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15th C-HPP Workshop at HUPO in Taipei, Taiwan, September 18-22, 2016

A Guide to HPP Workshops in Taipei

(Updated Final Circular: Sept 9, 2016, V11C6)

HUPO Taipei logo

Summary of HPP Workshop Programs in Taipei

Venue*

Taipei Int’l Convention Center, Taipei, Taiwan (9/18-9/21)

Fleur De Chine Hotel, Sun Moon Lake, Nantou, Taiwan (9/22)

SUN, Sept 18

HPP Investigators Meeting
08:00-15:30
Taipei Int’l Convention Center
Room 101B, 202A, South Lounge (3F)
MON, Sept 19

Joint Cluster Group Mtg.
07:30-08 :30

C-HPP Poster Session
9:30 - 10:30 & 16:20-17:30

PIC Meeting
12:20-13:30
THURS, Sept 22

HPP Post-Congress Day
08:30 - 18:00
Fleur de Chine Hotel,
Sun Moon Lake, Nantou
(Appendix 5)
HPP Plenary Session I
(Rm 101B: See Appendix 1)

Moderators: Young-Ki Paik & Fernando Corrales


8:00-08:55: Rm 101B
HPP Overview

Chair: Michael Snyder (SSAB Chair)
(C-HPP, B/D-HPP, Bioinformatics, Ab, MS)

09:00-09:30
HPP Plenary Lecture 1

Chair: Fernando Corrales
Genomics for HPP
Michael Snyder, Stanford Univ. CA

09:30-10:00
HPP Plenary Lecture 2

Chair: Christoph M. Overall
“Emerging Tech” -Small ORF Analysis
Alan Saghatelian, Salk Inst. CA

10:00-10:20
Coffee Breaks (Sign up the Cluster Meeting)


C- and B/D-HPP separate sessions

C-HPP Session 1

10:20-12:30
Rm 202A
(Appendix 1, 2)
1. Introduction (YK Paik)
2. Top 50 MP Marathon Challenge (CM Overall)
3. Reports on Missing Protein (Lydie Lane)
Chr 3 T. Nishimura
Chr 10 J. LaBaer
Chr 15 G. Domont
Chr 18 S. N. Naryzhny/A. Archakov
Chr 19 G. Marko-Varga
Chr 22 A. Pandey
Chr X T. Yamamoto
Chr Y G. Hosseini Salekdeh
4. Open Discussion
B/D-HPP Session 1**

10:20-12:30 Rm 101B
1. Extreme conditions proteomics (Eugene Nikolaev)
2. Glycoproteomics (Hisashi Narimatsu)
3. Brain Proteome Project (Peter Nilsson)
4. Cardiovascular Initiative (Maggie Lam & PeiPei Ping)
5. Plasma Initiative (Jochen Schwenk)
6. Food and Nutrition Initiative (Paola Roncada)
7. Diabetes Initiative (Loïc Dayon)
8. Mitochondria Initiative (Mauro Fassano)

HPP Plenary Session II (Appendix 1)
Joint Cluster Group Meeting for C-HPP and B/D-HPP (Rm101B)


12:30-13:10 Lunch

13:10-15:20 Joint Cluster Session

(1). Introduction (5-10 min)

-What is “Cluster Collaboration?” (Appendix 2) (Young-Ki Paik)
Move to each designated room for Break-out session

(2). Break-out Session (120 min)
A. Cancer Cluster Group (Rm 101B): Led by Siqi Liu, Ed Nice & Hui Zhang
International Cancer Collaboration: Australia and US (15 min)
Moonshot Project & Int’l Cancer Proteomics Collaboration
Mark Baker (HUPO President), Phil Robinson (ProCan) and Jerry Lee (NCI Office)
Introduction of B/D-HPP Cancer (20 min)
Hui Zhang and Colleagues
Discussion on the Strategic Points (Appendix 1) (85 min)

B. IVTT Cluster Group (Rm 202A) (120 min)
Led by Gyorgy Marko-Varga Joshua LaBaer
Discussion on the Strategic Points (Appendix 1)

C. Reproductive Disease (South Lounge) (120 min)
Led by Charles Pineau & Ghasem Hosseini Salekdeh
Discussion on the Strategic Points (Appendix 1)
Note: While both Membrane Proteins and Neurodegenerative Disease groups may join one of above groups, they may have their own Cluster meeting (203 and 102) on Monday early morning (07:30-8:30).

15:20 HPP Meeting Ends
07:30-08:30
Joint Cluster Mtg.
(C- and B/D-HPP)


Membrane Cluster Group (Rm 203)
Neurodegenerative Disease Group (Rm 102)
(subject to change w/o notice)


09:30-16:30
C-HPP Session 2
C-HPP Poster Session
(Chair: Lydie Lane, Co-Chair: Peter Horvatovich)
(Appendix 3)

09:30-10:30: Session 1
(Even Numbers of Chr. 2, 4, 6, 8, 10, 12, 14, 16,18, 20, 22.+X, Y)
15:30-16:30: Session 2
(Odd Numbers of Chr. 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, Mito)

Poster Awards (Cash Prize and -Award Certificate by HUPO President) will be given to Total 7 Best Outstanding Poster Presenters at the Closing Ceremony.


