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Génétique Quantitative et Évolution - Le Moulon

PAPPSO - Plateforme d'Analyse Protéomique de Paris Sud-Ouest

The PAPPSO facility carries out proteomic 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 :

  • X!TandemPipeline ( Langella et al. 2017) pour l'identification et l'inférence des protéines,
  • MassChroQ ( Valot et al. 2011) pour la quantification des peptides,
  • The ProticDB database ( Langella et al. 2013),
  • the MCQR R package dedicated to the statistical analysis of MS proteomic data.

Members

PAPPSO has ten permanent staff members spread over the two sites. At GQE-Le Moulon in February 2020 the team is composed of :

  • Thierry BALLIAU, AI Inra

  • Willy Bienvenut, CR CNRS

  • Mélisande BLEIN-NICOLAS, IR Inra

  • Marlène DAVANTURE, AI CNRS

  • Olivier LANGELLA, IR CNRS

  • Filippo RUSCONI, CR CNRS

  • Michel ZIVY, DR CNRS, team leader.

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

Publications

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, 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
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
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
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
Hasson A, Plessis A, Blein T, Adroher B, Grigg S, Tsiantis M, Boudaoud A, Damerval C, Laufs P. (2011) Evolution and diverse roles of the CUP-SHAPED COTYLEDON genes in Arabidopsis leaf development. The Plant cell, 1 (23) 54-68
Valot B, Langella O, Nano E, Zivy M. (2011) MassChroQ: a versatile tool for mass spectrometry quantification. Proteomics, 17 (11) 3572-7