A Guide to the C-HPP Activity in Yokohama
(August 5, 2013, final version)
Dear Colleagues,
As Yokohama congress approaches around the corner, we would like to make update on our workshop
schedules which have been finalized very recently (8/3/2013). Based on the recent communications between
the interesting groups and Jennifer Watson who is coordinating the HPP initiative program with Yokohama
team from the HUPO side, we came up with the final agenda as outlined below. Please make note of this
information on your traveling plans where appropriate.
Cheers!
Young-Ki, Bill and György
Co-Chairs of the C-HPP Consortium
1. Updated Schedule of the C-HPP workshops and HPP sessions (see Appendix 6, p11)
The C-HPP workshop schedule along with other programs is outlined below under the HPP initiative session.
●Saturday: Sept 14
PRE-CONGRESS HPP LEADERSHIP / COMMITTEE / PI MEETINGS
The following planning meetings for HPP leadership and PIs are scheduled in Yokohama.
SATURDAY, SEPTEMBER 14
9:00 - 9:45 am
HPP General Leadership Meeting
Room 311-312
HPP EC, SSAB, Pillar Chairs, B/D HPP, C-HPP Committees and All HPP
investigators involved in HPP
9:45 - 11:45 am
B/D HPP Group Break-out C-HPP Group Break-out*
Rm 311-312
Rm 313-314 (see Appendix 1, p5)
11:45 am - 12:45 pm
Lunch Break (lunch-on-your-own) C-HPP EC (TBA)
12:45 - 2:00 pm
HPP General Leadership Meeting
Room 311-312
All re-group for an update on the break-out meetings.
14:00 - 16:00 pm
Joint Meeting (C-HPP and B/D-HPP)**
"Consultations and Discussions for C-HPP and B/D-HPP investigators
with SSAB, resource pillars, and each other.
Room 311-312
*Agenda for the C-HPP Group Break-out at Rm 313-314 is listed in Appendix 1, p5. This will be used for sharing the
progress reported from several invited PIs who have missed a chance to introduce their works to the consortium due to
some reasons (e.g., leadership change, late participation etc).
Invited PIs to this session are; Lydie Lane for Chr 2, Joshua Labaer for Chr 10, Visith Thongboonkerd for Chr 12, Daniel
Figeys for Chr 21, Charles Lee and Akhileshi Pandey for Chr 22. However, if anyone wants to share some of progress made
during the past months, we always welcome him/her to this meeting.
1
**Note: A joint meeting between B/D-HPP and C-HPP at 14:00 - 16:00 pm. It was proposed at the July HPP EC meeting
that B/D-HPP and C-HPP co-chairs and their members get together to share their views on the cooperation for the
scientific matters (potential topics are: cancer, metabolic disease, disease biomarkers and others). It is anticipated that
some of SSAB members and key members of the HPP resource pillars would be available for this meeting. From the CHPP side, Gyorgy will lead the discussion session with help of Bill (Paik has another duty in Education session).
●Sunday through Wednesday (Sept 15-18)
SUN, SEPT 15
MON, SEPT 16
TUES, SEPT 17
WED, SEPT 18
8:15 - 9:30 am
8:15 - 9:30 am
8:15 - 9:30 am
8:15 - 9:30 am
Room 303-304
Exhibition Hall
Room 303-304
Room 318
C-HPP (Part 2) - Poster
Session
*C-HPP (Part 3) –
Bioinformatics
C-HPP (Part 1), jointly
with PSI/
ProteomeXchange
/KBpC
●Eric Deutsch (ISB, USA)
will present the PSI
efforts to develop
standardized data
formats and their
implementation
●Henning Hermjakob
(EBI, UK) will present
ProteomeXchange, that
simplifies and unifies
proteomics data
submission to PRIDE and
Peptide atlas
Agenda: Appendix 3 (p 7)
●Gyorgy will lead this
session. No abstract is
needed.
●Siqi Liu (BGI, China) will
present the survey results of
RNA-Seq service through
the C-HPP consortium and
give some update on the
RNA-Seq database which
can be useful for the
consortium members.
●Each team need to load
the poster no later than 5
pm, Sunday. In addition to
the C-HPP, Any papers
related to common
technology or resources
can be presented.
●Peter Horvatovich
(University of Groningen,
Netherlands) will present
recent progress in WiKi on
the C-HPP.
●Lydie Lane (SIB,
●Reports from the web
browsers (Rob Goode, Ping
Xu, Siqi Liu, Andrey
Lisita,and Seul-ki Jeong
Switzerland) will show
how human proteomics
data is handled in
neXtProt, and how it is
integrated with other
types of data
*C-HPP PIC Meeting
Topics: Std Metrics; 2014
workshop plan; MRM std,
JPR special issue
Agenda: Appendix 4
(page 8)
Wednesday, September
18
9:30 - 11:50 am
HPP Special Parallel
Session
Room 303-304
Featuring invited speaker
Opening Talk:Y. K. Paik
Keynote Speakers:
◎G. S. Omenn &
◎W. Hancock
Invited Speaker:
◎M. Y. White
●Updates from Protein atlas
and Monash antibody
initiative (Emma Lundberg
and Ed Nice)
●A panel composed of
the three speakers and
Bill Hancock
●Encode update (Kate
Rosenbloom and Mike
Snyder)
13:00-14:00, Rm TBA
C-HPP Wiki Workshop: Led by Peter Horvatovich
Agenda: Appendix 2 (page 6)
Bill Hancock will chair this session: A designated member
from each chromosome team will attend this meeting.
Wednesday, September
18
1:45 - 2:45 pm
HPP Plenary Session
Room 303-304
Featuring invited
speakers Jeremy
Nicholson and Heui-Soo
Kim
●Wiki workshop will be held at lunch time on Mon-Tues. Each team should send a delegate who can participate in this
two-day luncheon workshop. Agenda for all workshops is briefly outlined in p5-8.
●Special Note on the C-HPP Meeting
Poster session: György Marko-Varga will lead this session. In this session all PIs and their colleagues are
requested to bring their posters which should be hung on the poster board no later than 5 pm Sunday, Sept 15.
2
No abstract submission is necessary because most of the presenters may have submitted their manuscripts to
JPR. An additional instruction for grouping and organization for this session may be given further by György
later, if necessary.
●Duty assigned: Three co-chairs will share some workloads on the following sessions in Yokohama.
-Young-Ki -Paik: Overall administrative affairs, organization of the scientific programs and PIC meeting
-Bill Hancock: Bioinformatics sessions (Part I, 3), Liaise with HUPO (Activity Report at the Council)
-György Marko-Varga: Poster session (Part 2), Liaise with Yokohama Organizer for poster settings
●Election of the C-HPP Executive Committee Member: All C-HPP PIs are required to present and cast
votes on the election of EC member at large (term: September 2013 to August 2016) who takes over Charles
Lee’s seat (see below as described in the C-HPP Newsletter, June 11, 2013). We encourage you to send us
the names of nomination for this position by Sept 15. So far, we have received only one candidate name for
this seat.
Election: As discussed at the PIC meeting in Berlin, we are seeking nominations for individuals to replace Dr. Charles Lee,
whose term ends Sep 9, 2013. Once elected, she/he will serve as member-at-large (MAL) for the C-HPP EC. The
candidate will be an official member of PIC once elected. The term of this new MAL will be 3 years (Sep 10, 2013–Sep 9,
2016). The following procedure is proposed for this election:
●Sept 15, 2013: Closing nominations from PIC members
●Sept 16, 2013: Verification of his/her candidacy by the C-HPP EC
●Sept 18, 2013: Voting will take place during the PIC council meeting in Yokohama(6/11/2013, Newsletter)
2. C-HPP Activity Report to HUPO Council: As determined in the previous PIC meeting and also suggested
by HPP EC that C-HPP team is mandated to report their activity to HUPO council as well as SSAB members
for their invaluable inputs and advice.
The scientific annual report: Publication of papers that are relevant to the C-HPP is regarded as this type of
report and thus off-sets the obligation of report submission to C-HPP EC. We will formally submit the list of
papers with pdf files to SSAB which will also be shared with HPP EC. This will be done immediately after
Yokohama HUPO congress.