12:20-13:30
C-HPP Session 3

C-HPP PIC Meeting (with Lunch: Rm 202A)

(Appendix 4)
1. Report Session (L. Lane)
2. Approval of Pending. Agenda (YK Paik)
3. Nomination and Election (Chris Overall)
4. Future Plans (2016-19) (YK Paik)


List of Appendices
1. HPP Investigators Meeting Agenda
2. New C-HPP Strategies (Cluster Collaboration &Top 50 MP Marathon and)
3. C-HPP Poster Session Guides
4. C-HPP PIC Meeting Agenda
5. HPP Post-Congress Day Agenda
6. Bioinformatics HUB Program
7. Hotel Reservation Form (Fleur De Chine, Sun Moon Lake)
8. 16th C-HPP Workshop in Brazil
Moderator: Gil Omenn


07:30-08:20

Joint B/D and C-HPP EC meeting

08:30-09:00
HPP Update Session:
(1) Highlights from Congress and discussions of B/D, C-HPP, Resource Pillars

09:00-09:30
(2) Bioinformatics Hub, JPR special issue 2016 and future, experience with HPP MS Guidelines v2.1.

09:30-10:00
Open discussion about recent strategic successes and strategic planning for next year and for 5 years: aims, directions, changes, deliverables

10:00-10:20
Coffee Break

10:20-10:50
HPP Plenary Lecture 3, “Lung Cancer Genomics”, Dr. Sung-Liang Yu, NUT, Taiwan

10:50-12:30
Reports on the Cluster Meeting (C- & B/D-HPP+CPTAC)
1. Cancer
2. IVTT
3. Reproductive Dis
4. Membrane Proteins
5. Neurodegenerative Disease,

12:30-13:30
Lunch

13:30-15:30
HPP Concluding Session
1. SSAB Members’ Feedback, led by Cathy Costello
2. HPP Operations & Communication matters (C. Pineau, C. Borchers)
3. Resources and Funding
4. Publications, including assessment of 2016 JPR special issue.
5. Strategic objectives & planned meetings and workshops, Brazil, 2016, and beyond

16:00-18:00
Boat Tour with Informal Discussion

18:00-
Dinner and Social Mixer

*Venue: Taipei International Convention Center Address: 1 Hsin-Yi Rd., Sec.5, Taipei 11049, Taiwan, Tel:+886-2-2725-5200 Website: http://www.ticc.com.tw
**B/D-HPP initiatives sessions in the main program:
Monday Sept 19: Brain and EyeOME: connecting two images (10:30-12:15); Diabetes and Cardiovascular Diseases: Energy balance in disease phenotypes (13:45-15:30).
Tuesday Sept 20: Liver and Toxicoproteomics: Metabolism, drug transformation and toxicity (10:30-12:15); Protein Standards and model organisms: Expanding our horizons (13:45-15:30).
Wednesday Sep 21: Food &Nutrition and Immuno-Peptidome: Focus on food allergies (10:30-12:15); Kidney, Urine and Plasma: Opportunities for early diagnosis and risk assessment (13:45-15:30).
***Venue: Fleur de Chine Hotel Address: No.23, Zhongzhen Rd., Sun Moon Lake, Yuchi Township, Nantou County 55546, Taiwan, R.O.C. Tel: +886-49-285-6788 Website: http://en.fleurdechinehotel.com/

  1. Registration for HPP Workshop in Sun Moon Lake (~USD 100)
  2. Hotel Reservation in Sun Moon Lake: Visit website for hotel reservation: You may download the reservation form, fill-out and send it to hotel by fax (or email) (Download in Appendix 7 the Reservation Form)
  3. How to get Sun Moon Lake: The congress will arrange the shuttle bus from Taipei International Convention Center to Fleur de Chine Hotel, Sun Moon Lake, Nantou. Be sure there at 17:30 on 21st of September.
  4. How to get back to Taipei from Sun Moon Lake: You need to make your own arrangement by making reservation for High Speed Train (or Bus). On the evening of 22nd of September (Wed), the congress LOC will arrange the district shuttle bus from Sun Moon Lake directly to the Taiwan High Speed Rail Taichung Station. You need to get train-tickets at the rail station by yourself or make a reservation by online ahead of time, by visiting Taiwan High Speed Rail web site. There is also bus back to Taipei which should be arranged by each participant. LOC will provide the shuttle bus from Fleur de Chine Hotel to THSR Taichung Station. The Shuttle Bus (transit between FDC hotel and Bus station).
    Schedule as follows: (A) 20:30, September 22 the Fleur de Chine Hotel -> THSR Taichung Station and (B) 17:45, September 23 the Fleur de Chine Hotel -> THSR Taichung Station.

