, 6 (30) 1368-83
  • Langella O. , Valot B., Jacob D., Balliau T. , Flores R., Hoogland C., Joets J., Zivy M. . (2013) Management and dissemination of MS proteomic data with PROTICdb: Example of a quantitative comparison between methods of protein extraction. Proteomics, 9 (13) 1457-66
  • Blein-Nicolas M. , Xu H., de Vienne D., Giraud C., Huet S., Zivy M. . (2012) Including shared peptides for estimating protein abundances: a significant improvement for quantitative proteomics. Proteomics, 18 (12) 2797-801
  • Valot B., Langella O. , Nano E., Zivy M. . (2011) MassChroQ: a versatile tool for mass spectrometry quantification. Proteomics, 17 (11) 3572-7
  • Virlouvet L., Jacquemot MP., Gerentes D., Corti H., Bouton S., Gilard F., Valot B., Trouverie J., Tcherkez G., Falque M., Damerval C., Rogowsky P., Perez P., Noctor G., Zivy M. , Coursol S.. (2011) The ZmASR1 protein influences branched-chain amino acid biosynthesis and maintains kernel yield in maize under water-limited conditions. Plant physiology, 2 (157) 917-36