For those who have not published yet any scientific paper for their chromosome proteomics works, the
attached form (see Appendix 5, p9) which covers the period Sept 1, 2012 to August 31, 2013 will constitute
the annual report. Please submit it to HQ office at paikyk@yonsei.ac.kr by September 1st, 2013 for inclusion
in the council report. We thank the teams for their hard work and impressive achievements to date for the
C-HPP initiative and are proud to make this contribution to the scientific future of the HUPO organization.
If you have any question on this matter, please contact Young-Ki.
3. Dataset Submission through ProteomeXchange (update)
In St. Petersburg where the C-HPP scientific meeting was held, Juan-Pablo Albar presented his progress
report on chromosome 16 and agreed with Young-Ki and Gil on the suggestion that he and his colleagues
would prepare for a simple guideline and tutorial for submitting the C-HPP datasets to ProteomeXchange. After
a few round of discussion between the C-HPP leaders by email (Bill, Paik, Gil) and Juan-Pablo, he kindly
agreed to provide this manual to all C-HPP PIs. Once it is received, it will be uploaded at the web site (www.chpp.org) as a general instruction to the community.
In fact, as Gil mentioned in his earlier email, the HPP Executive Committee has emphasized the
importance of compliance with the HPP guidance for timely uploading of full datasets and sufficient metadata
for all papers to be published in the 2014 C-HPP special issue in JPR, even if in advance of such guidance
from the journals, given that the ProteomeXchange mechanism meets the needs and connects all the
individual data resources, specifically including PRIDE, PeptideAtlas, neXtProt, and GPMDB. SRM datasets
are to be submitted to PeptideAtlas at the Institute for Systems Biology, as stated in earlier guidance.
3
Juan Pablo suggested the pipeline of data submission (see the figure) which is based on the MIAPE
information extraction and storage in the ProteoRed Repository, followed by a data integration and a filtering
step
Here are some of his comments on this process which would be helpful for understanding what we
expect to see soon: -“The last step is the preparation of a ProteomeXchange bulk submission, including
MIAPE compliant PRIDE XML files, MIAPE human readable documents, peak lists, mzIdentML files and raw
files…all interrelated in a consistent way and ready to use in the ProteomeXchange submission tool (loading
the ProteomeXchange summary file and clicking next-next-next…). However, due to the high heterogeneity of
the available proteomics workflows we prefer to indicate a very concrete workflow which we have extensively
tested in the Spanish HPP consortium, consisting on the use of MGF or mzML files + MS metadata +
mzIdentML exported from a Mascot server. Any other pipeline will be incorporated as soon as we were sure
about all is going well.
We are planning to incorporate the use of X!Tandem as the search engine in the pipeline in the
following weeks. The complete pipeline is quite automatic, but anyway, we would like to create a HPP focused
tutorial for ProteomeXchange submissions using the ProteoRed MIAPE Extractor, in order to provide the more
comprehensive information for the potential users of the tool. We hope to provide a full and detailed description
of the whole wokflow submission process by the Yokohama meeting. Currently, we have a partial tutorial
available at www.proteored.org/MIAPEextractor but it is not updated. We will update along the next month.
(most of our bioinformatician team is currently on vacations).” (by Juan Pablo Albar).
4. The 8th C-HPP Workshop in 2014: We are currently working on this workshop which is more likely taking
place at the Samsung Conference Center in Seoul National University, March 26 (Wed), 2014 in conjunction
with KHUPO annual international meeting, if everything goes well (funding). Details on the agenda for this
workshop will be discussed and updated at the upcoming PIC meeting in Yokohama, Sept 18. Certainly, if an
opportunity would also be given at Thailand AOHUPO Congress (August 6-8, 2014 in Bangkok, Thailand), we
will make use of this slot as an additional discussion session before heading to Madrid Congress, Oct 5-8,
2014.
5. Follow Up Actions After the C-HPP Scientific Meeting in Russia (FEBS Congress): Alex and his
colleagues have recently hosted “Scientific Meeting of the C-HPP” in St. Petersburg, Russia from July 10 to 11.
The meeting was well attended where Gil, Juan Pablo Alba, Amos Bairoch, Christoph Borchers, Alex, Andrey,
Young-Ki and other colleagues had scientific presentations on the C-HPP as well as HPP. Before the C-HPP
session, Ruedi Aebersold presented a keynote lecture in the Proteomics session of the FEBS congress. This
was a great opportunity to show our activity to the European colleagues in FEBS congress.
Several items have been suggested in that meeting. For example, MRM standard for plasma, tissues and cell
samples for the community, update info on the standard metrics and more close cooperation between the CHPP and B/D-HPP. These items will be discussed at either Bioinformatics meeting or PIC meeting in
Yokohama. Gil will add more on this list when we are in Yokohama. In particular, we encourage you to commit
yourself to the Saturday 14 Sept, a day-long working meeting for C-HPP and B/D-HPP interactions.
We will count on all of you in Yokohama. See you soon!
Young-Ki, Bill and György
4
Appendix 1
Agenda for the C-HPP Group Break-out
Rm 313-4
Update progress on the C-HPP
We would like to invite the following PIs for their opportunity to present
Chair: Bill Hancock
1. Young-Ki Paik, Bill Hancock and György Marko-Varga, Co-Chairs of the C-HPP Consortium
Brief Report on the 1st year activity of the C-HPP consortium (2012/2013)
2. Lydie Lane (SIB, Switzerland): Progress in Chr 2 Project
3. Joshua Labaer (Arizona State Univ., USA): Progress in Chr 10 Project
4. Visith Thongboonkerd (Mahidol University , Bangkok, Thailand): Progress in Chr 12 Project
5. Daniel Figesys (Ottawa Univ., Canada): Progress in Chr 21 Project
6. Charles Lee (Harvard U., USA) and Akhleshi Pandey (Johns Hopkins Univ., USA): Progress
in Chr 22.
7. Additional Report from PIs
8. Free Discussion
5
Appendix 2
Agenda for the Wiki Workshop
Time: Monday Lunch Time
Venue: TBA
Agenda (Proposed)
This session is being planned for WiKi workshop for the C-HPP group by Peter Horvatovich
(University of Groningen; member of Chr 5 group) for. The proposed plans are as below.
Major topics to be proposed are:
1. Wiki writing skills and information management, overview on Wiki structure
2. Strategy for collection of news and report updates on the events and other activities of C-HPP
3. Information on research group resources, skills, research interests to enhance collaborations
between chromosome teams.
4. Publication of a monthly newsletter of C-HPP Wiki (http://c-hpp.webhosting.rug.nl/) giving overview
on the most important news, updates and announcements concerning C-HPP initiative.
5. Interaction with major public DBs and disseminate those updated info through the community
(GPMDB, NextProt)
6. Update on the missing protein list in a real time manner
7. Other topics (TBA)
Action Items: Each PI should designate someone who can participate in this workshop by Sept
1, 2013.
For more information, please contact Peter at p.l.horvatovich@rug.nl
6
Appendix 3
Agenda for C-HPP Bioinformatics (Part 3)
Date: Tuesday, September 17
Place: Room 303-304
Chair: Bill Hancock
In this session, the C-HPP consortium members from 25 countries will discuss general matters
related to protein database, updated status on the missing proteins, integration of both ENCODE and
Metabolomics data into the C-HPP scaffold.
Presentation by Speakers:

Siqi Liu (BGI, China) will present the survey results of RNA-Seq service through the C-HPP co
nsortium and give some update on the RNA-Seq database which can be useful for the consorti
um members.

Peter Horvatovich (University of Groningen, Netherlands) will present recent progress in WiKi
on the C-HPP.

Reports from the web browsers (Rob Goode, Ping Xu, Siqi Liu, Andrey Lisita,and Seul-ki Jeon
g

Updates from Protein atlas and Monash antibody initiative (Emma Lundberg and Ed Nice)

Encode update (Kate Rosenbloom and Mike Snyder)
Q&A

RNA Seq data acquisition and management

Wiki news management by each group

Web browsers-access statistics

mAb for validating missing proteins

Integration of ENCODE into the C-HPP dataset

AOB
7
Appendix 4
Agenda for PIC meeting
Time: Wednesday, 8:15 AM-9:30
Venue: Room 318
Chair: Young-Ki Paik,
Co-chair: Bill Hancock, György Marko-Varga
PIC Members Invited to This Meeting (as of August 1, 2013)
Fuchu He (Chr 1), Lydie Lane (Chr 2), Toshihide Nishimura (Chr 3), Yu Ju Chen (Chr 4), Rainer Bischoff (Chr
5), Paul Keown (Chr 6), Mark Baker (Chr 7), Pengyuan Yang (Chr 8), Je-Yoel Cho (Chr 9),
Joshua Labaer (Chr 10), Jong Shin Yoo (Chr 11), Visith Thongboonkerd (Chr 12), Young-Ki Paik (Chr 13),
Jérome Garin (Chr 14), Gilberto B Domont (Chr 15), Juan Pablo Albar (Chr 16), William S. Hancock (Chr 17),
Alexander Archakov (Chr 18), György Marko-Varga (Chr 19), Siqui Liu (Chr 20), Daniel Figeys (Chr 21),
Charles Lee and Akhileshi Pandey (Chr 22), Tadashi Yamamoto (Chr X), Ghasem Hosseini Salekdeh (Chr Y),
Andrea Urbani (Mit)
Additional Invitees: HPP EC, C-HPP EC, SSAB Members, Amos Bairoch, Emma Lundberg, Eric
Deutsch, Christoph Borchers and Associated members of each Chromosome team
Discussion Topics*
1. A New Policy to Recruit an Additional Chromosome Teams within the Consortium;
Evaluation system (spreadsheet)
2. Standard Metrics Updates: Comments by Amos, Emma, Gil, Bill, Eric and others.
3. MRM standard (presented by Christoph Borchers)
4. Update on the 2014 JPR special issue
5. 2014 C-HPP workshop plans
6. Election of the C-HPP EC member-at-large
7. AOB
(*order of the topics is subject to change depending on the priority)
8
Appendix 5
C-HPP Annual Report Form
(Period Covered: Year 1: Sept 1, 2012-August 31, 2012)
Project Name
Principal
Investigator (PI)
Co-PIs
Or
Co-workers
Chromosome-Centric Human Proteome Project (Chr 00)
Name:
Affiliation:
Name
Affiliation
Name
Affiliation
Name
Affiliation
Supporting
1
Grants
2
Contact Information
PI
Name
Assistant to PI
Name
Publications
Phone
E-mail
1. (sample) Liu S, et al., and Hancock WS. A chromosome-centric human proteome project (C-HPP) to
characterize the sets of proteins encoded in chromosome 17. J Proteome Res. 2013 Jan 4;12(1):45-57.
(any published
papers relevant to
the C-HPP during
the period of Sept
1-August 31, 2013)
Portal
Contents
Date
Data
Submission
Records
(sample)
Primary Aims
To map the entire proteins encoded in Chr 00 ….
To identify and characterize the missing proteins in Chr 00 which have not been well
characterized with respect to at least one of the following categories: MS evidence, biological
function and cellular location.
9
To …
Biological/Disease
Focus
1) Breast cancer
2) ERBB2 signaling pathway…
Research
(Sample) The work on chromosome 17 has focused on the identification of the missing
proteins in the context of chromosome parameters such as gene density and transcriptionally
active regions. The occurrence of alternative splice variants is also being explored as part of
the definition of the parts list. We are using data from ERBB2 driven colon cancers (breast,
(Abstracts or
colon and gastric) to identify processes for the integration of proteomics and transcriptomic
data. The data sets are also being explored for examples of the importance of co-location
List of
and co-expressed genes in which the corresponding proteins show evidence of biological
Accomplishment) significance such as with GO attributes, common tissue or subcellular location, involvement
in disease processes, protein interactions, expression in specific gene sets, or occurrence in
(up to 200 words) common pathways. The ERBB2 amplicon is a focus of this team as it shows an example of
amplification of a genomic region as part of the etiology of a driver oncogene.
Highlights
Remarks
(Suggestions etc.)
10
APPENDIX 6
HUMAN PROTEOME PROJECT - INITIATIVE SESSIONS
The Human Proteome Project (HPP) has grown to become a strong focus of HUPO activities. Most existing HUPO initiatives have
found a focus within the HPP. All congress attendees are invited to participate in the morning initiative sessions. These lively, smaller
sessions are an invaluable opportunity to connect with colleagues and contribute to the HPP.
At the conclusion of the congress two HPP-related sessions are scheduled where, in addition to invited speakers, the HPP Executive
Committee will report on progress and updates from the Sunday, Monday and Tuesday morning sessions.
See following pages for an overview of leadership meetings and initiatives sessions as well as detailed initiative session
descriptions.
MORE ABOUT THE HPP
An organizational chart for the Human Proteome Project showing the C-HPP, B/D-HPP, resource pillars, the HPP Executive Committee
(EC) and HPP Senior Scientific Advisory Board (SSAB). Please also visit www.thehpp.org and www.c-hpp.org for more information.
The teams for the chromosome-centric C-HPP and the biology and disease-driven B/D-HPP are shown here. Details about the
members of the teams and the activities of each can be found at www.thehpp.org and www.c-hpp.org.
The Journal of Proteome Research published progress updates from both the C-HPP and B/D HPP leadership in a special January
2013 issue. To-date a total of 48 C-HPP related articles have been published in JPR (January 2013 and June 2013).