Appendix 1

Sunday, Sept 18, 2016

HPP General Investigators Meeting in Taipei

(Last updated August 14, 2016)

Taipei International Convention Center

Plenary Session: Rm 101B

Break-out session: Rm 101B, 202A, South Lounge

08:00-15:20 HPP Investigators Meeting: Rm 101B (All HPP Investigators)

Moderators: Young-Ki Paik & Fernando Corrales

08:00-08:55 HPP Overview

Chair: Michael Snyder (SSAB Chair)
C-HPP: YK Paik, CM Overall, L. Lane. HPP C-HPP report summary in pdf format is available here.
B/D-HPP: JE van Eyk, FJ Corrales. This presentation is available in pdf format here.
Bioinformatics: Eric Deutsch (HPP MS data management guidelines). This presentation in pdf format is available here.
Antibodies: Emma Lundberg. This presentation in pdf format is available here.
MS: Susan Weintraub

09:00-09:30 HPP Plenary Lecture 1

Chair: Fernando Corrales
Genomics for HPP, Michael Snyder, Stanford Univ., CA, USA. This presentation in pdf format is available here.

09:30-10:00 HPP Plenary Lecture 2

Chair: Christopher M. Overall
Emerging Tech - Small ORF Analysis, Alan Saghatelian, Salk Inst. CA, USA

10:00-10:20 Coffee Break & Sign-up Cluster Meeting (Cancer, IVTT, Reproductive Disease)

10:20-12:30 C-HPP Session 1 (Rm 202A): Participants- C-HPP Investigators
  • Agenda 1: Brief Report on the Recapture of the HPP Cluster Concept (Young-Ki Paik) (Appendix 2)
  • Agenda 2: The C-HPP Top 50 MP Marathon Challenge with Cluster Collaboration (Chris Overall) (Appendix 2)
  • Agenda 3: Progress Reports on Missing Protein ID from PIs: 8 min each (Lydie Lane). This presentation in pdf format is available here.
    • Chr 3 Toshihide Nishimura, St. Marianna University School of Medicine, Kanagawa, Japan
    • Chr 10 Josh LaBaer, Arizona State University, USA
    • Chr 15 Gilberto Domont, Universidade Federal do Rio de Janeiro, Brazil
    • Chr 18 S.N. Naryzhny & A. Archakov, Institute of Biomedical Chemistry, Russia
    • Chr 19 György Marko-Varga, Lund University, Sweden
    • Chr 22 Akihlesh Pandey, Johns Hopkins University, USA
    • Chr X Tadashi Yamamoto, Niigata University, Japan
    • Chr Y Ghasem Hosseini Salekdeh, Royan Institute, Iran
  • Discussion

10:20-12:30 B/D-HPP Session 1 (Rm 101B) Participants-B/D-HPP and related HPP Investigators


10:20 Extreme conditions proteomics
Eugene Nikolaev, Inst Biomed Chem, Russia

10:35 Glycoproteomics
Hisashi Narimatsu, National Institute of Advanced Industrial Science and Technology, Japan

10:50 Brain Proteome Project
Peter Nilsson, SciLifeLab, KTH - Royal Institute of Technology, Stockholm, Sweden

11:05 Cardiovascular Initiative
Maggie Lam, University of California, Los Angeles, USA
PeiPei Ping, NHLBI Proteomics Center – UCLA, USA

11:20 Plasma Initiative
Jochen Schwenk, Science for Life Laboratory (KTH), Sweden

11:35 Food and Nutrition Initiative
Paola Roncada, Istituto Sperimentale Italiano Lazzaro Spallanzani, Italy

11:50 Diabetes Initiative
Loïc Dayon, Nestlé Institute of Health Sciences SA, Switzerland

12:05 Mitochondria Initiative
Mauro Fasano, University of Insubria, Italy

12:30-15:20 Joint Cluster Group Meeting (Lunch box provided) B/D-HPP and C-HPP Interactions (Room 101B)

Participants: HPP Investigators involved in C-HPP, B/D-HPP, Pillars & CPTAC groups are welcome.
Moderator: Young-Ki Paik. Introduction slides from Young-Ki Paik is available here.

12:30-13:10 Lunch

13:10-15:20 Joint Cluster Session

(1) Introduction (5-10 min)
-What is “Cluster Collaboration?” (Appendix 2)*
Move to each room for Break-out session

(2) Break-out Session (120 min) (see Table 1 below for composition)
A. Cancer Cluster Group (Rm 101B): Led by Siqi Liu, Ed Nice & Hui Zhang
▶ International Cancer Collaboration: Australia and US (15 min): Moonshot Project & Int’l Cancer Proteomics Collaboration, Mark Baker (HUPO President), Phil Robinson (ProCan) and Jerry Lee (NCI Office)
▶ Introduction of B/D-HPP Cancer (20 min): Hui Zhang (JHU), Chris Kinsinger (CPTAC), Jacob Kagan (EDRN), Shengtao Zhou (Sichuan Univ)
▶ Discussion on the Strategic Points (see below) (85 min)

