Major achievements

1.1. Chromosome 1

• Publications in 2015
  • PMID 26144840
  • PMID 26076724
  • PMID 26282447
  • PMID 26561870
  • PMID 25723528
  • PMID 26076068
  • PMID 25794139

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1.2. Chromosome 2

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.

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1.3. Chromosome 3

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1.4. Chromosome 4

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1.5. Chromosome 5

• Setup Wiki for C-HPP (13 January 2013).
• Poster at C-HPP poster session of HUPO 2013 (Yokohama, Japan): Chromosome-Centric Human Protein Project: Chromosome 5, Peter Horvatovich, Pei-Jing Pai, Henry Lam, Rainer Bischoff. Poster in pdf is available here.
• Oral presentation at Young Investigator session and poster at HUPO 2013 (Yokohama, Japan): Pei-Jing Pai, Yingwei Hu, Henry Lam, Site-Specific N-Linked Glycosylation Analysis by Nano-LC Tandem Mass Spectrometry Coupled with a Spectral Library Searching Approach, References: YI03-03 11:29-11:41 for oral presentation and POS-03-016 for poster presentation.
• Organizing a DTL focus meeting on "Data integration, standards and fair principles in proteomics" in Utrecht on August 29, 2016, Utrecht, The Netherlands. See program at DTL website and presentation on the C-HPP Wiki.
• PhP test page

• Publications in 2015
  • PMID 26076068
  • PMID 26155874
  • PMID 25982285 and PMID 26143031

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1.6. Chromosome 6

A review of the chromosome 6 project has been published, link
Borchers et al., 'The Human Proteome Organization Chromosome 6 Consortium: Integrating chromosome-centric and biology/disease driven strategies', Journal of Proteomics 100 (2014), 60-67.

Rare tissue analysis:

• Prudova, A., Serrano, K., Eckhard, U., Fortelny, N., Devine, D. V., Overall, C. M., TAILS N-terminomics of human platelets reveals pervasive metalloproteinase-dependent proteolytic processing in storage, e-Blood, 2014, 124(26):e49-e60.
• Lange, P.F., Huesgen, P.F., Nguyen, K., Overall, C. M., Annotating N Termini for the Human Proteome Project: N Termini and Nα-Acetylation Status Differentiate Stable Cleaved Protein Species from Degradation Remnants in the Human Erythrocyte Proteome, Journal of Proteome Research, 2014, 13, 2028−2044.
• Eckhard, U., Marino, G., Abbey, S. R., Tharmarajah, G., Matthew, I., Overall, C. M., The Human Dental Pulp Proteome and N‑Terminome: Levering the Unexplored Potential of Semitryptic Peptides Enriched by TAILS to Identify Missing Proteins in the Human Proteome Project in Underexplored Tissues, Journal of Proteome Research, 2015, 14, 3568−3582.
• Eckhard, U., Marino, G., Abbey, S. R., Matthew, I., Overall, C. M., TAILSN-terminomic and proteomic datasets of healthy human dental pulp, Data in Brief, 2015, 5, 542–548.
• Abbey, S. R., Eckhard, U., Solis, N., Marino, G., Matthew, I., Overall, C. M., The Human Odontoblast Cell Layer and Dental Pulp Proteomes and N-Terminomes, Journal of Dental Research, 2017.

Database search tool

• Lange, P. F., Huesgen, P. F., Overall, C. M., TopFIND 2.0 - linking protein termini with proteolytic processing and modifications altering protein function, Nucleic Acids Research, 2012, 40, D351–D361.
• Lange, P. F., Overall, C. M., TopFIND, a knowledgebase linking protein termini with function, Nature Methods, 2011, 8, pages 703–704.

Other papers:

• Overall, C. M., Can proteomics fill the gap between genomics and phenotypes? Journal of Proteomics, 2014, 100, 1-2.
• Borchers, C.H., Kast, J., Foster, L.J., Siud, K.W.M., Overall, C.M., Binkowski, T.A., Hildebrand, W.H., Scherer, A., Mansoor, M., Keown, P.A., for the Human Proteome Organization Chromosome 6 Consortium, The Human Proteome Organization Chromosome 6 Consortium: Integrating chromosome-centric and biology/disease driven strategies, Journal of Proteomics, 2014, 100, 60-67.
• Huesgen, P. F., Lange, P. F., Rogers, L. D., Solis, N., Eckhard, U., Kleifeld, O., Goulas, T., Gomis-Rüth, F. X., Overall, C.M., LysargiNase mirrors trypsin for protein C-terminal and methylation-site identification, Nature Methods, 2015, 12(1):55-58.
• Paik, Y.K., Omenn, G. S., Overall, C.M., Deutsch, E., W., Hancock, W. S., Recent Advances in the Chromosome-Centric Human Proteome Project: Missing Proteins in the Spot Light, Journal of Proteome Research, 2015, 14, 3409−3414.
• Marino, G., Eckhard, U., Overall, C. M., Protein Termini and Their Modifications Revealed by Positional Proteomics, Chemical Biology, 2015, 10(8):1754-1764.
• Eckhard U., Marino, G., Butler, G. S., Overall, C. M., Positional proteomics in the era of the human proteome project on the doorstep of precision medicine, Biochimie 2016, 122, 110e118.
• Deutsch, E.W., Overall, C.M., Van Eyk, J.E., Baker, M.S., Paik, Y.K., Weintraub, S.T., Lane, L., Martens, L., Vandenbrouck, Y., Kusebauch, U., Hancock, W.S., Hermjakob, H., Aebersold, R, Moritz R.L., Omenn, G. S., Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1., J Proteome Res., 2016, 15(11):3961-3970.
• Omenn, G.S., Lane, L., Lundberg, E.K., Beavis, R.C., Overall, C.M., Deutsch, E.W., Metrics for the Human Proteome Project 2016: Progress on Identifying and Characterizing the Human Proteome, Including Post-Translational Modifications, J Proteome Res., 2016, 15(11):3951-3960.
• Paik, Y.K., Overall, C.M., Deutsch, E.W., Hancock, W.S., Omenn, G.S., Progress in the Chromosome-Centric Human Proteome Project as Highlighted in the Annual Special Issue IV, J Proteome Res. 2016, 15(11):3945-3950.
• Paik, Y.K., Omenn, G.S., Hancock, W.S., Lane, L., Overall C.M., Advances in the Chromosome-Centric Human Proteome Project: looking to the future, Expert Rev Proteomics, 2017, 14(12):1059-1071.
• Klein, T., Eckhard, U., Dufour, A., Solis, N., Overall, C.M., Proteolytic Cleavage-Mechanisms, Function, and "Omic" Approaches for a Near-Ubiquitous Posttranslational Modification, Chem Rev., 2018, 118(3):1137-1168.
• Paik YK, Lane L, Kawamura T, Chen YJ, Cho JY, LaBaer J, Yoo JS, Domont G, Corrales F, Omenn GS, Archakov A, Encarnación-Guevara S, Lui S, Salekdeh GH, Cho JY, Kim CY, Overall C.M., Launching the C-HPP neXt-CP50 Pilot Project for Functional Characterization of Identified Proteins with No Known Function, J Proteome Res. 2018 Dec 7;17(12):4042-4050.
• Omenn GS, Lane L, Overall CM, Corrales FJ, Schwenk JM, Paik YK, Van Eyk JE, Liu S, Pennington S, Snyder MP, Baker MS, Deutsch EW., Progress on Identifying and Characterizing the Human Proteome: 2018-2019 Metrics from the HUPO Human Proteome Project, J Proteome Res. 2019.

Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome.
Kusebauch U, Campbell DS, Deutsch EW, Chu CS, Spicer DA, Brusniak MY, Slagel J, Sun Z, Stevens J, Grimes B, Shteynberg D, Hoopmann MR, Blattmann P, Ratushny AV, Rinner O, Picotti P, Carapito C, Huang CY, Kapousouz M, Lam H, Tran T, Demir E, Aitchison JD, Sander C, Hood L, Aebersold R, Moritz RL. Cell. 2016 Jul 28;166(3):766-778. doi: 10.1016/j.cell.2016.06.041. Epub 2016 Jul 21. PMID: 27453469

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1.7. Chromosome 7

• Publications in 2014
  • PMID 24861753
  • PMID 25171765
  • PMID 25277501
  • PMID 25405748
• Publications in 2015
  • PMID 26330117
  • PMID 26076068
  • PMID 25925208
  • PMID 26518147
  • PMID 25794139
  • PMID 27975291
  • PMID 26330117
• Publications in 2016
  • PMID 26680015

• Article entitled "Human Proteome Project Finds Outside Biological Knowledge Could Aid Effort" in GenomeWeb (account and login required).

