Group composition

1.1. Chromosome 1

Participating country(ies): China
Head: Ping Xu
Members:
Fuchu He

Participating country(ies): Switzerland
Head: Lydie Lane
Members:
Amos Bairoch (SIB, PI of neXtProt)
Frédérique Lisacek (SIB, glycomics, bioinformatics)
Paula Duek (SIB/University of Geneva)
Alain Gateau (SIB/University of Geneva)
Thibault Robin (SIB/University of Geneva)
Markus Mueller (SIB Lausanne)
Charlotte Macron (Nestlé Institute of Health Sciences)
Antonio Nunez-Galindo (Nestlé Institute of Health Sciences)
Loïc Dayon (Nestlé Institute of Health Sciences)
Camille Mary (University of Geneva)

1.3. Chromosome 3

Participating country(ies): Japan, Sweden, Singapore
Head: Takeshi Kawamura, Associate Professor, Proteomics Laboratory, Isotope Science Center, The University of Tokyo, Tokyo, Japan
Members:

Co-PI: Toshihide Nishimura, Professor, Department of Translational Medicine Informatics, St. Marianna University School of Medicine, Kanagawa, Japan
Co-PI: Hiromasa Tojo, Associate Professor, Department of Biophysics and Biochemistry, Osaka University; Graduate School of Medicine, Osaka, Japan (Current address: Visiting Professor, Translational Medicine Informatics, St. Marianna University School of Medicine, Kanagawa, Japan)
International Collaborative Team Member: György Marko-Varga, Professor, Center of Excellence in Biological and Medical Mass Spectrometry, Lund University, Lund, Sweden
International Collaborative Team Member: Dr. Siu Kwan Sze, Assistant Professor, Director of Proteomics Core of Bioscience Research Centre, Office: 03n-37, Singapore

1.4. Chromosome 4

Participating country(ies): Taiwan
Head: Yu-Ju Chen
Members:

Yu-Ju Chen/Yet-Ran Chen (Academia Sinica) - LC-MS/MS analysis and Proteomics
Wen-Lian Hsu/Ting-Yi Sung (Academia Sinica) - Bioinformatics
Shih-Feng Tsai (National Health Research Institute/National Yang-Ming University) - Genomics
Jau-Song Yu (Chang Gung University)
Pao-Chi Liao (National Cheng Kung University)
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1.5. Chromosome 5

Participating country(ies): Netherlands, Belgium
Head: Péter Horvatovich
Members:

Rainer Bischoff clinical proteomics, PTM analysis
Péter Horvatovich (bioinformatics, LC-MS analysis)
Peter Verhaert (top-down analysis, proteomics and LC-MS analysis)

1.6. Chromosome 6

Participating country(ies): USA\Canada\Qatar
Head: Robert Moritz - Institute for Systems Biology, USA
Co-Lead:Christopher Overall - U. British Columbia, Canada
Member:Frank Schmidt - Weill-Cornell, Qatar
Member:John Wilson - Protifi, USA
Member:Eric Deutsch - Institute for Systems Biology, USA

1.7. Chromosome 7

Participating country(ies): Australia, NewZealand
Head: Ed Nice
Members: Mark Baker
William S. Hancock,
Bill Jordan

1.8. Chromosome 8

Participating country(ies): China
Head: Gong Zhang, Jinan University
Members:

1.9. Chromosome 9

Participating country(ies): South-Korea
Head: Je-Yoel Cho
Members:

Soo-Youn Lee
Suk-Ki Cho
Byung-Gyu Kim
Jung-Mo Ahn
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1.10. Chromosome 10

Participating country(ies): USA
Head: Joshua Labaer
Members:

1.11. Chromosome 11

Participating country(ies): South Korean
Head: Jong Shin Yoo
Members: Young Mok Park: Human Brain Proteome Project Leader, Biological experiments
Kyung-Hoon Kwon : Bioinformatics
Jin Young Kim : LC-MS analysis

1.12. Chromosome 12

Participating country(ies): India, Singapore, Taiwan, Thailand
Head: Ravi Sirdeshmukh (India)
Members:

Maxey Chung (Singapore)
Yu-ju Chen (Taiwan)
Terence Poon (Hong Kong)

1.13. Chromosome 13

Participating country(ies): South Korea
Head: Min-Sik Kim
Members:

Keun Na (Functional study, C. elegans)
Ju-Wan Kim (LC-MS analysis)
Jin-Young Cho (Proteomics, LC-MS analysis)
Chae-Yeon Kim (Bioinformatics)
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1.14. Chromosome 14

Participating country(ies): France
Head: Charles Pineau
Members:

1.15. Chromosome 15

Participating country(ies): Brazil
Head: Gilberto B Domont
Members:
Paulo Costa Carvalho - Computational Proteomics
Magno Junqueira
Fabio Nogueira

1.16. Chromosome 16

Participating country(ies): Spain
Head: Fernando J Corrales
Members:

Concha Gil
Francisco J. Blanco

1.17. Chromosome 17

Participating country(ies): USA
Head: Gilbert S. Omenn
Members: Gilbert S. Omenn, Michael Snyder and Ronald C. Beavis, William S. Hancock (honorary member)

1.18. Chromosome 18

Participating country(ies): Russia
Principal Investigator: Alexander Archakov
co-PIs: Elena Ponomarenko (bioinformatics), Andrey Lisitsa (standardization)
Members:
Institute of Biomedical Chemistry (core facility), Moscow
Institute of Physical-Chemical Medicine of the FMBA, Moscow
Centre "Bioengineering", Moscow
Institute of Bioorganic Chemistry, Moscow
Institute of Molecular Biology, Moscow
Institute of Biomedical Problems, Moscow
International Tomography Center, Novosibirsk

Roadmap available at http://www.ibmc.msk.ru/content/intelligence/RHUPO_Roadmap.pdf
Key issues:

The size of the human proteome requires estimates of number of protein species (proteome width) and number of copies of the same protein molecules in a biosample (proteome depth).
Master proteome of a single chromosome is the results of the identification and measurement of all master proteins encoded by the selected chromosome and expressed in the selected type of biological material, there master protein is the primary translation of the coding sequence resembling at least one of the known protein forms, coded by the gene.
Complete human proteome in this context is the result of (1) constellation of master proteomes of different chromosomes and types of biological material and (2) data about modified (AS, SAP, PTM) protein species.
In case PTM and SAP can occur both in the proteins encoded by gene with canonical sequence and splice variants, the number of human protein species (proteome width) was estimated based on the NeXtProt (v2013) data as 1.8 million, which correspond to 2-DE based experimental estimations. Using the assumption that PTMs appear exclusively in sequences of master proteins, but not in splice variants, the width of the human proteome contains approximately 650 000 protein species. If all types of modifications (AS, SAP and PTM) are independent events, the potential proteome width is approximately 8.5 million.
One of the most sensitive SRM technology available detection with sensitivity limit of 10^-18 M for BSA standard, but additional sample treatment with irreversible binding onto BrCN-Sepharose beads allowed a sensitivity of 10^–18 M to be achieved (the proteins CYP102 and BSA was used for calibration), which corresponds to one protein copy/µl of blood plasma.
Operating within an ultra-low concentration range, it is convenient to refer to protein copies rather than concentrations because it allows comparison of results of transcriptomic and proteomic experiments.
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