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Chromosome 2

1.1. Group composition


Participating country(ies): Switzerland
Head: Lydie Lane
Members:
Amos Bairoch (SIB, PI of neXtProt)
Frédérique Lisacek (SIB, glycomics, bioinformatics)
Paula Duek (SIB/University of Geneva)
Alain Gateau (SIB/University of Geneva)
Thibault Robin (SIB/University of Geneva)
Markus Mueller (SIB Lausanne)
Charlotte Macron (Nestlé Institute of Health Sciences)
Antonio Nunez-Galindo (Nestlé Institute of Health Sciences)
Loïc Dayon (Nestlé Institute of Health Sciences)
Camille Mary (University of Geneva)

1.2. Missing proteins


Protein evidence according to NeXtProt for Chromosome 2:
Protein evidence status in text format is available here.

1.3. Bioinformatics protocols


We are developing https://www.nextprot.org/, the reference knowledgebase for C-HPP projects contact : lydie.lane at sib.swiss
We have set up data mining workflows to prioritize missing proteins for targeted studies contact : lydie.lane at sib.swiss or paula.duek at sib.swiss

1.4. Analytical protocols


1.5. Biological projects


Identification of missing proteins in sperm samples, in collaboration with Chromosome 14 team
Functional characterization of unknown proteins

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(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.

1.8. Special expertise


1.9. Major achievements


We maintain neXtProt as the reference protein database for the C-HPP and provide yearly metrics to assess project advances
In collaboration with Chromosome 14 team, we have been looking for missing proteins from chromosome 2 in human sperm samples
We have highlighted a role for the unknown protein C2orf62 in ciliogenesis

C-HPP metrics

  • PMID 27487407. Omenn GS, Lane L, Lundberg EK, Beavis RC, Overall CM, Deutsch EW. Metrics for the Human Proteome Project 2016: Progress on Identifying and Characterizing the Human Proteome, Including Post-Translational Modifications. J Proteome Res. 2016 Nov 4;15(11):3951-3960.
  • PMID 26155816. Omenn GS, Lane L, Lundberg EK, Beavis RC, Nesvizhskii AI, Deutsch EW. Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification. J Proteome Res. 2015 Sep 4;14(9):3452-60. doi: 10.1021/acs.jproteome.5b00499.
  • PMID 24364385 . Lane L, Bairoch A, Beavis RC, Deutsch EW, Gaudet P, Lundberg E, Omenn GS. Metrics for the Human Proteome Project 2013-2014 and strategies for finding missing proteins. J Proteome Res. 2014 Jan 3;13(1):15-20. doi: 10.1021/pr401144x.


Standardization and guidelines

  • 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:26367542. Bruford EA, Lane L, Harrow J. Devising a Consensus Framework for Validation of Novel Human Coding Loci. J Proteome Res. 2015 Dec 4;14(12):4945-8. doi: 10.1021/acs.jproteome.5b00688.


neXtProt and associated tools

  • PMID 27899619 . Gaudet P, Michel PA, Zahn-Zabal M, Britan A, Cusin I, Domagalski M, Duek PD, Gateau A, Gleizes A, Hinard V, Rech de Laval V, Lin J, Nikitin F, Schaeffer M, Teixeira D, Lane L, Bairoch A. Nucleic Acids Res. 2017 Jan 4;45(D1):D177-D182. doi: 10.1093/nar/gkw1062.
  • PMID 24364385 . Gaudet P, Argoud-Puy G, Cusin I, Duek P, Evalet O, Gateau A, Gleizes A, Pereira M, Zahn-Zabal M, Zwahlen C, Bairoch A, Lane L. neXtProt: organizing protein knowledge in the context of human proteome projects. J Proteome Res. 2013 Jan 4;12(1):293-8. doi: 10.1021/pr300830v.
  • PMID 27173522 . Sallou O, Duek PD, Darde TA, Collin O, Lane L, Chalmel F. PepPSy: a web server to prioritize gene products in experimental and biocuration workflows. Database (Oxford). 2016 May 12;2016. pii: baw070. doi: 10.1093/database/baw070.


Reviews

  • PMID 26680015 . Liu F, Koval M, Ranganathan S, Fanayan S, Hancock WS, Lundberg EK, Beavis RC, Lane L, Duek P, McQuade L, Kelleher NL, Baker MS. Systems Proteomics View of the Endogenous Human Claudin Protein Family. J Proteome Res. 2016 Feb 5;15(2):339-59. doi: 10.1021/acs.jproteome.5b00769. Review.


Identification of missing proteins

  • 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 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.
  • 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.


Functional characterization of chromosome 2 proteins

  • PMID 24475127. Bontems F, Fish RJ, Borlat I, Lembo F, Chocu S, Chalmel F, Borg JP, Pineau C, Neerman-Arbez M, Bairoch A, Lane L. PLoS One. 2014 Jan 27;9(1):e86476. doi: 10.1371/journal.pone.0086476.

1.10. The neXt-MP50 challenge


Plans:

  • Complete reannotation of the 33 missing proteins from chr 2 with associated literature - expected validation of ~20 proteins in September 2017
  • Targeted studies (SRM, IHC) on the 40 probable sperm proteins listed in Duek et al. 2016 - expected validation of ~10 chromosome 2 proteins in April 2017 (collaboration with Chromosome 14 team)
  • Data mining on the remaining chr2 MPs to define the best samples to track them - prioritized list expected May 2017