Quest for Missing Proteins: Update 2015 on Chromosome-Centric Human Proteome Project

Péter Horvatovich; Emma Lundberg; Yu-Ju Chen; Ting-Yi Sung; Fuchu He; Edouard Nice; Robert Goode; Simon Yu; Shoba Ranganathan; Mark Baker; Roberto Domont; Erika Valesquez; Dong Li; Siqi Liu; Quanhui Wang; Qing-Yu He; Rajasree Menon; Yuangfang Guan; Fernando Corrales; Victor Segura; Ignacio Casal; Alberto Pascual-Montano; Juan Pablo Albar; Manuel Fuentes; Maria Gonzalez-Gonzalez; Paula Diez; Nieves Ibarolla; Rosa Degano; Yassane Mohammed; Christoph Borchers; Andrea Urbani; Alessio Soggiu; Tadashi Yamamoto; Alexander Archakov; Elena Ponomarenko; Andrey Lisitsa; Cheryl Lichti; Ekaterina Mostovenko; Roger Kroes; Melinda Rezeli; Ákos Végvári; Thomas Fehniger; Rainer Bischoff; Juan Antonio Vizcaíno; Eric Deutsch; Lydie Lane; Carol Nilsson; György Marko-Varga; Gilbert Omenn; Seul-Ki Jeong; Jin-Young Cho; Young-Ki Paik; William Hancock

doi:10.1021/pr5013009

Quest for Missing Proteins: Update 2015 on Chromosome-Centric Human Proteome Project

Péter Horvatovich, Emma Lundberg, Yu-Ju Chen, Ting-Yi Sung, Fuchu He, Edouard Nice, Robert Goode, Simon Yu, Shoba Ranganathan, Mark Baker, Roberto Domont, Erika Valesquez, Dong Li, Siqi Liu, Quanhui Wang, Qing-Yu He, Rajasree Menon, Yuangfang Guan, Fernando Corrales, Victor SeguraIgnacio Casal, Alberto Pascual-Montano, Juan Pablo Albar, Manuel Fuentes, Maria Gonzalez-Gonzalez, Paula Diez, Nieves Ibarolla, Rosa Degano, Yassane Mohammed, Christoph Borchers, Andrea Urbani, Alessio Soggiu, Tadashi Yamamoto, Alexander Archakov, Elena Ponomarenko, Andrey Lisitsa, Cheryl Lichti, Ekaterina Mostovenko, Roger Kroes, Melinda Rezeli, Ákos Végvári, Thomas Fehniger, Rainer Bischoff, Juan Antonio Vizcaíno, Eric Deutsch, Lydie Lane, Carol Nilsson, György Marko-Varga, Gilbert Omenn, Seul-Ki Jeong, Jin-Young Cho, Young-Ki Paik, William Hancock

Research output: Contribution to journal › Article › peer-review

Abstract

This paper summarizes the recent activities of the Chromosome-Centric Human Proteome Project (CHPP)
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 key
approaches and their roles in the project. We present new analytical technologies that improve the
chemical space and lower detection limits coupled with 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 contents have 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
Pages (from-to)	3415-3431
Journal	Journal of Proteome Research
Volume	14
Issue number	9
DOIs	https://doi.org/10.1021/pr5013009
Publication status	Published - 2015

Subject classification (UKÄ)

Bioinformatics and Computational Biology

Free keywords

missing proteins
chromosome centric human proteome project
LC-MS
antibody enrichment
proteomics
bioinformatics

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10.1021/pr5013009

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Horvatovich, P., Lundberg, E., Chen, Y.-J., Sung, T.-Y., He, F., Nice, E., Goode, R., Yu, S., Ranganathan, S., Baker, M., Domont, R., Valesquez, E., Li, D., Liu, S., Wang, Q., He, Q.-Y., Menon, R., Guan, Y., Corrales, F., ... Hancock, W. (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

@article{8867145d7a114e6682745a31aaf0bb89,

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 (CHPP) 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{\textquoteright}s activities; therefore, we have summarized some of key approaches and their roles in the project. We present new analytical technologies that improve the chemical space and lower detection limits coupled with 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{\textquoteright}s contents have 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 = "missing proteins, chromosome centric human proteome project, LC-MS, antibody enrichment, proteomics, bioinformatics",

author = "P{\'e}ter Horvatovich and Emma Lundberg and Yu-Ju Chen and Ting-Yi Sung and Fuchu He and Edouard Nice and Robert Goode and Simon Yu and Shoba Ranganathan and Mark Baker and Roberto Domont and Erika Valesquez and Dong Li and Siqi Liu and Quanhui Wang and Qing-Yu He and Rajasree Menon and Yuangfang Guan and Fernando Corrales and Victor Segura and Ignacio Casal and Alberto Pascual-Montano and Albar, {Juan Pablo} and Manuel Fuentes and Maria Gonzalez-Gonzalez and Paula Diez and Nieves Ibarolla and Rosa Degano and Yassane Mohammed and Christoph Borchers and Andrea Urbani and Alessio Soggiu and Tadashi Yamamoto and Alexander Archakov and Elena Ponomarenko and Andrey Lisitsa and Cheryl Lichti and Ekaterina Mostovenko and Roger Kroes and Melinda Rezeli and {\'A}kos V{\'e}gv{\'a}ri and Thomas Fehniger and Rainer Bischoff and Vizca{\'i}no, {Juan Antonio} and Eric Deutsch and Lydie Lane and Carol Nilsson and Gy{\"o}rgy Marko-Varga and Gilbert Omenn and Seul-Ki Jeong and Jin-Young Cho and Young-Ki Paik and William Hancock",