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1.8. Chromosome 8

• Publications in 2015
  • PMID 26144840
  • PMID 26282447
  • PMID 26202631
  • PMID 25574523
  • PMID 26202631

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1.9. Chromosome 9

• Publications in 2015
  • PMID 26043090

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1.10. Chromosome 10

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1.11. Chromosome 11

• Publications in 2015
  • PMID 26549206
• Publications in 2016
  • PMID 27601894

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1.12. Chromosome 12

• Publications in 2014
  • PMID 24831074
  • PMID 24960282
  • PMID 24804578
• Publications in 2015
  • PMID 26143930
  • PMID 26464075
  • PMID 26407240

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1.13. Chromosome 13

1. Set up home page for C-HPP (April 2012)
2. Construct GenomewidePDB (December 2012)
3. Update GenomewidePDB 2.0 (November 2015)

Publications

• Paik,Y. et al. (2012) The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome. Nat Biotechnol, 30, 221-3. (PMID 22398612)
• Paik, Y. K. and Hancock, W. S. (2012) Uniting ENCODE with genome-wide proteomics. Nat. Biotechnol. 30, 1065-1067. (PMID 23138303))
• Lee, H. J. et al. (2013) Comprehensive genome-wide proteomic analysis of human placental tissue for the Chromosome-Centric Human Proteome Project. J. Proteome Res., 12, 2458-2466. (PMID 23362793)
• Jeong, S. K. et al. (2013) GenomewidePDB, a proteomic database exploring the comprehensive protein parts list and transcriptome landscape in human chromosomes. J. Proteome Res., 12, 106-111. (PMID 23252913)
• Paik, Y. K. et al. (2014) Genome-wide proteomics, Chromosome-Centric Human Proteome Project (C-HPP), part II. J. Proteome Res., 13, 1-4. (PMID 24328071)
• Paik, Y. K. et al. (2015) Recent Advances in the Chromosome-Centric Human Proteome Project: Missing Proteins in the Spot Light. J. Proteome Res., 14, 3409-3414. (PMID 26337862)
• Jeong, S. K. et al. (2015) GenomewidePDB 2.0: A Newly Upgraded Versatile Proteogenomic Database for the Chromosome-Centric Human Proteome Project. J. Proteome Res., 14, 3710-3719. (PMID 26272709)
• Cho, J. Y. et al. (2015) Combination of Multiple Spectral Libraries Improves the Current Search Methods Used to Identify Missing Proteins in the Chromosome-Centric Human Proteome Project. J. Proteome Res., 14, 4959-4966. (PMID 26330117)
• Paik, Y. K. et al. (2016) Progress in the Chromosome-Centric Human Proteome Project as Highlighted in the Annual Special Issue IV. J. Proteome Res., 15, 3945-3950. (PMID 27809547)
• Kim, J. W. et al. (2016) gFinder: A Web-Based Bioinformatics Tool for the Analysis of N-Glycopeptides. J. Proteome Res., 15, 4116-4125. (PMID 27573070)
• Paik YK et al. (2018) Launching the C-HPP neXt-CP50 Pilot Project for Functional Characterization of Identified Proteins with No Known Function. J Proteome Res. 7;17(12):4042-4050. (PMID 30269496).
• Paik YK et al. (2018) Toward Completion of the Human Proteome Parts List: Progress Uncovering Proteins That Are Missing or Have Unknown Function and Developing Analytical Methods. J Proteome Res. 7;17(12):4023-4030. (PMID 30985145)
• Jeong SK et al. (2018) ASV-ID, a Proteogenomic Workflow to Predict the Candidate Protein Isoforms based on Transcript Evidence. J Proteome Res. 7;17(12):4235-4242. (PMID 30289715)

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1.14. Chromosome 14

• 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

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1.15. Chromosome 15

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1.16. Chromosome 16

Publications:

• PMID 23234512
• PMID 24138474
• PMID 25612097
• PMID 26076068
• PMID 26144527
• PMID 26155874
• PMID 26216070
• PMID 27686808
• PMID 27581094
• PMID 27885863

Posters presented in the HUPO 2013 (Yokohama, Japan) Meeeting:
Bioinformatic workflow for Chr16 characterization using proteomic shotgun and transcriptomic RNA-seq experiments
Development of SRM methods for the detection and quantification of chromosome 16 proteins
Dissecting subcellular compartments for deep proteome coverage of chromosome 16 in t cells
Improving Chr-16 proteins coverage with high confidence and MIAPE compliant MS data
Missing proteins in Chromosome 16 - Spanish HPP