B. IVTT Cluster Group (Rm 202A) (120 min) Led by Gyorgy Marko-Varga, Joshua LaBaer
▶ Discussion on the Strategic Points (Appendix 1)

C. Reproductive Disease (South Lounge) (120 min) Led by Charles Pineau & Ghasem Hosseini Salekdeh
▶ Discussion on the Strategic Points (see below)

Note: While both Membrane Proteins and Neurodegenerative Disease groups may join one of above groups, they may use 202A (Membrane Cluster) and 101B (Neurodegenerative D.) on Monday early morning (07:30-8:30) for their own Cluster meeting.{DIV}

Table 1. A Proposed List of Cluster Groups and Meeting Rooms (ver 2)*

Cluster Gr. Coordinators Joint Members Time Room
Cancer Siqi Liu, Ed Nice, Hui Zhang, Chris Kinsinger, Jacob Kagan, Shengtao Zhou B/D-Cancer (CPTAC), + more Chr. 1, 7, 8, 9, 11, 12, 13, 17, 20 Sun, 9/18/2016 12:30-15:20 (lunch included) Rm 101B
IVTT Gyorgy Marko-Varga, Joshua LaBaer HAI, Protein Std, + More (open to all HPP groups) Chr. 5, 10, 15, 16, 19 Sun, 9/18/2016 12:30-15:20 (lunch included) Rm 202A
Reproductive Disease Charles Pineau, Ghasem Hosseini Salekdeh Model Organism and more (open to whole HPP groups), Chr. 2, 14, X, Y Sun, 9/18/2016 12:30-15:20 (lunch included) South Lounge 3F

Responsibility of Coordinators (Proposed)
1. To preside the joint cluster meeting on Sunday (13:10-15:20)

  • Ask attendees to fill out the signup sheet provided in the room and hand in the list to HUPO Admin Office (Chelsea or Joanna).
  • Lead discussion session by presenting first their own short talks (5-7) that are followed by the additional invited presenters whom the coordinators have previously arranged.
  • Open discussion on the joint cluster efforts on
    1. The common scientific interests.
    2. Building a cooperative working cluster on the specific targets or technology or resource (e.g., discussion on the appointment of each group’s coordinators for next meeting, suggestions to HPP leadership, networking, more etc.).

2. To report the meeting results at the Cluster Report Session (led by Gil Omenn) during the Post-Congress Workshop in Sun Moon Lake, Thursday (10:50 to 12:30).

15:30- Adjourn

Definition of Cluster Collaboration The term “cluster" can be defined as an informal grouping to facilitate communications between the formal groups (i.e. B/D-HPP, C-HPP, Pillars, CPTAC and related HPP groups) that the HUPO membership and general public see it as a way to organize sessions and workshops rather than setting up a parallel set of groups (Chris Overall) (Appendix 2)

Floor Plan

FloorPlan

Appendix 2

New C-HPP Strategy*

1. Revised “HPP Cluster Collaboration Strategy” (2016 version), by Young-Ki Paik, Chair of C-HPP

A. Background and Aims

As the technology in proteomics moves rapidly along with the publication of large-scale competitive publications, it was necessary for us to closely re-examine the direction of ongoing projects and the operation of HPP teams to ensure that we are continually at the forefront in the study of chromosome-based or biology/disease-based proteomics (Fig. 1). In an attempt to introduce some changes in our cooperative consortia operation, the concept of cluster collaboration strategy was initially coined during the 12th C-HPP workshop at Milano 2015 but now being expanded into all HPP area as a pilot case.
HUPO_HPP_structure.png
Fig. 1. The concept of cluster group collaboration between HPP Initiatives. Once missing proteins involved in various diseases (e.g., cancer, membrane function, reproductive disease etc.) are newly identified, they are annotated by neXtProt and released on the web site. Any interesting investigator will pick up one or some of these newly identified proteins and start characterizing their functions. In practice, the initial findings of missingproteins (MPs) by a C-HPP team may be validated or shown orthogonally, perhaps by antibodies-based approaches, perhaps by SRMs etc. It is anticipated that the B/D-HPP investigators will seize upon these interesting MPs and others that remain under-investigated that may be relevant to a disease process, Thus translation with the B/D group is hoped to be stimulated to develop mechanistic and novel biological insights into a disease leveraged by the new MPs.

The purposes of this cluster group formation included, but were not limited to, (i) stimulating the activity of each team and the work performance of chromosome-based or biology/disease-based proteomics research in a cooperative manner, (ii) effecting a closer working relationship between chromosome teams and other related consortia (e.g., B/D-HPP, Pillars and CPTAC) toward completion of the scientific goals and (iii) strengthening of the research focus of HPP teams using advanced proteomics platform technologies and resources.

