View a presentation about HUPO's mission and its initiatives

HUPO:
THE HUMAN
PROTEOME
O
ORGANIZATION
Bruno Domon
Membership Committee Chair, HUPO
Congreso Biotecnología Habana 2012, Havana, Cuba,
March 6, 2012

HUPO: Mission
HPP will
The
deliver
Human
a
Proteome
comprehensive
Organization
map
(HUPO)
of the
represents
human
and
proteins in
their biological
promotes proteomics
context.
through international cooperation and
collaborations by fostering collaboration for the development
HPP will
of
provide
new technologies,
tools for
techniques,
the scientific
training,
community
and ethical
that will
allow each guidelines,
scientist in order
to design to better experiments understand human in a
disease better
and
way, as the
Human
other
Genome
aspects
Project
of human
did.
well-being. and by supporting related
research into plants, livestock and pathogens.
HPP will inspire, beyond the scientific community, other
stakeholders for diagnosis, prevention, therapy and cure of
diseases and improved health worldwide.

HUPO: Structure
HPP will The deliver Council a comprehensive is the governing body map of HUPO. of the It human meets proteins in
their biological annually and context. implements HUPO functions throughout the
year; its 48 members are equally distributed among
HPP will Europe/Africa, provide tools the for Americas the scientific and Asia/Oceana. community The Executive that will
allow each Committee scientist confers to design monthly experiments and oversees day-to-day
in a better way, as the
Human Genome activities. Committees Project did. and Initiatives involve many members
HPP will and engage in fulfilling specific scientific and practical goals
of inspire, HUPO.
beyond the scientific community, other
stakeholders for diagnosis, prevention, therapy and cure of
diseases and improved health worldwide.

HUPO: Goals
•Represent and promote proteomics: international cooperation/collaboration
• HPP Foster will development: deliver a new comprehensive technologies, techniques map of , bioinformatics, the human proteins training in
• their Play a biological leading role context. in:
1.definition of protein location/functions in human health/disease
HPP 2. will development provide of tools common for and the specific scientific standards community for peptide/protein that will
Goals: HUPO
allow characterization each scientist of human/model to design experiments organism specimens; in a data better evaluation way, as the
Human storageGenome Project did.
3.the creation of country-based ethical and legal policy for large-scale
HPP proteomics will inspire, projects.
beyond the scientific community, other
• stakeholders Support large-scale for diagnosis, proteomics projects prevention, mechanistic therapy understanding cure of
diseases fundamental and improved biological processes health worldwide.
• Coordinate/enable communication with funding agencies, industry

HUPO Committees
HUPO Committees: carry out HUPO objectives; worldwide membership
HPP will deliver a comprehensive map of the human proteins in
their biological HUPO Initiatives context. Committee
HUPO Industrial Advisory Board
Nomination & Elections Committee
New Technology & Resources Committee
Education and Training Committee
Ethics Committee
Meetings Committee
Membership Committee
Awards Committee
Finance Committee
Publications Committee
HPP will provide tools for the scientific community that will
allow each scientist to design experiments in a better way, as the
Human Genome Project did.
HPP will inspire, beyond the scientific community, other
stakeholders for diagnosis, prevention, therapy and cure of
diseases and improved health worldwide.

HUPO Initiatives
HUPO Initiatives: participants from many countries
HPP will deliver a comprehensive map of the human proteins in
Human Proteome Project (HPP)
their biological context.
Plasma Proteome Project (PPP)
Human Liver Proteome Project (HLPP)
Human Brain Proteome Project (HBPP)
Human Antibody Initiative (HAI)
Proteomic Standards Initiative (PSI)
Human Disease Glycomics/Proteome Initiative (HGPI)
Kidney and Urine Initiative (HKUPP)
Mouse Models of Human Disease (MMHD)
HUPO Cardiovascular Initiative (HUPO CVI)
Proteome Biology of Stem Cells Initiative
Disease Biomarkers Initiatives (DBI)
Initiative on Model Organism Proteomes (iMOP)
HPP will provide tools for the scientific community that will
allow Proteomic each Standards scientist Initiative to (PSI) design experiments in a better way, as the
Human Genome Project did.
HPP will inspire, beyond the scientific community, other
stakeholders for diagnosis, prevention, therapy and cure of
diseases and improved health worldwide.