Presentations:
Identification of proteins driving the progression of liver injury and potential biomarkers
How to submit MIAPE compliant data to ProteomeXchange Repository in the context of the human proteome project
Chromosome 16 Update: Surfing transcriptomics landscapes. A step beyond the annota=on of Chr-­‐16 proteome
European initiatives in the field of Proteomics Standarization

Other files:
SpanishContributiontoPX_Jan16.xlsx

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1.17. Chromosome 17

We list here those.
proteins that were correlated with higher levels of EGFR or ERBB2 transcript, respectively.
EGFR signaling: caveolin 1 (CAV1), plectin (PLEC) (EGFR); growth factor receptor bound protein 7 (GRB7), Crk-like protein (CRKL) and Catenin delta-1 (CTNND1) (ERBB2).
Integrin signaling: filamin A (FLNA) and actinin alpha1 (ACTN1) (EGFR). MYC signaling: branched chain amino-acid transaminase 1 (BCAT1), carbamoyl-phosphate synthetase (CAD), nucleolin (NCL) (EGFR); transferrin receptor (TFRC), metadherin (MTDH) (ERBB2). p53 signaling: S100-A2 protein (S100A2), caveolin 1 (CAV1), Serpin B5 (SERPINB5), stratifin (SFN), PYD and CARD domain containing (PYCARD), and EPH receptor A2 (EPHA2) (EGFR).

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1.18. Chromosome 18

• Transcriptome profiling for chr18 in liver tissue and HepG2 cell line using RNA-Seq (Illumina and SOLiD) and RT-PCR protocols.
• Proteome profiling for 276 master proteins coding on Chr18 in blood plasma, liver tissue and HepG2 cell line using SRM.

Vienn diagram representing the number of chromosome 18 proteins detected by SRM in three types of biomaterial.

• Construction Gene-Centric Knowledgebase(kb18) and SRM Registry (pikb18.ru) database for post-genomic data of Chr18.