B. Approaches

This collaborative strategy will be applied to all areas of the C-HPP first and then extended to other HPP teams, if necessary, during the process of MP discovery and validation, data integration, disease mechanisms and biological studies. Teams can use or share the common resources (cell types, tissues or biological conditions) and technology platform in the hope of ensuring the highest probability of detecting a given protein/proteoforms. With collaborative networks, more efforts will be placed on devising metrics to unequivocally define these newly detected protein/proteoforms.

This cluster strategy plan was accepted unanimously during the PIC meeting at the Vancouver 2015 congress at which we had an opportunity to organize and discuss various tactics. As a pilot plan, initially, four groups were initially created: IVTT (Chr 5, 10, 15, 16, 19), Cancer (Chr 1, 8, 20, 9, 11, 13, 7, 17), Reproduction (Chr 2, 14, X, Y) and Membrane (Chr 4, 18, 21). At the Vancouver HUPO congress, the IVTT, cancer and membrane proteins cluster teams met for the first time during the breakout session. At the 14th C-HPP workshop in Xiamen, the creation of one more cluster, called the “Neurodegenerative disease group (Chr 1, 3, 6, 11 and 12)” was suggested. Of course, this structure is rather flexible in that one chromosome team can join multiple clusters depending on the specific goals of their projects or temporal need of assistance from other expert teams. Each group would have some consensus on their future activity. It was recommended that any team having a similar target disease or biological questions should share their data and resources to deepen the scientific insight and promote their activity during the 14th C-HPP Xiamen Workshop (May 2016). For example, the cancer cluster collaboration group meeting was held on May 20th with great participation (>60 people).

Currently, the Chinese (Chr 20) and Korean Team (Chr 11) have now explored such possibilities to share their specialty database (e.g., RNA Seq and MS profiling of SAAVs). As suggested by Gil Omenn in Xiamen, we look for some additional targets for our study in Taipei workshop. For example, cancer stem cells may be good targets for PE2 proteomic analysis due to their heterogeneous nature, which makes easy to find MPs. As such, lnc RNA, Amplicon and SAAVs will also be good targets for cluster group studies. We anticipate that restructuring our C-HPP associated teams with a strong focus on the project will bring streamline in the leadership of each team and logistical strategy on completing the project. It will also be a good chance in getting more efficient research works for clustered teams.

C. Perspectives

This new move will not only stimulate less active teams by giving them an opportunity to identify a new PI as well as additional working members but also make synergistic outputs by working together with other teams across chromosomes under the specific goals (e.g., missing protein validation, data integration, disease mechanism, biological studies using the same resources and technology platform). Regarding more efficient collaboration within HPP group, since C-HPP has a strong technological aspect to improve detection of proteoforms (including missing proteins), we can enhance our collaboration with B/D-HPP teams and CPTAC led by NCI. For instance, if we identify a missing protein or a proteoforms, we can provide the analytical method to study their functionalities. This should define the collaboration with B/D-HPP teams with addition that they can be a source of precious sample collection for the studies of biological/pathological implications of missing proteins, important for both teams. With an informal coalition, more efforts will be put on metrics to unequivocally define those newly detected protein/proteoforms. Further to this, we can build a consensus on identification of cell types, tissues or biological conditions providing the highest probability of detecting a given protein/proteoform. This also brings improved methods and workflows allowing detection and quantification of missing proteins/proteoforms.

*Note: The part of content was taken from Editorials of 2016 JPR Special Issue (Paik et al., 2016).

2. The C-HPP 50 MP Marathon Challenge: Not Missing the End game, by Christopher M. Overall, Co-Chair of C-HP

A. Background and Aims

As missing proteins (MPs) are gradually discovered, attainment of the goal of the HPP is coming ever closer. However, the barely hidden proteins that are close by or in plain sight are likely the first to be found. We expect the law of diminishing returns to dominate more and more in specific MP hunts. Had the HPP been organized differently, we could envision that groups would leave the hard MPs for someone else: what is everybody’s is nobody’s! Hence, the beautiful hidden underlying structure of the C-HPP provides a particularly strong strategy to deal with this challenge. A notable strength of the C-HPP approach is that it breaks down the human proteome into more reasonable bins based on chromosomes. Thus, although most proteomic studies are chromosome agnostic, the data management is not, nor is the responsibility for everyone doing their fair share of the MP work. We strongly feel that the individual chromosome groups will increasingly take on the responsibility of completing the protein list for each chromosome to fill in the last MPs, the ones hardest to find, the ones that no one else will tackle.

B. Approaches

We suggest that group or national pride will soon start to be a driver for the first group to produce a high-accuracy protein part list for their chromosome. As seen in many papers in this issue, several approaches to the search for MPs include less accessible or poorly studied tissues, common tissues but at different developmental stages, stem cells and human mutations that alter pathways that perhaps invoke compensatory paths that use a former low-abundance MP (e.g., an MP once active in development), dedicated SRM and SWATH searches, new technologies and antibody pull out as a few examples. All of these and more can be levered upon RNA Seq analyses of different human tissues to optimize searches for the right tissue and developmental stage, e.g., to increase the probability of revealing a shy MP.