New Initiatives
HPP will deliver a comprehensive map of the human proteins in
their biological HUPO Criteria context. for Starting New Initiatives:
Endorsement by HUPO of a new Initiative requires an international
HPP will provide collaboration---not tools for the a project scientific dominated ifi community d by one laboratory that or will
allow each scientist even one to nation. design experiments in a better way, as the
The initiative organizers will propose or negotiate with the EC/IC who
Human Genome Project did.
would be appropriate cochairs, reflecting prominence in the
subfield and geography.
The endorsement requires a compelling research plan with deliverables,
milestones, and potential timelines.
HPP will inspire, beyond the scientific community, other
stakeholders for diagnosis, prevention, therapy and cure of
diseases and improved health worldwide.

National and regional proteomics groups

HUPO website, newsletter and journals
HPP
HUPO
will
Website:
deliver
www.hupo.org
a comprehensive map of the human proteins in
their biological context.
HUPOST: the quarterly newsletter of HUPO; download from HUPO website
HPP will provide tools for the scientific community that will
allow
HUPO
each
Journals:
scientist
cooperate
to design
with the
experiments
goals of HUPO
in a better way, as the
Human Genome
Molecular
Project
and Cellular
did.
Proteomics
Journal of Proteomics
HPP will inspire,
Journal beyond
of Clinical the
Proteomics
scientific community, other
stakeholders for diagnosis, prevention, therapy and cure of
diseases and improved health worldwide.

HUPO educational activities
HPP
Short
will
courses
deliver
at
a
HUPO
comprehensive
meetings
map of the human proteins in
their biological context.
Workshops
HPP will provide tools for the scientific community that will
allow
Support
each
for
scientist
regional
to
meetings
design experiments in a better way, as the
Human Genome Project did.
HPP will inspire beyond the scientific community other
HPP will inspire, beyond the scientific community, other
stakeholders for diagnosis, prevention, therapy and cure of
diseases and improved health worldwide.

HUPO awards
HUPO Distinguished i Achievement in Proteomic Sciences
HPP will deliver
2011: Amos
a comprehensive
Bairoch, Switzerland
map of the human proteins in
their biological context.
HUPO Discovery Award in Proteomic Sciences
HPP will provide
2011: Steve
tools
Carr,
for
USA
the scientific community that will
allow each scientist to design experiments in a better way, as the
Human
HUPO
Genome
Distinguished
Project
Service
did.
Award
2011: Fuchu He, China
HPP will inspire, beyond the scientific community, other
stakeholders HUPO Science for and diagnosis, Technology prevention, Award therapy and cure of
diseases and 2011: improved Alexander Markarov, health Germany worldwide.

HUPO annual meetings
HPP will HUPO deliver International a comprehensive Meetings
map of the human proteins in
• 2002 Versailles, France
their biological context.
• 2003 Montreal, Canada
• 2004 Beijing, China
HPP will • 2005 provide Munich, tools Germany
for the scientific ifi community that will
allow each • 2006 scientist Long Beach, to USAdesign experiments in a better way, as the
Human • Genome 2007 Seoul, Korea Project did.
• 2008 Amsterdam, The Netherlands
• 2009 Toronto, Canada
• 2010 Sydney, Australia
• 2011 Geneva, Switzerland
• 2012 Boston, USA September 9-13
• 2013 Yokohama, Japan September 14-18
• 2014 Madrid, Spain October 5-8HUPO 11th Annual World
HPP will inspire, beyond the scientific community, other
stakeholders for diagnosis, prevention, therapy and cure of
diseases and improved health worldwide.

Human Proteome Project (HPP): Mission
HPP will deliver a comprehensive map of the human proteins in
their biological context.
HPP will provide tools for the scientific community that will
allow each scientist to design experiments in a better way, as the
Human Genome Project did.
HPP will inspire beyond the scientific community other
HPP will inspire, beyond the scientific community, other
stakeholders for diagnosis, prevention, therapy and cure of
diseases and improved health worldwide.

HPP: Essential elements
• mass-spectrometry-based proteomics for protein
signatures
• antibody-based proteomics for protein expression/localization
• data format and interconnected databases
• HPP pilot projects
www.thehpp.org

Creation of the HPP Working Group
• Creation of an international working ggroup for a “Human Proteome
Project” (HPP) follows decision of HUPO EC in October 2009
• Mandate voiced by the international scientific community, major
scientific journals, industry representatives and funding agencies from
around the world.
• Working Group for the huge undertaking built on foundation of major
g p g g j
progress in mass spectrometry, protein capture knowledge base and
open sharing of proteome data sets

HPP: Working Group

Huntington: 1 st
disease mapped
(1983)

Human Proteome Project: Objectives
• To map the human proteins (gene by gene)
• Molecular isoforms (including PTMs)
• Cellular, tissue, fluid and organ expression
• Protein quantification in biological samples
• To annotate the human proteins in their biological
• To annotate the human proteins in their biological
context:
• Interaction networks
• Comparison of samples (normal/diseased)
• Integration of data (genomics, clinical, etc.)