Publications

1. Alexander I. Archakov, Elena A. Ponomarenko, Ekaterina V. Poverennaya, Andrey V. Lisitsa, Ekaterina V. Ilgisonis, Mikhail A. Pyatnitskiy, Arthur T. Kopylov, Victor G. Zgoda. The size of the human proteome: the width and depth. 2014 (submitted).
2. Lisitsa A, Moshkovskii S, Chernobrovkin A, Ponomarenko E, Archakov A. Profiling proteoforms: promising follow-up of proteomics for biomarker discovery. Expert Rev Proteomics. 2014 Feb;11(1):121-9. doi: 10.1586/14789450.2014.878652. PubMed PMID: 24437377.
3. Ponomarenko EA, Kopylov AT, Lisitsa AV, Radko SP, Kiseleva YY, Kurbatov LK,Ptitsyn KG, Tikhonova OV, Moisa AA, Novikova SE, Poverennaya EV, Ilgisonis EV,Filimonov AD, Bogolubova NA, Averchuk VV, Karalkin PA, Vakhrushev IV, Yarygin KN,Moshkovskii SA, Zgoda VG, Sokolov AS, Mazur AM, Prokhortchouck EB, Skryabin KG,Ilina EN, Kostrjukova ES, Alexeev DG, Tyakht AV, Gorbachev AY, Govorun VM,Archakov AI. Chromosome 18 transcriptoproteome of liver tissue and HepG2 cells and targeted proteome mapping in depleted plasma: update 2013. J Proteome Res. 2014 Jan 3;13(1):183-90. doi: 10.1021/pr400883x. Epub 2013 Dec 13. PubMed PMID: 24328317.
4. Shargunov AV, Krasnov GS, Ponomarenko EA, Lisitsa AV, Shurdov MA, Zverev VV, Archakov AI, Blinov VM. Tissue-specific alternative splicing analysis reveals the diversity of chromosome 18 transcriptome. J Proteome Res. 2014 Jan 3;13(1):173-82. doi: 10.1021/pr400808u. Epub 2013 Dec 9. PubMed PMID: 24320163.
5. Poverennaya EV, Bogolubova NA, Bylko NN, Ponomarenko EA, Lisitsa AV, Archakov AI. Gene-centric content management system. Biochim Biophys Acta. 2014 Jan;1844(1 Pt A):77-81. doi: 10.1016/j.bbapap.2013.08.006. Epub 2013 Aug 27. PubMed PMID: 23994227.
6. Ponomarenko E, Baranova A, Lisitsa A, Albar JP, Archakov A. The Chromosome-Centric Human Proteome Project at FEBS Congress. Proteomics. 2013 Nov 28. doi: 10.1002/pmic.201300373. Epub ahead of print PubMed PMID: 24285571.
7. Naryzhny SN, Lisitsa AV, Zgoda VG, Ponomarenko EA, Archakov AI. 2DE-based approach for estimation of number of protein species in cell. Electrophoresis.2013 Nov 20. doi: 10.1002/elps.201300525. Epub ahead of print PubMed PMID:24259369.
8. Kopylov AT, Zgoda VG, Lisitsa AV, Archakov AI. Combined use of irreversible binding and MRM technology for low- and ultralow copy-number protein detection and quantitation. Proteomics. 2013 Mar;13(5):727-42. doi: 10.1002/pmic.201100460. PubMed PMID: 23281252.
9. Zgoda VG, Kopylov AT, Tikhonova OV, Moisa AA, Pyndyk NV, Farafonova TE, Novikova SE, Lisitsa AV, Ponomarenko EA, Poverennaya EV, Radko SP, Khmeleva SA, Kurbatov LK, Filimonov AD, Bogolyubova NA, Ilgisonis EV, Chernobrovkin AL, Ivanov AS, Medvedev AE, Mezentsev YV, Moshkovskii SA, Naryzhny SN, Ilina EN, Kostrjukova ES, Alexeev DG, Tyakht AV, Govorun VM, Archakov AI. Chromosome 18 transcriptome profiling and targeted proteome mapping in depleted plasma, liver tissue and HepG2 cells. J Proteome Res. 2013 Jan 4;12(1):123-34. doi: 10.1021/pr300821n. Epub 2012 Dec 20. PubMed PMID: 23256950.
10. Archakov A, Zgoda V, Kopylov A, Naryzhny S, Chernobrovkin A, Ponomarenko E, Lisitsa A. Chromosome-centric approach to overcoming bottlenecks in the Human Proteome Project. Expert Rev Proteomics. 2012 Dec;9(6):667-76. doi: 10.1586/epr.12.54. Review. PubMed PMID: 23256676.
11. Ponomarenko E, Poverennaya E, Pyatnitskiy M, Lisitsa A, Moshkovskii S, Ilgisonis E, Chernobrovkin A, Archakov A. Comparative ranking of human chromosomes based on post-genomic data. OMICS. 2012 Nov;16(11):604-11. doi: 10.1089/omi.2012.0034. Epub 2012 Sep 11. PubMed PMID: 22966780.
12. Ershov P, Mezentsev Y, Gnedenko O, Mukha D, Yantsevich A, Britikov V, Kaluzhskiy L, Yablokov E, Molnar A, Ivanov A, Lisitsa A, Gilep A, Usanov S, Archakov A. Protein interactomics based on direct molecular fishing on paramagnetic particles: experimental simulation and SPR validation. Proteomics. 2012 Nov;12(22):3295-8. doi: 10.1002/pmic.201200135. Epub 2012 Nov 2. PubMed PMID: 23001861.
13. Medvedev A, Kopylov A, Buneeva O, Zgoda V, Archakov A. Affinity-based proteomic profiling: problems and achievements. Proteomics. 2012 Feb;12(4-5):621-37. doi: 10.1002/pmic.201100373. Epub 2012 Jan 19. Review. PubMed PMID: 22246677.
14. Archakov A, Aseev A, Bykov V, Grigoriev A, Govorun V, Ivanov V, Khlunov A, Lisitsa A, Mazurenko S, Makarov AA, Ponomarenko E, Sagdeev R, Skryabin K. Gene-centric view on the human proteome project: the example of the Russian roadmap for chromosome 18. Proteomics. 2011 May;11(10):1853-6. doi: 10.1002/pmic.201000540. PubMed PMID: 21563312.
15. Archakov A, Ivanov Y, Lisitsa A, Zgoda V. Biospecific irreversible fishing coupled with atomic force microscopy for detection of extremely low-abundant proteins. Proteomics. 2009 Mar;9(5):1326-43. doi: 10.1002/pmic.200800598. PubMed PMID: 19253286.
16. Archakov AI, Ivanov YD, Lisitsa AV, Zgoda VG. AFM fishing nanotechnology is the way to reverse the Avogadro number in proteomics. Proteomics. 2007 Jan;7(1):4-9. PubMed PMID: 17154275.