C. Perspectives

Thus, with this being the sixth year since the announcement of the HPP at the Sydney HUPO meeting, with many approaches having now been distilled and circulated and initiatives started, we feel it is now time for the C-HPP as a team to really get serious! Thus, we are challenging each chromosome group to target 50 MPs for discovery this year before the Dublin HUPO! Perhaps these MPs could all be on either the long or short arm of a chromosome to come closer to reaching the goal (completing one arm of a chromosome), or the teams could go for all members of a family of proteins encoded on a chromosome or track their chromosome proteins during fetal or tissue development. In any case, at the C-HPP workshop this year in Taipei, these strategies will have been discussed as a means to really start closing the numbers of MPs found to complete the first draft of the Human Proteome. Get ready, get set, go!
Collaboration of C-HPP and B/D-HPP
Fig. 2. Perspectives: A possible direction of harmonized collaboration between C-HPP and B/D-HPP (plus Pillars) Initiatives. (from Paik et al., 2014, JPR Editorials, 13, 1-4).

Appendix 3

Monday, Sept 19, 2016

Additional Cluster Group Meetings and C-HPP Poster Session

1. C-HPP and B/D-HPP Joint Cluster Group Meeting (07:30-08:30)


Table 2. A Proposed List of Cluster Groups and Meeting Rooms

Cluster Group Coordinators** C-HPP Members B/D- and CPTAC*** Meeting Room
Membrane Protein Daniel Figeys, Yu-Ju Chen Chr. 3, 4, 6, 7, 18, 21 Open to all HPP groups Rm 203
Neurodegenerative Disease Jong Shin Yoo, Andrea Urbani Chr. 1, 6, 11, 12, Mt. HBPP, Autoimmune, open to all HPP groups Rm 102

Poster size figure

2. C-HPP Poster Session (Exhibit Hall)

Exhibit Hall: 09:30-10:30 Even No Chr Teams and 15:30-16:30 Odd No Chr Teams

Co-Chairs: Lydie Lane and Peter Horvatovich

Poster sessions are intended to showcase research in a format that is easy to scan and absorb quickly. This session is designed to facilitate more in-depth discussion of the research than is typically possible in a symposium format.

Session 1: 09:30 - 10:30, Monday, Sept 19
Chromosomes #-Even Number of Chromosome Teams (2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, X, Y)

Session 2: 15:30 - 16:30, Monday, Sept 19
Chromosomes #-Odd Number of Chromosome Teams (1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, Mitochondria) and Related Technologies (Pillars: Bioinformatics, MS and Ab)

  • Evaluation Team for the Best Posters: Lydie Lane and Peter Horvatovich will organize the evaluation committee for selecting the awardees.
  • Poster Awards (Cash Prize and Award Certificate Issued by HUPO President) will be given to 7 Best Outstanding Poster Presenters based on the merits of contents, the significance of discovery and deliverables.
  • In addition to the C-HPP research subjects (e.g., mapping missing proteins, ASV, PTM on each chromosome), any papers related to common technology or resources applicable to C-HPP can also be presented. All eligible presenters (first authors or senior authors) should be one of the C-HPP members (PI, co-PI or participating members).
  • Posters should be prepared according to the guideline set by HUPO Congress organizer. Poster Presentation Guidelines (see details at here)

The purpose of the poster sessions is to offer another type of opportunity to present up-to-date researches, new ideas, or best practices. Authors are requested to meet and discuss their work with interested parties on the days of presentation.

  • Poster Display
    Dimension of Display board is 100cm width by 200cm height. The paper number will be mounted on the top of the board by the Congress staff. The poster should be measured within horizontally 90cm max and vertically 120cm max.
  • Preparation
    • The presentation number assigned to your poster must be placed in the upper left corner of the poster.
    • Be sure to include the Abstract Title, Authors’ Names and Affiliations centered at the top of the poster.
    • Use the headings “Introduction, Methods, Results, Conclusions” to identify the poster layout.
    • The text of your presentation should be visible from 3 feet away. Therefore, a large font (20 point or larger) for the primary text should be applied for, and an even larger font for headings.
    • DO NOT MAIL YOUR POSTER to the HUPO 2016 Congress venue but hand carry to the meeting site.
  • Please add your abstract on the Wiki or send it to Peter Horvatovich.