Marko-Varga G, Omenn GS, Paik YK, Hancock WS. A first step toward completion of a genome-wide characterization of
the human proteome. J Proteome Res. 2013;12:1-5.
11

Aebersold R, Bader GD, Edwards AM, van Eyk JE, Kussmann M, Qin J, et al. The biology/disease-driven human proteome
project (B/D-HPP): enabling protein research for the life sciences community. J Proteome Res. 2013;12:23-7.
HPP LEADERSHIP MEETINGS - INITIATIVE SESSIONS OVERVIEW
PRE-CONGRESS HPP LEADERSHIP / COMMITTEE / PI MEETINGS
The following planning meetings for HPP leadership and PIs are scheduled in Yokohama.
SATURDAY, SEPTEMBER 14
9:00 - 9:45 am
HPP General Leadership Meeting
Room 311-312
HPP EC, SSAB, Pillar Chairs, B/D HPP and C-HPP Committees
9:45 - 11:45 am
B/D HPP Group Break-out
C-HPP Group Break-out
Room 311-312
Room 313-314
11:45 am - 12:45 pm
Lunch Break (lunch-on-your-own)
12:45 - 2:00 pm
HPP General Leadership Meeting
Room 311-312
All re-group for an update on the break-out meetings.
OVERVIEW OF HPP CONGRESS SESSIONS - OPEN TO ALL CONGRESS ATTENDEES
Refer to the following pages for detailed description of the initiative sessions Sunday, Monday and Tuesday mornings 8:15 - 9:30 am.
For details on the Wednesday, September 18 HPP Parallel and Plenary Sessions, please refer to the main congress program.
SUNDAY, SEPTEMBER 15
8:15 - 9:30 am
PSI / ProteomeXchange / KBpC +
C-HPP (Part 1)
Room 303-304
MONDAY, SEPTEMBER 16
8:15 - 9:30 am
C-HPP (Part 2) - Poster Session
Exhibition Hall
TUESDAY, SEPTEMBER 17
8:15 - 9:30 am
C-HPP (Part 3) - Bioinformatics
Room 303-304
WEDNESDAY, SEPTEMBER 18
8:15 - 9:30 am
B/D-HPP PI Meeting
Room 317
EyeOME
Room 301
Liver (HLPP and B/D-HPP-Liver)
Room 303-304
HGPI Glycoproteomics
Room 301
Proteome Biology of Stem Cells
Room 311-312
Human Protein Atlas / ABpC
Room 301
iMOP
Room 302
C-HPP PI Meeting
Room 318
Topics: Std Metrics; 2014
workshop plan; MRM std, JPR
special issue
Human Brain Proteome Project
(HBPP)
Room 313-314
Cancer
Room 302
Proteome Analyzer: A New High
Throughput Platform
Room 311-312
HKUPP + HPPP
Room 311-312
Cardiovascular
Room 313-314
Human Diabetes Proteome
Project
Room 313-314
Wednesday, September 18
9:30 - 11:50 am
HPP Special Parallel Session
Room 303-304
Featuring invited speaker Melanie
Y. White and HPP Progress
Update from HPP Leadership,
General Discussion
Wednesday, September 18
1:45 - 2:45 pm
HPP Plenary Session
Room 303-304
Featuring invited speakers Jeremy
Nicholson and Heui-Soo Kim
12
HPP INITIATIVE SESSIONS - SUNDAY, SEPTEMBER 15, 8:15 - 9:30 AM
PSI/ProteomeXchange/KBpC + C-HPP (Part 1)
Organizers: Eric Deutsch, Henning Hermjakob, Lydie Lane, Bill Hancock
Abstracts available for this session.
Room 303-304
HPP projects are generating massive amounts of proteomics data using a large variety of MS-based techniques. To be exploitable, this
data need to be stored and and precisely documented, and made available in a standardized format. To answer these needs, several
resources are being developed.