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1.19. Chromosome 19

Chromosome 19 Team meeting, Salamanca, Spain, October 2-4, 2014

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1.20. Chromosome 20

Publications in 2015

• PMID 26144840
• PMID 26076724
• PMID 26282447
• PMID 26500078
• PMID 26456862
• PMID 26258396
• PMID 26076068
• PMID 25574523
• PMID 26202631
• PMID 26108252

Publications in 2016

• PMID 27457664
• PMID 27316337

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1.21. Chromosome 21

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1.22. Chromosome 22

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1.23. Chromosome X

• Publications in 2013
  • PMID 23253012
• Publications in 2015
  • PMID 26162278
  • PMID 25982285
  • PMID 26143031
  • PMID 26144214
  • PMID 26215926
  • PMID 26162009

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1.24. Chromosome Y

2017

• Meyfour A, Pooyan P, Pahlavan S, Rezaei-Tavirani M, Gourabi H, Baharvand H, Salekdeh GH. Chromosome-Centric Human Proteome Project Allies with Developmental Biology: a Case Study of the Role of Y chromosome Genes in Organ Development. J Proteome Res. 2017 Sep 15. doi: 10.1021/acs.jproteome.7b00446. PuMed PMID: 28914051.
• Meyfour A, Ansari H, Pahlavan S, Mirshahvaladi S, Rezaei-Tavirani M, Gourabi H, Baharvand H, Salekdeh GH. Y Chromosome Missing Protein, TBL1Y, May Play an Important Role in Cardiac Differentiation. J Proteome Res. 2017 Sep 13. doi: 10.1021/acs.jproteome.7b00391. PuMed PMID: 28853286.

2015

• Jangravi Z, Tabar MS, Mirzaei M, Parsamatin P, Vakilian H, Alikhani M, Shabani M, Haynes PA, Goodchild AK, Gourabi H, Baharvand H, Salekdeh GH. Two Splice Variants of Y Chromosome-Located Lysine-Specific Demethylase 5D Have Distinct Function in Prostate Cancer Cell Line (DU-145). J Proteome Res. 2015 Sep 4;14(9):3492-502. doi: 10.1021/acs.jproteome.5b00333. Epub 2015 Aug 10. PubMed PMID: 26215926.
• Ahmadi Rastegar D, Sharifi Tabar M, Alikhani M, Parsamatin P, Sahraneshin Samani F, Sabbaghian M, Sadighi Gilani MA, Mohammad Ahadi A, Mohseni Meybodi A, Piryaei A, Ansari-Pour N, Gourabi H, Baharvand H, Salekdeh GH. Isoform-Level Gene Expression Profiles of Human Y Chromosome Azoospermia Factor Genes and Their X Chromosome Paralogs in the Testicular Tissue of Non-Obstructive Azoospermia Patients. J Proteome Res. 2015 Sep 4;14(9):3595-605. doi: 10.1021/acs.jproteome.5b00520. PubMed PMID: 26162009.
• Vakilian H, Mirzaei M, Sharifi Tabar M, Pooyan P, Habibi Rezaee L, Parker L, Haynes PA, Gourabi H, Baharvand H, Salekdeh GH. DDX3Y, a Male-Specific Region of Y Chromosome Gene, May Modulate Neuronal Differentiation. J Proteome Res. 2015 Sep 4;14(9):3474-83. doi: 10.1021/acs.jproteome.5b00512. PubMed PMID: 26144214.

2013

• Jangravi Z, Alikhani M, Arefnezhad B, Sharifi Tabar M, Taleahmad S, Karamzadeh R, Jadaliha M, Mousavi SA, Ahmadi Rastegar D, Parsamatin P, Vakilian H, Mirshahvaladi S, Sabbaghian M, Mohseni Meybodi A, Mirzaei M, Shahhoseini M, Ebrahimi M, Piryaei A, Moosavi-Movahedi AA, Haynes PA, Goodchild AK, Nasr-Esfahani MH, Jabbari E, Baharvand H, Sedighi Gilani MA, Gourabi H, Salekdeh GH. A fresh look at the male-specific region of the human Y chromosome. J Proteome Res. 2013 Jan 4;12(1):6-22. doi: 10.1021/pr300864k. PubMed PMID: 23253012.

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1.25. Mitochondrial Chromosome

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