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

被引：51

作者：

Horvatovich, Peter ^{[1
]}

Lundberg, Emma K. ^{[2
]}

Chen, Yu-Ju ^{[3
]}

Sung, Ting-Yi ^{[4
]}

He, Fuchu ^{[5
]}

Nice, Edouard C. ^{[6
]}

Goode, Robert J. ^{[6
]}

Yu, Simon ^{[6
]}

Ranganathan, Shoba ^{[7
,8
]}

Baker, Mark S. ^{[9
]}

Domont, Gilberto B. ^{[10
]}

Velasquez, Erika ^{[10
]}

Li, Dong ^{[5
]}

Liu, Siqi ^{[11
,12
,45
]}

Wang, Quanhui ^{[11
,12
]}

He, Qing-Yu ^{[13
]}

Menon, Rajasree ^{[14
]}

Guan, Yuanfang ^{[15
,16
]}

Corrales, Fernando J. ^{[17
,18
]}

Segura, Victor ^{[17
,18
]}

Casal, J. Ignacio ^{[19
]}

Pascual-Montano, Alberto ^{[20
]}

Albar, Juan P. ^{[20
]}

Fuentes, Manuel ^{[21
,22
]}

Gonzalez-Gonzalez, Maria ^{[21
,22
]}

Diez, Paula ^{[21
,22
]}

Ibarrola, Nieves ^{[21
,22
]}

Degano, Rosa M. ^{[21
,22
]}

Mohammed, Yassene ^{[23
,24
]}

Borchers, Christoph H. ^{[23
]}

Urbani, Andrea ^{[25
,26
]}

Soggiu, Alessio ^{[27
]}

Yamamoto, Tadashi ^{[28
]}

Salekdeh, Ghasem Hosseini ^{[29
,30
]}

Archakov, Alexander ^{[31
]}

Ponomarenko, Elena ^{[31
]}

Lisitsa, Andrey ^{[31
]}

Lichti, Cheryl F. ^{[32
]}

Mostovenko, Ekaterina ^{[32
]}

Kroes, Roger A. ^{[33
]}

Rezeli, Melinda ^{[34
]}

Vegvari, Akos ^{[34
]}

Fehniger, Thomas E. ^{[34
]}

Bischoff, Rainer ^{[1
]}

Vizcaino, Juan Antonio ^{[35
]}

Deutsch, Eric W. ^{[36
]}

Lane, Lydie ^{[37
,38
]}

Nilsson, Carol L. ^{[32
]}

Marko-Varga, Gyorgy ^{[34
]}

Omenn, Gilbert S. ^{[39
,40
,41
]}

机构：

[1] Univ Groningen, Dept Pharm, Analyt Biochem, NL-9713 AV Groningen, Netherlands

[2] KTH Royal Inst Technol, Sci Life Lab, SE-17121 Stockholm, Sweden

[3] Acad Sinica, Inst Chem, Taipei 115, Taiwan

[4] Acad Sinica, Inst Informat Sci, Taipei 115, Taiwan

[5] Beijing Inst Radiat Med, Beijing Proteome Res Ctr, State Key Lab Prote, Beijing 100850, Peoples R China

[6] Monash Univ, Dept Biochem & Mol Biol, Clayton, Vic 3800, Australia

[7] Macquarie Univ, Dept Chem & Biomol Sci, Sydney, NSW 2109, Australia

[8] Macquarie Univ, ARC Ctr Excellence Bioinformat, Sydney, NSW 2109, Australia

[9] Macquarie Univ, Australian Sch Adv Med, Sydney, NSW 2109, Australia

[10] Univ Fed Rio de Janeiro, Inst Chem, Prote Unit, BR-21941909 Rio De Janeiro, RJ, Brazil

[11] Beijing Inst Genom, Beijing 100101, Peoples R China

[12] BGI Shenzhen, Beijing 100101, Peoples R China

[13] Jinan Univ, Coll Life Sci & Technol, Guangdong Higher Educ Inst, Key Lab Funct Prot Res, Guangzhou 510632, Guangdong, Peoples R China

