Quest for missing proteins: Update 2015 on chromosome-centric human proteome project

Péter Horvatovich, Emma K. Lundberg, Yu Ju Chen, Ting Yi Sung, Fuchu He, Edouard C. Nice, Robert J. Goode, Simon Yu, Shoba Ranganathan, Mark S. Baker, Gilberto B. Domont, Erika Velasquez, Dong Li, Siqi Liu, Quanhui Wang, Qing Yu He, Rajasree Menon, Yuanfang Guan, Fernando J. Corrales, Victor SeguraJ. Ignacio Casal, Alberto Pascual-Montano, Juan P. Albar, Manuel Fuentes, Maria Gonzalez-Gonzalez, Paula Diez, Nieves Ibarrola, Rosa M. Degano, Yassene Mohammed, Christoph H. Borchers, Andrea Urbani, Alessio Soggiu, Tadashi Yamamoto, Ghasem Hosseini Salekdeh, Alexander Archakov, Elena Ponomarenko, Andrey Lisitsa, Cheryl F. Lichti, Ekaterina Mostovenko, Roger A. Kroes, Melinda Rezeli, Ákos Végvári, Thomas E. Fehniger, Rainer Bischoff, Juan Antonio Vizcaíno, Eric W. Deutsch, Lydie Lane, Carol L. Nilsson, György Marko-Varga, Gilbert S. Omenn, Seul Ki Jeong, Jong Sun Lim, Young Ki Paik, William S. Hancock

Research output: Contribution to journalArticle

45 Citations (Scopus)

Abstract

This paper summarizes the recent activities of the Chromosome-Centric Human Proteome Project (C-HPP) consortium, which develops new technologies to identify yet-to-be annotated proteins (termed "missing proteins") in biological samples that lack sufficient experimental evidence at the protein level for confident protein identification. The C-HPP also aims to identify new protein forms that may be caused by genetic variability, post-translational modifications, and alternative splicing. Proteogenomic data integration forms the basis of the C-HPP's activities; therefore, we have summarized some of the key approaches and their roles in the project. We present new analytical technologies that improve the chemical space and lower detection limits coupled to bioinformatics tools and some publicly available resources that can be used to improve data analysis or support the development of analytical assays. Most of this paper's content has been compiled from posters, slides, and discussions presented in the series of C-HPP workshops held during 2014. All data (posters, presentations) used are available at the C-HPP Wiki (http://c-hpp.webhosting.rug.nl/) and in the Supporting Information.

Original languageEnglish (US)
Pages (from-to)3415-3431
Number of pages17
JournalJournal of Proteome Research
Volume14
Issue number9
DOIs
StatePublished - Sep 4 2015

Fingerprint

Human Chromosomes
Proteome
Chromosomes
Posters
Proteins
Technology
Data integration
Alternative Splicing
Post Translational Protein Processing
Bioinformatics
Computational Biology
Limit of Detection
Assays
Education

Keywords

  • antibody enrichment
  • bioinformatics
  • Chromosome-Centric Human Proteome Project
  • LC-MS
  • missing proteins
  • proteomics

ASJC Scopus subject areas

  • Biochemistry
  • Chemistry(all)

Cite this

Horvatovich, P., Lundberg, E. K., Chen, Y. J., Sung, T. Y., He, F., Nice, E. C., ... Hancock, W. S. (2015). Quest for missing proteins: Update 2015 on chromosome-centric human proteome project. Journal of Proteome Research, 14(9), 3415-3431. https://doi.org/10.1021/pr5013009

Quest for missing proteins : Update 2015 on chromosome-centric human proteome project. / Horvatovich, Péter; Lundberg, Emma K.; Chen, Yu Ju; Sung, Ting Yi; He, Fuchu; Nice, Edouard C.; Goode, Robert J.; Yu, Simon; Ranganathan, Shoba; Baker, Mark S.; Domont, Gilberto B.; Velasquez, Erika; Li, Dong; Liu, Siqi; Wang, Quanhui; He, Qing Yu; Menon, Rajasree; Guan, Yuanfang; Corrales, Fernando J.; Segura, Victor; Casal, J. Ignacio; Pascual-Montano, Alberto; Albar, Juan P.; Fuentes, Manuel; Gonzalez-Gonzalez, Maria; Diez, Paula; Ibarrola, Nieves; Degano, Rosa M.; Mohammed, Yassene; Borchers, Christoph H.; Urbani, Andrea; Soggiu, Alessio; Yamamoto, Tadashi; Salekdeh, Ghasem Hosseini; Archakov, Alexander; Ponomarenko, Elena; Lisitsa, Andrey; Lichti, Cheryl F.; Mostovenko, Ekaterina; Kroes, Roger A.; Rezeli, Melinda; Végvári, Ákos; Fehniger, Thomas E.; Bischoff, Rainer; Vizcaíno, Juan Antonio; Deutsch, Eric W.; Lane, Lydie; Nilsson, Carol L.; Marko-Varga, György; Omenn, Gilbert S.; Jeong, Seul Ki; Lim, Jong Sun; Paik, Young Ki; Hancock, William S.