2015 C-HPP Poster Awardees 1. Amr Elguoshy (Chr X); 2. Qidan Li (Chr 1, 8, 20); 3. Ekaterina Mostovenko (Chr 19); 4. Concha Gil (Chr 16); 5. Mauricio Ronci (Mito); 6. Weiming Zhang (Chr 1, 8, 20); 7. Dong Yang (Chr 1, 8, 20); 8. Young-In Kim (Chr 9); 9. Jin-Young Cho (Chr 13); 10. Gilberto Domont (Chr 15)

Appendix 4

Monday, Sept 19, 2016

C-HPP Principal Investigator Council Meeting

12:20-13:30, Room 202A (with Lunch)

Chair: Young-Ki Paik and Co-Chairs: Lydie Lane and Chris Overall

PIC Members Invited to This Meeting (as of August 1, 2016)

C-HPP EC Members:

Young-Ki Paik, Lydie Lane, Chris Overall, Peter Horvatovich, Fuchu He, Fernando Corrales, Daniel Figeys

C-HPP PIC Members:

Ping Xu (Chr 1), Lydie Lane (Chr 2), Toshihide Nishimura (Chr 3), Yu Ju Chen (Chr 4), Peter Horvatovich (Chr 5), Paul Keown (Chr 6), Ed Nice (Chr 7), Pengyuan Yang (Chr 8), Je-Yoel Cho (Chr 9), Joshua Labaer (Chr 10), Jong Shin Yoo (Chr 11), Ravi Sirdeshmukh (Chr 12), Young-Ki Paik (Chr 13), Jérome Garin (Chr 14), Gilberto B Domont (Chr 15), Fernando Corrales (Chr 16), William S. Hancock (Chr 17), Alexander Archakov (Chr 18), György Marko-Varga (Chr 19), Siqui Liu (Chr 20), Daniel Figeys (Chr 21), Akhileshi Pandey (Chr 22), Tadashi Yamamoto (Chr X), Ghasem Hosseini Salekdeh (Chr Y), Andrea Urbani (Mito)

Agenda

  • Quorum Report
  • Welcome Remarks: Young-Ki Paik, Chair of the C-HPP Consortium

Part I. Report Session (by Slide Presentations): Chair: Lydie Lane

1. Report from Co-Chairs: Organization matter (Paik), JPR SI (Overall), neXtProt (Lane)

2. Report from Secretary General: Minutes of 2015 PIC meeting by Peter Horvatovich

3. An Informal Ceremony of Appreciation for Dr. William S. Hancock, Wiki and Biobanks

Part II. Discussion Session: Chair: Young-Ki Paik

4. Discussion and Approval of Top 50 Missing Protein Marathon Strategy: Chris Overall, Co-Chair of C-HPP

(Details on this plan will be discussed during the afternoon session,15:20-18:00)

5. Discussion and Approval of the Rules Set for Hosting the Annual C-HPP Workshop
Proposed Rule for Hosting an Annual C-HPP Workshop Meeting
(1) Time and Interval (between workshop/symposium and HUPO congress)
▶at least 3 months (Feb-June)
(2) Responsibility of Host
▶Provides Room and Board (3 days), local guidance and organization of the meeting in coordination with Co-Chairs.

6. Discussion and Approval of the Following Agenda
(1) Confirmation of each cluster group coordinator (name, roles etc.)
(2) Evaluation Plans of Whole C-HPP in 2017/2018
(3) New Research Topics for the C-HPP Groups: Amplicon, Stem cells, lnc RNA, Small ORF etc.

(4) Misc.

Part III. Nomination and Election Session: Chair: Chris Overall

(1) Discussion and Approval of Procedure for Nomination and Election of the C-HPP EC members (Chair, MAL)
(2) Elections: Nomination & Voting

Position Name Affiliation Term Ends Remarks
Chair Young-Ki Paik
(Asia Oceania)
Yonsei Univ., Seoul, Korea Dec 31, 2016 PI, Chr 13
Secretary General Peter Horvatovich
(Europe)
Univ. Groningen, Groningen, Netherlands Dec 31, 2016 PI, Chr 5
WiKi Manager
MAL Fernando Corrales
(Europe)
CIMA, University of Navarra, Spain Dec 31, 2016 PI, Chr 16

Part IV. Future C-HPP Workshop/Symposium Plans: 2016-2019: Chair, Young-Ki Paik

  • 16th C-HPP Workshop in Rio de Janeiro, Brazil, 12/10-12, 2016 (by Gilberto Domont)
  • 17th C-HPP Symposium/Workshop, April in 2017 (by Ghasem Hosseini Salekdeh) (TBA)
  • 18th C-HPP Workshop in Dublin during 16th HUPO Congress, 9/17-20, 2017
  • 19th C-HPP Workshop in Santiago, Spain (Jointly with EuPA) Last week June, 2018 (TBA)
  • 20th C-HPP Workshop in Chicago, USA (TBA), 2018
  • 21st C-HPP Workshop in St. Malo, France, May 13-14, 2019 (by Charles Peneau)

Appendix 5

Thursday, Sept 22, 2016

HPP Post-Congress Day

Venue: Fleur de Chine Hotel, Sun Moon Lake, Nantou

Moderator: Gilbert S. Omenn (Chair, HPP)

07:30-08:30 Joint B/D- and C-HPP EC meeting (TBA)

08:30-09:00 HPP Update Session.

Moderators: Gil Omenn, Young-Ki Paik, Jennifer van Eyk
Highlights from Congress and Discussions on B/D-, C-HPP, and Resources Pillars.
Introduction of Gilbert Omenn is available in pdf format here.
Summary of HPP HUPO day from Young-Ki Paik is available in pdf format here.
Report presentation of B/D-HPP is available here.