Eric Deutsch (ISB, USA) will present the PSI efforts to develop standardized data formats and their implementation

Henning Hermjakob (EBI, UK) will present ProteomeXchange, that simplifies and unifies proteomics data submission to
PRIDE and Peptide atlas

Lydie Lane (SIB, Switzerland) will show how human proteomics data is handled in neXtProt, and how it is integrated with other
types of data
Finally, a panel composed of the three speakers and Bill Hancock will host 15 min of Q&A about the optimization of data resources
within the HPP.
EyeOME
Organizers: Richard Semba and Roger Beuerman
Abstracts available for this session.
Room 301
In this session, we introduce the Human Eye Proteome Project (HEPP), one of the most recent components of the Biology/Diseasedriven Human Proteome Project (B/D-HPP) whose overarching goal is to support the broad application of state-of-the-art
measurements of proteins and proteomes by life scientists studying the molecular mechanisms of biological processes and human
disease. The goals of the HEPP will be presented (Richard Semba, Baltimore). The session will cover the proteome of human tears and
murine retina (Zhou Lei, Roger Beuerman, Singapore), the anterior segment in relation to glaucoma (Deepak Edward, Riyadh, Saudi
Arabia), the vitreous proteome in diabetic retinopathy (Edward Feener, Boston), and personalized proteomics for therapy of
inflammatory retinal disease (Vinit Mahajan, Iowa City).
Speakers:
1
2
3

Introduction to the Human Eye Proteome Project; Richard Semba ; Jan J. Enghild ; Vidya Venkatraman ; Thomas F.
2
3 1
Dyrlund ; Jennifer E. Van Eyk ; Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA;
2
3
Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark; Johns Hopkins Bayview Proteomics
Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA

1,2,4
1-4 1
Proteome of Human Tears and the Mouse Retina; Zhou Lei , Roger Beuerman , Singapore Eye Research Institute,
Duke-NUS, SRP Neuroscience and Behavioral Disorders, 3Ophthalmology, Yong Loo Lin School of Medicine, National
4
University of Singapore, Ophthalmology, University of Tampere Medical Center, Tampere, Finland
2
1,2
3 1

The Proteome of the Anterior Segment in Relation to Glaucoma; Deepak Edward ; Rachida Bouhenni ; King Khalid Eye
2
Hospital,Riyadh, Kingdom of Saudi Arabia; Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore,
3
MD, USA; Summa Health System, Akron, OH, USA

Vitreous Proteome in Diabetic Retinopathy; Edward P. Feener , Lloyd P. Aiello ; Joslin Diabetes Center and
2
3
Departments of Medicine and Ophthalmology, Harvard Medical School, Boston, MA, USA

Personalized Proteomics for Inflammatory Retinal Disease Therapy; Vinit B. Mahajan ; Jessica M. Skeie ; Omics
2
Laboratory, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, USA

The Tears as a Source for Proteomic Biomarkers of Human Eye Diseases; Roger Beuerman ; Zhou Lei ; Singapore
2
3
Eye Research Institute, Duke-NUS, SRP Neuroscience and Behavioral Disorders, Ophthalmology, Yong Loo Lin School of
4
Medicine, National University of Singapore, Ophthalmology, University of Tampere Medical Center, Tampere, Finland
1,2
1,3 1
1,2
1,2 1
1-4
13
1,2,4 1
HPP INITIATIVE SESSIONS - SUNDAY, SEPTEMBER 15, 8:15 - 9:30 AM (Cont'd.)
Proteome Biology of Stem Cells
Organizers: Albert Heck and Jeroen Krijgsveld
Abstracts available for this session.
Room 311-312
This session will provide an update of recent efforts gaining insight into various aspects of both embryonic, induced pluripotent and
adult stem cell biology using advanced proteomic approaches.
Three talks will be presented followed by discussion.
Speakers:

Deep Subcellular Proteome Profiling of Human Induced Pluripotent Stem Cell by One-Shot Nanolc-MS/MS Analyses
1
1
2
1,3 1
with Meter-Scale Monolithic Silica Columns; Mio Iwasaki , Masato Nakagawa , Yasushi Ishihama , Shinya Yamanaka ;
2
Center for iPS Cell Research and Application, Kyoto University, Japan; Graduate School of Pharmaceutical Sciences, Kyoto
3
University, Japan; Gladstone Institute of Cardiovascular Disease, San Francisco, USA

Proteomic Analysis OF LGR5+ve Intestinal Adult Stem Cells and Their Immediate Undifferentiated Daughters; Javier
1,2
3
3
1,2
3
1,2 1
Muñoz , Daniel E. Stange , Marc van de Wetering , Shabaz Mohammed , Hans Clevers , Albert J. R. Heck ;
2
Biomolecular Mass Spectrometry and Proteomics Group, Utrecht University, The Netherlands; Netherlands Proteomics
3
Center, Utrecht, The Netherlands; Hubrecht Institute, KNAW, Utrecht, The Netherlands

Stem Cells and Neural Development; Akhilesh Pandey, Johns Hopkins University, Baltimore, USA
Human Brain Proteome Project (HBPP)
Organizers: Lea Grinberg, Young-Mok Park, Helmut E. Meyer
Abstracts available for this session.
Room 313-314
The Human Brain Proteome Project is one of the international initiatives of the Human Proteome Organization (HUPO). Since its
initiation in 2003, the HUPO Brain Proteome Project (HUPO BPP) organizes workshops on a regular basis. The main goal was to
intensify collaboration between fundamental research and clinics as well as to discuss recent sub-project results in the field of clinical
th
Neuroproteomics and to establish guidelines and requirements for the future HBPP. At the 16 HUPO BPP workshop which was held in
2011 during the HUPO 10th Annual World Congress in Geneva, Human Brain Proteome Atlas Project (HBPAP) was launched as an
international, multidisciplinary initiative by HUPO BPP. The overarching goal of HBPAP is to analyze what are the proteomic
compositions of distinctive areas of healthy human brain and how it changes during aging and disease. At HBPAP, several groups will
analyze human brain samples using their expertise, and the results will be compared using robust and integrative bioinformatics. This
well-orchestrated international collaboration will maximize the project potential and the chances of identifying biomarkers and novel
therapeutic targets for Alzheimer’s disease.
Speakers:

The Role of Neuroproteomics to Elucidate Neurodegenerative Disease Mechanisms; Lea T. Grinberg, University of Sao
Paulo (Brazil) and University of California, San Francisco (USA)