year = "2015",

doi = "10.1021/pr5013009",

language = "English",

volume = "14",

pages = "3415--3431",

journal = "Journal of Proteome Research",

issn = "1535-3893",

publisher = "The American Chemical Society (ACS)",

number = "9",

}

Horvatovich, P, Lundberg, E, Chen, Y-J, Sung, T-Y, He, F, Nice, E, Goode, R, Yu, S, Ranganathan, S, Baker, M, Domont, R, Valesquez, E, Li, D, Liu, S, Wang, Q, He, Q-Y, Menon, R, Guan, Y, Corrales, F, Segura, V, Casal, I, Pascual-Montano, A, Albar, JP, Fuentes, M, Gonzalez-Gonzalez, M, Diez, P, Ibarolla, N, Degano, R, Mohammed, Y, Borchers, C, Urbani, A, Soggiu, A, Yamamoto, T, Archakov, A, Ponomarenko, E, Lisitsa, A, Lichti, C, Mostovenko, E, Kroes, R, Rezeli, M, Végvári, Á, Fehniger, T, Bischoff, R, Vizcaíno, JA, Deutsch, E, Lane, L, Nilsson, C, Marko-Varga, G, Omenn, G, Jeong, S-K, Cho, J-Y, Paik, Y-K & Hancock, W 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

TY - JOUR

T1 - Quest for Missing Proteins: Update 2015 on Chromosome-Centric Human Proteome Project

AU - Horvatovich, Péter

AU - Lundberg, Emma

AU - Chen, Yu-Ju

AU - Sung, Ting-Yi

AU - He, Fuchu

AU - Nice, Edouard

AU - Goode, Robert

AU - Yu, Simon

AU - Ranganathan, Shoba

AU - Baker, Mark

AU - Domont, Roberto

AU - Valesquez, Erika

AU - Li, Dong

AU - Liu, Siqi

AU - Wang, Quanhui

AU - He, Qing-Yu

AU - Menon, Rajasree

AU - Guan, Yuangfang

AU - Corrales, Fernando

AU - Segura, Victor

AU - Casal, Ignacio

AU - Pascual-Montano, Alberto

AU - Albar, Juan Pablo

AU - Fuentes, Manuel

AU - Gonzalez-Gonzalez, Maria

AU - Diez, Paula

AU - Ibarolla, Nieves

AU - Degano, Rosa

AU - Mohammed, Yassane

AU - Borchers, Christoph

AU - Urbani, Andrea

AU - Soggiu, Alessio

AU - Yamamoto, Tadashi

AU - Archakov, Alexander

AU - Ponomarenko, Elena

AU - Lisitsa, Andrey

AU - Lichti, Cheryl

AU - Mostovenko, Ekaterina

AU - Kroes, Roger

AU - Rezeli, Melinda

AU - Végvári, Ákos

AU - Fehniger, Thomas

AU - Bischoff, Rainer

AU - Vizcaíno, Juan Antonio

AU - Deutsch, Eric

AU - Lane, Lydie

AU - Nilsson, Carol

AU - Marko-Varga, György

AU - Omenn, Gilbert

AU - Jeong, Seul-Ki

AU - Cho, Jin-Young

AU - Paik, Young-Ki

AU - Hancock, William

PY - 2015

Y1 - 2015

N2 - This paper summarizes the recent activities of the Chromosome-Centric Human Proteome Project (CHPP) 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 key approaches and their roles in the project. We present new analytical technologies that improve the chemical space and lower detection limits coupled with 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 contents have 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.

AB - This paper summarizes the recent activities of the Chromosome-Centric Human Proteome Project (CHPP) 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 key approaches and their roles in the project. We present new analytical technologies that improve the chemical space and lower detection limits coupled with 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 contents have 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.

KW - missing proteins

KW - chromosome centric human proteome project

KW - LC-MS

KW - antibody enrichment

KW - proteomics

KW - bioinformatics

U2 - 10.1021/pr5013009

DO - 10.1021/pr5013009

M3 - Article

C2 - 26076068

SN - 1535-3893

VL - 14

SP - 3415

EP - 3431

JO - Journal of Proteome Research

JF - Journal of Proteome Research

IS - 9

ER -

Quest for Missing Proteins: Update 2015 on Chromosome-Centric Human Proteome Project

Abstract

Subject classification (UKÄ)

Free keywords

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