Human Proteome Project: Organization
HPP
General Assembly
HPP EC
SSAB
Chromosome-centric HPP
C-HPP
EC / PI Council
Biology/Disease HPP
B/D-HPP
EC / PI Council
Ab
Committee
KB
Committee
MS
Committee
Three Resource Pillars

Integration of human proteome information and . resources
Disease or
Biology
di
driven
projects
MS
KB
Abs
“Adopt-a-
Adopt a
chromosome”
groups

Human Proteome Project: Implementation
• Chromosome‐ and Disease‐based projects
• Collection of data for the full set of proteins of the chromosome
• Cross‐analyses of data for these proteins
• In‐depth annotation of these proteins
• Unknown/poorly known proteins as specific targets
• Relationships of specific proteins and PTMs to diseases
• Use all available/Develop technology platforms:
• Mass spectrometry
• Antibodies and protein capture reagents
• Algorithms for cross‐analyses

HPP launch in Sydney, September 2010

HPP launch in Sydney, September 2010

MS‐based HPP: Current developments and
next phase for the MS pillar
Ruedi Aebersold

HUPO 2010
Significant advance was achieved towards:
• Completion of reference spectra database for all
yeast proteins
• Completion of reference spectra database tb for all
*Uniprot) human proteins
• New technology to use the maps for quantitative
proteomic measurement

Human proteome SRM coverage

Distribution of Peptide/Protein SRM/MRM coverage
by chromosome (August 2010)

Next phases of MS pillar
• Make data from first phase publicly accessible
• Extend SRM library approach
• ‐ PTMs
• ‐ SNPs
• Generate database for registering SRM data
• Extend SRM resources to other species
• Create additional resources at Uniprot level
• ‐ GFP libraries
• ‐ Isotopic reference molecules
• Create links to antibody and informatics pillars

Contribution to the HPP by
antibody‐based proteomics
Mathias Uhlen

Knowledge‐based resource (normal profiles)
For each protein:
All data available to the public
All data available to the public
(with no IPR restrictions)

Knowledge‐based resource (disease profiles)
For each protein:
• Disease specific projects
• Investigator‐driven
• Possible to seek IPR‐protection

Physical resources
• All resources available to the public (with no IPR restrictions titi
• Decentralized resource with international coordination
• Academic and commercial partnerships
p

Long term antibody objectives of HPP (2020)

Five‐year antibody objectives of HPP (2015)

Database and knowledge resources
Building on present achievements
Amos Bairoch

HPP Knowledge resources: Main points

Existing resources (1/2)

Existing resources (2/2)

New resource!
now includes

The HPP portal
• A web portal is being developed as the focal point of HPP in terms of
publicizing the project, its goals and its results
• It will be populated by appropriate documents, time lines and links to the
participating p laboratories, funding agencies and proteomic resources and
initiatives.
• It will provide deep links to the data and knowledge resources described in
previous slides.
• It will also provide access to proteomics identification and analysis tools.
• To engage the participation of the broad scientific community, the design
and development of the portal are driven by user requirements.
http://www.thehpp.org

Cross‐analysis of HUPO Initiative data collections
Eric Deutsch, Terry Farrah, Laura Beretta
Tadashi Yamamoto, Gilbert Omenn

Comparing 4 human data collections

Total counts and global FDRs in the 4 atlases

201 Proteins common to all atlases
(excluding keratins and immunoglobulins)

Proteins unique to each atlas

Collective analysis in PeptideAtlas

Chromosome‐based proteome survey
Young‐Ki Paik
On behalf of 9 chromosome‐based HPP working groups

Big picture of HPP

Strategy of Chr‐based HPP working group
(e.g., Chr13)

Status in May 2010

Selected chromosomes…..

Still available……

more help needs to be found…
St. Petersburg, June 2010

Key questions (1/4)

Key questions (2/4)

Key questions (3/4)

Key questions (4/4)

Communication with the public is key to gaining support.

HPP progress in 2011
‐Creation of the HPP International Consortium
‐Establishment of national/regional HPP consortia
‐Establishment/Implementation/ p of means for building guidelines for
MS and Ab based human proteomics fitting standards for a Human
proteome Knowledge Base
‐Establishment/Implementation of the guidelines for the
chromosome‐based consortium
‐Efforts to make the HPP more visible, associate with major scientific
international programs dealing with human biology/medicine.
‐Launch of Web Portal

Special Acknowledgements
Ruedi Aebersold
Catherine E Costello
Pierre Legrain
Gil Omenn
Yong-Ki Paik
Matthias Uhlen

Paik