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Chromosome 14


1. Group composition


Participating country(ies): France
Head: Charles Pineau
Members:

2. Missing proteins


Protein evidence according to NeXtProt for Chromosome 14(external link):



3. Bioinformatics protocols


We are developping Proline a data integration framework and a software suite for mass spectrometry based proteomics (software availability: http://proline.profiproteomics.fr/)(external link) . Proline algorithms focus on: result validation (using custom filters and target decoy analysis), merge/comparison of datasets and label-free quantification (spectral count and LC-MS analyses).
Contact: christophe.bruley at cea.fr

4. Analytical protocols


nano-LC MS-based workflows (Q-exactive plus, Orbitrap XL, Orbitrap Velos-pro, Triple-TOF 5600 and QTrap 4000, 5500 and 6500) for:
  • proteins identification
  • quantitative proteomics
  • targeted analysis
  • top-down analysis
Contact: jerome.garin at cea.fr

5. Biological projects


  • Proteomics for testicular pathophysiology, reproductive toxicology and male infertility research projects; contact: charles.pineau at inserm.fr
  • Targeted MS-based assays for a multiplex quantification of liver injury biomarkers candidates in plasma; contact: virginie.brun at cea.fr
  • Infectious diseases (malaria, toxoplasma, lyme disease); contact: ccarapito at unistra.fr

6. Biomaterials



7. Data sets


  • Missing proteins mapping human chromosome 2 and 14 detected in different samples (tissues, cell type names, type of fraction): PXD002131(external link). Contact: Anne Gonzalez.
  • Missing protein mapping human chromosomes detected in the spermatozoa: PXD002367(external link). Contact: Charles Pineau.
  • Missing protein mapping human chromosomes detected in the spermatozoa: an update: PXD003947(external link). Contact: Yves Vandenbrouck.

8. Special expertise


Absolute quantification (PSAQ technology); contact: virginie.brun at cea.fr

9. Major achievements


  • Publications
    • PMID: 28891297(external link). Carapito C, Duek P, Macron C, Seffals M, Rondel K, Delalande F, Lindskog C, Freour T, Vandenbrouck Y, Lane L, Pineau C. Validating missing proteins in human sperm cells by targeted mass spectrometry- and antibody-based methods. J Proteome Res. 2017 Sep 11 doi: 10.1021/acs.jproteome.7b00374. Epub ahead of print
    • PMID 27444420(external link). Vandenbrouck Y, Lane L, Carapito C, Duek P, Rondel K, Bruley C, Macron C, Gonzalez de Peredo A, Couté Y, Chaoui K, Com E, Gateau A, Hesse AM, Marcellin M, Méar L, Mouton-Barbosa E, Robin T, Burlet-Schiltz O, Cianferani S, Ferro M,Fréour T, Lindskog C, Garin J, Pineau C. Looking for Missing Proteins in the Proteome of Human Spermatozoa: An Update. J Proteome Res. 2016 Nov 4;15(11):3998-4019.
    • PMID: 27487287(external link). Duek P, Bairoch A, Gateau A, Vandenbrouck Y, Lane L. Missing Protein Landscape of Human Chromosomes 2 and 14: Progress and Current Status. J Proteome Res. 2016 Nov 4;15(11):3971-3978. PubMed
    • PMID:27490519(external link). Deutsch EW, Overall CM, Van Eyk JE, Baker MS, Paik YK, Weintraub ST, Lane L, Martens L, Vandenbrouck Y, Kusebauch U, Hancock WS, Hermjakob H, Aebersold R, Moritz RL, Omenn GS. Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1. J Proteome Res. 2016 Nov 4;15(11):3961-3970.
    • PMID 26132440(external link). Carapito C, Lane L, Benama M, Opsomer A, Mouton-Barbosa E, Garrigues L, Gonzalez de Peredo A, Burel A, Bruley C, Gateau A, Bouyssié D, Jaquinod M, Cianférani S, Burlet-Schiltz O, Van Dorsselaer A, Garin J, Vandenbrouck Y. Computational and mass spectrometry-based workflow for the discovery and validation of missing human proteins: application to chromosomes 2 and 14. J Proteome Res. 2015 Jul 1.
    • PMID 26168773(external link). Jumeau F, Com E, Lane L, Duek P, Lagarrigue M, Lavigne R, Guillot L, Rondel K, Gateau A, Melaine N, Guével B, Sergeant N, Mitchell V, Pineau C. Human spermatozoa as a model for detecting missing proteins in the context of the chromosome-centric Human Proteome Project. J. Proteome Res. 2015 Sep 4;14(9):3621-34.
  • Posters and other media
    • Carapito C, Macron C, Duek P, Rondel K, Seffals M, Fréour T, Lindskog C, Vandenbrouck Y, Pineau C, Lane L. Taking up the “neXt50 challenge” using human sperm. 16th Human Proteome Organization World Congress, September 17-21, 2017, Dublin, Ireland. Poster
    • The French-Swiss Human Chromosome 2 and 14 consortium: Looking for missing proteins in the proteome of human spermatozoa. 15th Human Proteome Organization World Congress, September 18-22, 2016, Taipei, Taiwan. Oral communication
    • Vandenbrouck Y, Lane L, Pineau C, et al. The French-Swiss Human chromosome 2 and 14 consortium: looking for missing proteins in the proteome of human spermatozoa. 15th Human Proteome Organization (HUPO). Taipei, Taïwan. September 18-21th2016. Poster (C-HPP investigator award).
    • Pineau C. & Lane L. Call for a Testis/Epididymis proteome Project. 14th Human Proteome Organization (HUPO). Oral communication. Vancouver, Canada. September 27-30th 2015. Oral communication.
    • Vandenbrouck Y et al. Finding Missing Proteins in the Human Proteome. 10th Mass Spectrometry Applied to Proteomics (SMAP) congress. Ajaccio, France. September 15-18th 2015. Invited speaker.
    • Vandenbrouck Y et al. Computational and mass spectrometry-based workflow for the discovery and validation of missing proteins: the case of human chromosomes 2 and 14. 13th Human Proteome Organization (HUPO). Madrid, Spain. October 5-8th 2014. Oral communication.
    • Opsomer A, Benama M, Garrigues L, Lennon S, Mouton-Barbosa E, Van Dorsselaer A, Garin J, Vandenbrouck Y, Carapito C. Targeted proteomics experiments to validate so far “missing” human proteins. 10th Sienna Meeting. Italy, 31 August – 4 September 2014. Poster
    • Lane L, Bruley C, Christine Carapito C, Gateau A, Burel A, Gonzales de Peredo A, Bouyssié D, Schiltz-Burlet O, Monsarrat B, Van Dorsselaer A, Bairoch A, Garin J and Vandenbrouck Y. The Franco-Swiss c-HPP project: identifying missing proteins from chromosomes 2 and 14 using existing datasets and neXtProt annotations. HUPO 2013. Yokohama, Japan. 14-18th September 2013. Poster


10. The neXt50 challenge