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 Segura; J. 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

doi:10.1021/pr5013009

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

Pharmacology & Toxicology

Research output: Contribution to journal › Review article › peer-review

52 Scopus citations

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 language	English (US)
Pages (from-to)	3415-3431
Number of pages	17
Journal	Journal of Proteome Research
Volume	14
Issue number	9
DOIs	https://doi.org/10.1021/pr5013009
State	Published - Sep 4 2015

Keywords

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

ASJC Scopus subject areas

General Chemistry
Biochemistry

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10.1021/pr5013009

Cite this

Horvatovich, P., Lundberg, E. K., Chen, Y. J., Sung, T. Y., He, F., Nice, E. C., Goode, R. J., Yu, S., Ranganathan, S., Baker, M. S., Domont, G. B., Velasquez, E., Li, D., Liu, S., Wang, Q., He, Q. Y., Menon, R., Guan, Y., Corrales, F. J., ... 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

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

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title = "Quest for missing proteins: Update 2015 on chromosome-centric human proteome project",

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.",

keywords = "Chromosome-Centric Human Proteome Project, LC-MS, antibody enrichment, bioinformatics, missing proteins, proteomics",

author = "P{\'e}ter Horvatovich and Lundberg, {Emma K.} and Chen, {Yu Ju} and Sung, {Ting Yi} and Fuchu He and Nice, {Edouard C.} and Goode, {Robert J.} and Simon Yu and Shoba Ranganathan and Baker, {Mark S.} and Domont, {Gilberto B.} and Erika Velasquez and Dong Li and Siqi Liu and Quanhui Wang and He, {Qing Yu} and Rajasree Menon and Yuanfang Guan and Corrales, {Fernando J.} and Victor Segura and Casal, {J. Ignacio} and Alberto Pascual-Montano and Albar, {Juan P.} and Manuel Fuentes and Maria Gonzalez-Gonzalez and Paula Diez and Nieves Ibarrola and Degano, {Rosa M.} and Yassene Mohammed and Borchers, {Christoph H.} and Andrea Urbani and Alessio Soggiu and Tadashi Yamamoto and Salekdeh, {Ghasem Hosseini} and Alexander Archakov and Elena Ponomarenko and Andrey Lisitsa and Lichti, {Cheryl F.} and Ekaterina Mostovenko and Kroes, {Roger A.} and Melinda Rezeli and {\'A}kos V{\'e}gv{\'a}ri and Fehniger, {Thomas E.} and Rainer Bischoff and Vizca{\'i}no, {Juan Antonio} and Deutsch, {Eric W.} and Lydie Lane and Nilsson, {Carol L.} and Gy{\"o}rgy Marko-Varga and Omenn, {Gilbert S.} and Jeong, {Seul Ki} and Lim, {Jong Sun} and Paik, {Young Ki} and Hancock, {William S.}",

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AU - He, Fuchu

AU - Nice, Edouard C.

AU - Goode, Robert J.

AU - Yu, Simon

AU - Ranganathan, Shoba

AU - Baker, Mark S.

AU - Domont, Gilberto B.

AU - Velasquez, Erika

AU - Li, Dong

AU - Liu, Siqi

AU - Wang, Quanhui

AU - He, Qing Yu

AU - Menon, Rajasree

AU - Guan, Yuanfang

AU - Corrales, Fernando J.

AU - Segura, Victor

AU - Casal, J. Ignacio

AU - Pascual-Montano, Alberto

AU - Albar, Juan P.

AU - Fuentes, Manuel

AU - Gonzalez-Gonzalez, Maria

AU - Diez, Paula

AU - Ibarrola, Nieves

AU - Degano, Rosa M.

AU - Mohammed, Yassene

AU - Borchers, Christoph H.

AU - Urbani, Andrea

AU - Soggiu, Alessio

AU - Yamamoto, Tadashi

AU - Salekdeh, Ghasem Hosseini

AU - Archakov, Alexander

AU - Ponomarenko, Elena

AU - Lisitsa, Andrey

AU - Lichti, Cheryl F.

AU - Mostovenko, Ekaterina

AU - Kroes, Roger A.

AU - Rezeli, Melinda

AU - Végvári, Ákos

AU - Fehniger, Thomas E.

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AU - Vizcaíno, Juan Antonio

AU - Deutsch, Eric W.

AU - Lane, Lydie

AU - Nilsson, Carol L.

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AU - Paik, Young Ki

AU - Hancock, William S.

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

Abstract

Keywords

ASJC Scopus subject areas

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