Biomarker Discovery for Alzheimer and Parkinson Disease; Helmut E. Meyer, Medical Proteom-Center, Ruhr-University
Bochum, Germany
14
HPP INITIATIVE SESSIONS - MONDAY, SEPTEMBER 16, 8:15 - 9:30 AM
C-HPP (Part 2) - Poster Session
Organizers: Bill Hancock, Young-Ki Paik, and Gyorgy Marko-Vargas
Exhibition Hall
There is a special section within the Exhibition Hall dedicated to HPP-related posters. For C-HPP there will be a number of posters
representing each chromosome. Chromosome/C-HPP-related posters will be attended during this special early morning poster session.
Posters relating to both the B/D-HPP and C-HPP are welcome in this special section of the exhibition hall. Posters may be displayed
throughout the congress week to maximize viewing opportunities.
Liver (HLPP and B/D-HPP-Liver)
Organizers: Pumin Zhang and Fernando Corrales
Abstracts available for this session.
Room 303-304
Liver is the central metabolic organ in human body that maintains blood sugar and lipid homeostasis. It also performs many other
critical functions essential for survival. Human Liver Proteome Project (HLPP) was launched in 2002 with three objectives: 1) generate
an integrative approach leading to a comprehensive protein atlas of the liver, 2) expand the liver proteome to its physiome and pathome
to dramatically accelerate the development of diagnostics and therapeutics toward liver diseases, and 3) develop standard operating
procedures (SOPs) for other HUPO initiatives. The HLPP Workshop will summarize the progresses made in past few years towards the
objectives and discuss plans to move the initiative forward. HLPP participants and everyone else with an interest in liver function are
welcome to attend the workshop.
Speakers:

Urine as a Source of Liver Disease Biomarkers and Proteomics Studies with Human Hepatoblastoma Samples; Felix
Elortza; CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Technology Park of Bizkaia, Derio, Spain

Identification of Proteins Driving the Progression of Liver Injury and Potential Biomarkers; Fernando J. Corrales;
Division of Hepatology and Gene Therapy, CIMA, University of Navarra, Pamplona, Spain

Towards the System Medicine of Non-Alcoholic Fatty Liver Disease; Tommy Nilsson, The Research Institute of the McGill
University Health Centre, the McGill University Health Centre & McGill University, Montreal, Quebec, Canada

HLPP, A Progress Report from Team China; Pumin Zhang; Beijing Proteome Research Center, China and Baylor College
of Medicine, Houston, TX, USA
Human Protein Atlas / ABpC
Organizers: Jochen Schwenk, Emma Lundberg and Mathias Uhlen
Room 301
The Human Antibody Initiative (HAI) aims to promote and facilitate the use of antibodies for proteomics research. In this session we will
present recent developments in antibody technologies as well as alternative affinity reagents. In addition to this we will report on the
current status of available antibody collections for the human proteome and discuss how to best integrate the antibody-based research
with other data in the Human Proteome Project.

Welcome and Introduction; Mathias Uhlén, Science for Life Laboratory, KTH, Sweden and Michael Snyder, Stanford Center
for Genomics and Personalized Medicine, USA

Programs for Antibody Generation at NIH and NCI; Salvatore Sechi, NIH, USA

Programs for Antibody and Protein Binder Generation in Europe; Mike Taussig (not confirmed yet), Babraham Institute,
Cambridge, UK

Programs for Generation of Antibodies in Australia; Ed Nice, Monash University, Australia

Availability of Commercially Antibodies to the Human Proteome; Tove Alm, Antibodypedia, KTH, Sweden

Discussion - the Role of HAI for the HPP; Mathias Uhlén and Michael Snyder
15
HPP INITIATIVE SESSIONS - MONDAY, SEPTEMBER 16, 8:15 - 9:30 AM (Cont'd.)
Cancer
Organizers: Hui Zhang (Center for Biomarker Discovery and Translation, Department of Pathology, Johns Hopkins University, USA)
and Juan Pablo Albar (CEI-UAM+CSIC Proteomics Platform, Spain)
Abstracts available for this session.
Room 302
The Cancer-HPP attempts to generate and disseminate the assays and resources to support the analysis of biological networks
underlying biological processes and cancer. The use of emerging mass spectrometry (MS)-based platforms such as selected reaction
monitoring (SRM) or targeted data extraction for candidate proteins from SWATH MS data has become an increasingly popular method
for quantitative analysis of target proteins. It has been shown that the use of synthetic peptide standards and isotope dilution makes
identification and accurate quantitation of proteins in a multiple laboratories possible. Therefore, the assays, once developed, can be
easily transferred and used in other laboratories. Acceptance of high throughput MS assays for proteins or protein modifications has
been limited due to the difficulty in establishing assays and the availability of the assays comparing to using traditional antibody based
assays, here we propose an international effort to target cancer proteins in each cancer type. By working together, we can create a
synergistic effort to work with a list of cancer protein targets, develop assays, and make assays available. We further discuss the
procedure to accrue a list of target proteins from each cancer type, the strategy for assay development, quality control, and procedure
and materials needed for transferring the established assays to a new laboratory.
Speakers:

CPTAC - a Proteogenomics Network for Cancer; Christopher Kinsinger, Clinical Proteomic Tumor Analysis Consortium
(CPTAC), National Cancer Institute, USA

Analysis of Tissue Biopsies by PCT-SWATH; Guo Tiannan, ETH Zurich, Institute of Molecular Systems Biology,
Switzerland

Proteomics-Based Studies on Colorectal Cancer; Edouard Nice, Clinical Biomarker Discovery and Validation, Monash
Antibody Technologies Facility, Monash University, Australia

Integrative Analysis - Bridging the Gaps in Genetic Information Flow between Genomic and Proteomic Data; Zhen
Zhang, Biomarker Discovery and Translation, Johns Hopkins University, USA

Breast Cell Index and Atlas Projects; Peter James, Department of Immunotechnology, Lund University, Sweden

Human Proteome Knowledge Discovery Gateway: Progress and Perspective; Dong Li and Fuchu He, State Key
Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, National Center for
Protein Sciences, National Engineering Research Center for Protein Drugs, China
Panel Discussion including:

Hisashi Narimatsu, Glycogene Function Team, Research Center for Medical Glycoscience (RCMG), National Institute of
Advanced Industrial Science and Technology (AIST), Open Space laboratory (OSL), Japan

Tadashi Kondo, Division of Pharmacoproteomics, National Cancer Center Research Institute, Japan

Sam Hanash, Clinical Cancer Prevention-Research, Red & Charline McCombs Institute for the Early Detection and Treatment
of Cancer, The University of Texas MD Anderson Cancer Center, USA

Leigh Anderson , SISCAPA Assay Technologies, Inc, USA

Ignacio Casal, ProteoRed-ISCIII, CIB-CSIC, Spain
16
HPP INITIATIVE SESSIONS - MONDAY, SEPTEMBER 16, 8:15 - 9:30 AM (Cont'd)
HKUPP + HPP
Organizers: Mark Baker and Tadashi Yamamoto
Abstracts available for this session.
Room 311-312
The following topics will be discussed: (1) comparative analyses across plasma and other biofluid and organ proteomes, like the
plasma/urine/kidney study pending; (2) joint workshops, like Plasma & CVD in Sydney and Plasma and HKUPP in Boston and
Yokohama; (3) the move from shotgun to targeted proteomics in biomarker discovery especially to overcome the domineering effect of
highly abundant proteins and their peptides in plasma; (4) the strategy of identifying biomarker candidates in diseased tissues and then
following the proteins into the periphery for convenient analysis; and (5) emphasis on protein variants from alternative splicing, PTMs,
and mutations.
Speakers:

Proteomic Analysis of Nephron Segments of Formalin-Fixed Paraffin-Embedded Human Kidney Tissues; Tadashi
Yamamoto, Keiko Yamamoto, Yutaka Yoshida, Bo Xu, Ying Zhang, Sameh Magdeldin; HKUPP

A Collective Analysis of Three Human Subproteomes using PeptideAtlas; Eric Deutsch, Terry Farrah, Tadashi
Yamamoto, Julian Watts, Micheleen Harris, Zhi Sun, Gil Omenn; HPPP

Different Levels of Variability in the Human Plasma Proteome; Yansheng Liu, Ben Collins, Ludovic CJ Gillet, Alfonso Buil,
Emmanouil T. Dermitzakis, Lin-Yang Cheng, Olga Vitek, Ruedi Aebersold, Institute of Molecular Systems Biology, ETH Zurich

Quantification of Peptides in Clinical Samples Based on High-Resolution Mass Measurements; Bruno Domon,
Luxembourg Clinical Proteomics Center, Luxembourg
Human Diabetes Proteome Project (HDPP)
Organizers: Jean-Charles Sanchez, Peter Bergsten, Martin Kussmann
Abstract available for this session.
Room 313-314
Diabetes mellitus is a complex multifactorial disease characterized by hyperglycemia and deranged lipids, which have been linked to
diabetes-related complications. The Human Diabetes Proteome Project (HDPP) consortium was created at HUPO 2012 to unravel
molecular mechanisms leading to diabetes and to understand the dysfunctions induced by glucose and free fatty acids. During the first
year, the partners of HDPP identified the short-to-mid term objectives of the project. Various omics datasets will be collected, mainly by
analyzing insulin producing cell lines, islets, and human blood from different conditions. Data integration as well as network biology
approaches will be applied to enhance our knowledge of pathways centrally involved and deregulated in diabetes. Existing projects
from the partners are already delivering omics data on human islets, rodent beta-cells, mitochondria, glycation in human blood as well
as key results on modifications associated to beta-cell dysfunction. Based on the three pillars of the B/D-HPP projects, HDPP has
already made publicly available (www.hdpp.info) three key protein resources [1]: (1) the 1’000 diabetes-associated protein (the 1000HDPP) database with links to their neXtProt, Peptide Atlas and Human Protein Atlas references; (2) a list of 5’300 human islet proteins;
and (3) a list of 2’500 rodent beta-cell proteins. All results obtained so far through the HDPP initiative will be presented in the HDPP
th
workshop held at the 12 HUPO world congress.
[1]
Topf F., Schvartz D. et al. The Human Diabetes Proteome Project (HDPP): From Network Biology to Targets for Therapies and Prevention. Translational Proteomics 2013,
in press.
Speakers:

The Human Diabetes Proteome Project (HDPP): 2013 Update; Jean-Charles Sanchez, Geneva University, Switzerland

A Systems Omics Perspective of Diabetes; Michael Snyder, Stanford University, USA

Beta-cells and mitochondrial function; Martin Kussmann, NIHS, Switzerland

The Study of Glucotoxicity on Rat INS-1E Pancreatic Beta-Cells; Domitille Schvartz, Geneva University, Switzerland

Genome Wide Methods and Proteomics in Biomarker Discovery for Type 1 Diabetes; Dave Goodlett, University of
Maryland, USA

NIDDK Funding Opportunities; Salvatore Sechi, NIH, USA
17
HPP INITIATIVE SESSIONS - TUESDAY, SEPTEMBER 17, 8:15 - 9:30 AM
C-HPP (Part 3) - Bioinformatics Session
Organizers: Young-Ki Paik, Bill Hancock, and Gyorgy Marko-Vargas
Room 303-304
In this session, chaired by Bill Hancock, the C-HPP consortium members from 25 countries will discuss general matters related to
protein database, updated status on the missing proteins, integration of both ENCODE and Metabolomics data into the C-HPP scaffold.
Speakers:

Siqi Liu (BGI, China) will present the survey results of RNA-Seq service through the C-HPP consortium and give some update
on the RNA-Seq database which can be useful for the consortium members.

Peter Horvatovich (University of Groningen, Netherlands) will present recent progress in WiKi on the C-HPP.

Reports from the web browsers (Rob Goode, Ping Xu, Siqi Liu, Andrey Lisita,and Seul-ki Jeong

Updates from Protein atlas and Monash antibody initiative (Emma Lundberg and Ed Nice)

Encode update (Kate Rosenbloom and Mike Snyder)
HGPI Glycoproteomics
Organizer: Hisashi Narimatsu
Abstracts available for this session.
Room 301
The aim of Human Disease Glycomics / Proteome Initiative (HGPI) is to identify disease-related glycosylation changes in blood and
other body fluids for developing glycobiomarkers of cancer, inflammation, auto-immune disease, other chronic fibrotic disease and so
forth. To discover such glycan alterations, development of reliable technologies to reveal glycan structures was necessary. Thus, the
pilot studies for standardization of glycan structural analyses were carried out as international collaboration with participation of
worldwide laboratories with various distinctive technologies. Thus far, two pilot studies were completed successfully on the analyses of
1,2
common purified glycoproteins for each of N- and O-glycans. The results and assessment of the used methodologies were published .
Presently, the third pilot study on glycan structural analyses of complex mixtures (soluble and insoluble fractions of two kinds of cell
lysates) is progressing; now the analyses of the data contributed by 10 participants have been ongoing. The overview will be reported in
the initiative session in Yokohama.
3
Recently, as described by P. Lagrain et al. , HUPO launched a global Human Proteome Project (HPP), which was designed to map the
entire protein set in humans. HPP consists of two major branches: C-HPP (Chromosome-Centric HPP) and B/D HPP (Biology and
Disease-driven HPP). Through this organizational reformation, all pre-existing initiatives will be incorporated into one of the B/D-HPP.
Then, taking upon this opportunity, a new international collaboration project was proposed by the current chair of HGPI, Narimatsu, in
th
11 Annual World Congress held in Boston, 2012. The new project is designed to expand disease glycomics to glycoproteomics and
named tentatively as the B/D-driven Glycoproteome Project (B/D-GPP). In this initiative session in Yokohama, the proposal to the
project and latest technologies on N- and O-glycoproteomics will be introduced.
1, Wada Y, et al. (2007) Glycobiol.
2, Wada Y, et al. (2010) MCP
3, Legrain P, et al. (2011) MCP
Speakers:

Summary of the First to Third Pilot Studies of Human Disease Glycomics/Proteome Initiative (HGPI); Hiromi Ito,
Department of Biochemistry, Fukushima Medical University

Proposal of a New International Collaboration under the HPP: Biology/Disease-driven Glycoproteome Project (B/DGPP) and Current Resources; Hisashi Narimatsu, Research Center for Medical Glycoscience (RCMG), National Institute of
Advanced Industrial Science and Technology (AIST)

Dissection of the Human GalNAc O-glycoproteome? Mapping Specific Functions of Individual Polypeptide GalNActransferase Isoforms by Zinc-finger Gene Engineering of Human Cells; Katrine ter-Borch Gram Schjoldager, Department
of Cellular and Molecular Medicine, University of Copenhagen
18
HPP INITIATIVE SESSIONS - TUESDAY, SEPTEMBER 17, 8:15 - 9:30 AM (Cont'd)
iMOP - Initiative on Model Organism Proteomes
Organizers: Michael Hengartner and Sabine Schrimpf
Abstracts available for this session.
Room 302
Fundamental pathways and biological processes are conserved across species, and studies of model organisms play an important role
for understanding human biology and health. The continuous improvement and use of mass spectrometry have led to a dramatic
increase in proteome coverage, and to the inclusion of an increasingly broad range of model organisms over the recent years.
However, new model organism species are typically supported by only small communities. To form a broader model organism
proteomics community, the initiative on model organism proteomes (iMOP; www.imop.uzh.ch) was integrated into HUPO. The research
interest of the iMOP community is already quite diverse; however, we still encourage more research groups to join iMOP. Current iMOP
members either focus on the interaction between humans and other organisms at the proteome level or and they are interested in the
relevance of model organism proteomes to the human proteome. They run inter- and intra-species proteome and transcriptome
comparisons to address evolutionary aspects and pathway development. iMOP members also focus on species that are important for
food production and on host-pathogen-interactions. The iMOP initiative distributes proteomics knowledge to a wide range of model
organism communities that are otherwise not closely linked. iMOP will contribute to the human proteome project (HPP) by providing
comparative studies across species.
We will take the opportunity to discuss the future aims and focus of iMOP during the session. The following speakers will give 15-min
talks followed by five minute discussion. The session will conclude with general discussion.
Speakers:

The Methylproteome Network of Saccharomyces cerevisiae; Marc R. Wilkins, University of New South Wales, Australia

Secretome Protein Profiling of growth Interaction between Listeria monocytogenes and Lactobacillus lactis subsp.
lactis; Paola Roncada, Lazzaro Spallanzani, Italian Experimental Institute, Milan, Italy

Acetyl-phosphate Links Metabolism to Global Acetylation Dynamics in E. coli; Brian Tate Weinert, University of
Copenhagen, Denmark
Proteome Analyzer: A New High Throughput Platform
Organizer: Bruno Domon, representing the Mass Spec HPP Pillar
Room 311-312
The proteomics community consistently seeks simple, cost-effective tools to analyze full proteomes (or part thereof) that are routinely
applicable in research laboratories. Consequently, there is thus an immediate need for instruments and solutions that enable a rapid,
simultaneous, and systematic analysis of very large sets of proteins Over the past decades, RNA-sequencing has shown a successful
path forward in the genomics arena, which could provide guidance as a model for proteomics community.
This session aims to be a forum to discuss and to delineate the characteristics of an ideal analytical platform allowing routine proteomic
experiments, where end-users (biologists, clinicians), manufacturers, and analytical biochemists share their experience and needs. This
should guide the design of a “generic proteome analyzer” and to formulate engineering requirements. The discussion will cover all
aspects of a proteomic experiment, including the sample preparation, the separation of the peptides, the mass spectrometric analyses,
and the analysis of the data, thus providing an integrated solution.
Two working groups will be formed with the objectives of discussing issues, and needs for different types of applications, and to outline
engineering requirements of a Proteome Analyzer.
Two “variants” of a Proteome Analyzer will be considered during this session, which fulfill distinct purposes and needs, and thus may
(or may not) have different requirements:

“High-throughput western blot like Proteome Analyzer” to help biologists to identify and detect proteins in samples in a
targeted way, and

The proteomic analog of a “RNA-Seq” Analyzer”: that could perform routine and systematical characterization of the proteome
components.
This session will meet for a brief introduction and then break into two working groups for guided discussion. At the end of the session,
both working groups will come back together for a brief summary.

Working Group I: Proteome Analyzer I: Large-scale Western Blot Surrogate. Chairs Ruedi Aebersold and Mark Cafazzo
(representative of IAB)
19

Working Group II: Proteome Analyzer II: RNA-Seq Proteome Analog. Chairs Mike Snyder and Andreas Huhmer
(representative of IAB)
HPP INITIATIVE SESSIONS - TUESDAY, SEPTEMBER 17, 8:15 - 9:30 AM (Cont'd)
Cardiovascular
Organizer: Jenny Van Eyk, Cathy Costello, Peipei Ping
Room 313-314
Worldwide, cardiovascular disease is the number one cause of mortality. Understanding the physiological and pathological proteomes
of the many cell types and organs that comprise the heart and vascular system is required for improved diagnosis and therapies. The
aim of this initiative is to i) bring together a diverse group of investigators in the area of heart and vascular diseases, ii) to support
scientists in basic, clinical and translation research with respect to training and the application of proteomics and iii) to assist in the
translation of proteomics into clinical medicine.
Session will include:

The initiative for cardiovascular translation (What are the big clinical questions? ). Peipei Ping and young clinical investigator
awardee

Challenges in CVD tissue analysis (Proteomic analysis of left ventricular tissues in dilated cardiomyopathy mouse models).
Mitsuhiro Nishigori

How to handle the really difficult and challenging cardiovascular proteomes (Systematic characterization of human platelets in
arterial vascular disorders by quantitative proteomics). Albert Sickman

Global thoughts across species and cardiovascular proteomes (A plasma membrane proteomic analysis of mouse and human
cardiovascular proteins). Antony Gramolini

Thoughts on proteome analysis of disease stage classification (Aortic aneurysm stage classification utilizing protein profiles),
Hiroaki Yaji

Summary and next steps. Cathy Costello and Jenny Van Eyk
20