In: Journal of Proteome Research, Vol. 14, No. 9, 04.09.2015, p. 3415-3431.

Research output: Contribution to journalArticle

Horvatovich, P, Lundberg, EK, Chen, YJ, Sung, TY, He, F, Nice, EC, Goode, RJ, Yu, S, Ranganathan, S, Baker, MS, Domont, GB, Velasquez, E, Li, D, Liu, S, Wang, Q, He, QY, Menon, R, Guan, Y, Corrales, FJ, Segura, V, Casal, JI, Pascual-Montano, A, Albar, JP, Fuentes, M, Gonzalez-Gonzalez, M, Diez, P, Ibarrola, N, Degano, RM, Mohammed, Y, Borchers, CH, Urbani, A, Soggiu, A, Yamamoto, T, Salekdeh, GH, Archakov, A, Ponomarenko, E, Lisitsa, A, Lichti, CF, Mostovenko, E, Kroes, RA, Rezeli, M, Végvári, Á, Fehniger, TE, Bischoff, R, Vizcaíno, JA, Deutsch, EW, Lane, L, Nilsson, CL, Marko-Varga, G, Omenn, GS, Jeong, SK, Lim, JS, Paik, YK & Hancock, WS 2015, 'Quest for missing proteins: Update 2015 on chromosome-centric human proteome project', Journal of Proteome Research, vol. 14, no. 9, pp. 3415-3431. https://doi.org/10.1021/pr5013009
Horvatovich P, Lundberg EK, Chen YJ, Sung TY, He F, Nice EC et al. Quest for missing proteins: Update 2015 on chromosome-centric human proteome project. Journal of Proteome Research. 2015 Sep 4;14(9):3415-3431. https://doi.org/10.1021/pr5013009
Horvatovich, Péter ; Lundberg, Emma K. ; Chen, Yu Ju ; Sung, Ting Yi ; He, Fuchu ; Nice, Edouard C. ; Goode, Robert J. ; Yu, Simon ; Ranganathan, Shoba ; Baker, Mark S. ; Domont, Gilberto B. ; Velasquez, Erika ; Li, Dong ; Liu, Siqi ; Wang, Quanhui ; He, Qing Yu ; Menon, Rajasree ; Guan, Yuanfang ; Corrales, Fernando J. ; Segura, Victor ; Casal, J. Ignacio ; Pascual-Montano, Alberto ; Albar, Juan P. ; Fuentes, Manuel ; Gonzalez-Gonzalez, Maria ; Diez, Paula ; Ibarrola, Nieves ; Degano, Rosa M. ; Mohammed, Yassene ; Borchers, Christoph H. ; Urbani, Andrea ; Soggiu, Alessio ; Yamamoto, Tadashi ; Salekdeh, Ghasem Hosseini ; Archakov, Alexander ; Ponomarenko, Elena ; Lisitsa, Andrey ; Lichti, Cheryl F. ; Mostovenko, Ekaterina ; Kroes, Roger A. ; Rezeli, Melinda ; Végvári, Ákos ; Fehniger, Thomas E. ; Bischoff, Rainer ; Vizcaíno, Juan Antonio ; Deutsch, Eric W. ; Lane, Lydie ; Nilsson, Carol L. ; Marko-Varga, György ; Omenn, Gilbert S. ; Jeong, Seul Ki ; Lim, Jong Sun ; Paik, Young Ki ; Hancock, William S. / Quest for missing proteins : Update 2015 on chromosome-centric human proteome project. In: Journal of Proteome Research. 2015 ; Vol. 14, No. 9. pp. 3415-3431.
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