Chromosome 14

1.1. Group composition

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

• Yves Vandenbrouck, co-PI (Bioinformatics)
• Christine Carapito (LC-MS analysis, SRM, bioinformatics)
• Anne Gonzalez de Peredo (LC-MS analysis, Quantitative proteomics)
• Christophe Bruley (IT, Bioinformatics)
• Jérôme Garin, French Proteomics Infrastructure, Head
• Myram Ferro, French Proteomics Infrastructure, Manager

1.2. Missing proteins

Protein evidence according to NeXtProt for Chromosome 14:
Protein evidence status in text format is available here.

1.3. 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/) . 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

1.4. 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

1.5. 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

1.6. Biomaterials

1.7. Data sets

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

1.8. Special expertise

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

1.9. Major achievements

• Publications
  • PMID: 31429579. Pineau C, Hikmet Noraddin F, Zhang C, Oksvold P, Chen S, Fagerberg L, Uhlén M, Lindskog C. Cell type-specific expression of testis elevated genes based on transcriptomics and antibody-based proteomics. J. Proteome Res. 2019; In Press.
  • PMID: 30130116 . Melaine N, Com E, Bellaud P, Guillot L, Lagarrigue M, Morrice NA, Guevel B, Lavigne R, Velez de la Calle JF, Dojahn J, Pineau C. Deciphering the Dark Proteome: Use of the Testis and Characterization of Two Dark Proteins. J Proteome Res. 2018; 17: 4197-4210.
  • PMID: 28891297. 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. 2016 Nov 4;15(11):3998-4019.
  • PMID 27444420. 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. 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. 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. 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. 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. 15^th Human Proteome Organization (HUPO). Taipei, Taïwan. September 18-21^th2016. Poster (C-HPP investigator award).
  • Pineau C. & Lane L. Call for a Testis/Epididymis proteome Project. 14^th Human Proteome Organization (HUPO). Oral communication. Vancouver, Canada. September 27-30^th 2015. Oral communication.
  • Vandenbrouck Y et al. Finding Missing Proteins in the Human Proteome. 10^th Mass Spectrometry Applied to Proteomics (SMAP) congress. Ajaccio, France. September 15-18^th 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

1.10. The neXt-MP50 challenge