[14] Univ Michigan, Dept Computat Med & Bioinformat, Ann Arbor, MI 48109 USA

[15] Univ Michigan, Dept Computat Med & Bioinformat, Ann Arbor, MI 48109 USA

[16] Univ Michigan, Dept Comp Sci, Ann Arbor, MI 48109 USA

[17] Univ Navarra, ProteoRed ISCIII, Spanish Consortium CHPP Chr 16, CIMA,Biomol & Bioinformat Resources PRB2, Pamplona 31008, Spain

[18] Univ Navarra, CIMA, Chr16 SpHPP Consortium, Pamplona 31008, Spain

[19] CSIC, CIB, Dept Cellular & Mol Med, E-28040 Madrid, Spain

[20] CSIC, CNB, E-28049 Madrid, Spain

[21] Univ Salamanca, CSIC, IBSAL, Ctr Canc Res,Prote Unit, Salamanca 37007, Spain

[22] Univ Salamanca, CSIC, IBSAL, Ctr Canc Res,Gen Serv Cytometry,Dept Med, Salamanca 37007, Spain

[23] Univ Victoria, Genome British Columbia Prote Ctr, Victoria, BC V8Z 7X8, Canada

[24] Leiden Univ, Med Ctr, Ctr Prote & Metabol, NL-2333 ZA Leiden, Netherlands

[25] Fdn Santa Lucia, Prote & Metabon Lab, Rome, Italy

[26] Univ Roma Tor Vergata, Dept Expt Med & Surg, Rome, Italy

[27] Univ Milan, Dept Vet Sci & Publ Hlth DIVET, I-20133 Milan, Italy

[28] Niigata Univ, Grad Sch Med & Dent Sci, Inst Nephrol, Niigata, Japan

[29] ACECR, Royan Inst Stem Cell Biol & Technol, Cell Sci Res Ctr, Dept Mol Syst Biol, Tehran, Iran

[30] Agr Biotechnol Res Inst Iran, Dept Syst Biol, Karaj, Iran

[31] Orechovich Inst Biomed Chem, Moscow, Russia

[32] Univ Texas Med Branch, Dept Pharmacol & Toxicol, Galveston, TX 77555 USA

[33] Northwestern Univ, Dept Biomed Engn, Falk Ctr Mol Therapeut, Evanston, IL 60201 USA

[34] Lund Univ, Dept Biomed Engn, Clin Prot Sci & Imaging, S-22184 Lund, Sweden

[35] EMBL EBI, Cambridge CB10 1SD, England

[36] Inst Syst Biol, Seattle, WA 98109 USA

[37] SIB Swiss Inst Bioinformat, Geneva, Switzerland

[38] Univ Geneva, Fac Med, Dept Human Prot Sci, Geneva, Switzerland

[39] Univ Michigan, Dept Computat Med & Bioinformat, Ann Arbor, MI 48109 USA

[40] Univ Michigan, Dept Human Genet, Ann Arbor, MI 48109 USA

[41] Univ Michigan, Sch Publ Hlth, Ann Arbor, MI 48109 USA

[42] Yonsei Univ, Yonsei Proteome Res Ctr, Coll Life Sci & Technol, Dept Integrated Omics Biomed Sci, Seoul 120749, South Korea

[43] Yonsei Univ, Yonsei Proteome Res Ctr, Coll Life Sci & Technol, Dept Biochem, Seoul 120749, South Korea

[44] Northeastern Univ, Barnett Inst Chem & Biol Anal, Boston, MA 02115 USA

[45] BGI Shenzhen, Shenzhen 518083, Peoples R China

来源：

JOURNAL OF PROTEOME RESEARCH | 2015年 / 14卷 / 09期

基金：

英国生物技术与生命科学研究理事会;

关键词：

missing proteins; Chromosome-Centric Human Proteome Project; LC-MS; antibody enrichment; proteomics; bioinformatics; POSTTRANSLATIONAL MODIFICATIONS; FUNCTIONAL ANNOTATION; INTERNATIONAL-SOCIETY; STATISTICAL-MODEL; ELECTRON-TRANSFER; GENE-EXPRESSION; DATA SETS; DATABASE; TRANSCRIPTOME; PEPTIDES;

D O I：

10.1021/pr5013009

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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 Wild (http://c-hpp.webhosting.rug.nl/) and in the Supporting Information.

引用

页码：3415 / 3431

页数：17

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