09:00-09:30 Bioinformatics Hub, JPR Special Issue 2016 and Future, Experience with HPP MS Guidelines v2.1

Eric Deutsch and Christoph Overall
Summary of HUPO Bioinformatics HUB and experience on HPP MS Guidelines v2.1 by Eric Deutsch is available in pdf format here.

09:30-10:00 Open discussion about recent strategic successes and strategic planning for next year and for 5 years: aims, directions, changes and deliverables

Gil Omenn

10:00-10:20 Coffee Break

10:20-10:50 HPP Plenary Lecture 3

Lung Cancer Genomics (With Cancer Cluster & CPTAC Group)
Dr. Sung-Liang Yu, NUT, Taiwan

10:50-12:30 Reports on the Cluster Group Meetings (C-HPP and B/D-HPP)

Leaders of Each Cluster Group will present highlights of Joint Cluster Meeting held on Sunday (9/18)

Table 1. A Proposed List of Cluster Groups and Meeting Rooms (ver 1)*

Cluster Group Coordinators Joint Members Time
(1) Cancer (report is available here) Siqi Liu, Ed Nice, Hui Zhang, Chris Kinsinger, Jacob Kagan, Shengtao Zhou B/D-Cancer (CPTAC), + more Chr. 1, 7, 8, 9, 11, 12, 13, 17, 20 Sun, 9/18/2016 12:30-15:20 (lunch included)
(2) IVTT (In Vitro Transcription/Translation Platform, report is available here) Gyorgy Marko-Varga, Joshua LaBaer HAI, Protein Std, + More (open to all HPP groups) Chr. 5, 10, 15, 16, 19. This presentation is available in here. Sun, 9/18/2016 12:30-15:20 (lunch included)
(3) Reproductive Biology (report is available here) Charles Peneau, Ghasem Hosseini Salekdeh Model Organism and more (open to whole HPP groups), Chr. 2, 14, X, Y Sun, 9/18/2016 12:30-15:20 (lunch included)
(4) Membrane Proteins Daniel Figeys, Yu-Ju Chen Open to all HPP groups Chr. 3, 4, 6, 7, 18, 21, Mon, 9/19/2016 07:30-08:30
(5) Neuro-degenerative Disorders (report is available here) Jong Shin Yoo, Andrea Urbani HBPP, Autoimmune, open to all HPP groups, Chr. 1, 6, 11, 12, Mt. Mon, 9/19/2016 07:30-08:30
*The term “cluster" can be defined as an informal grouping to facilitate communications between the formal groups (i.e. B/D-HPP, C-HPP, Pillars, CPTAC and related HPP groups) that the HUPO membership and general public see it as a way to organize sessions and workshops rather than setting up a parallel set of groups (Chris Overall) (Appendix 2)

Summary of SRM cluster by Alexander I. Archakov in pdf format is available here.

12:30-13:30 Lunch (Report Session continued, if necessary)

13:30-14:30 HPP Strategy Session
  • Strategic Evaluation by members of SSAB, led by Cathy Costello, Naoyuki Taniguchi, Mathias Uhlen and John Yates
  • HPP Operations & Communication matters (Pineau, Borchers)
  • Resources and Funding

14:30-15:30 Communications, Publications, Resources
  • Publications, including assessment of 2016 JPR special issue and plans for 2017
  • HPP Operations & Communication matters (C. Pineau, C. Borchers)
  • HPP Resources and Funding
  • Upcoming Workshops and Meetings: Brazil, 10-12 Dec 2016; C-HPP WS, Tehran, Iran, May 2017; C-HPP WS joint with EuPA (June, 2018, Santiago, Spain), C-HPP WS St. Malo, May, 2019

16:00-18:00 Boat Tour with Informal Discussion

Travel Information

Venue: Fleur de Chine Hotel. Address: No.23, Zhongzhen Rd., Sun Moon Lake, Yuchi Township, Nantou County 55546, Taiwan, R.O.C. Tel: +886-49-285-6788

  1. Registration for HPP Workshop in Sun Moon Lake (USD 100)
  2. Hotel Reservation in Sun Moon Lake: Visit website for hotel reservation: You may download the reservation form, fill-out and send it to hotel by fax (or email) (See Appendix 7)
  3. How to get Sun Moon Lake: The congress will arrange the shuttle bus from Taipei International Convention Center to Fleur de Chine Hotel, Sun Moon Lake, Nantou. Be sure there at 17:30 on 21st of September:
  4. How to get back to Taipei from Sun Moon Lake: You need to make your own arrangement by making reservation for High Speed Train (or Bus). On the evening of September 22 (Thurs), the congress LOC will arrange the district shuttle bus from Sun Moon Lake directly to the Taiwan High Speed Rail Taichung Station. You need to get train-tickets at the rail station by yourself or make a reservation by online ahead of time, by visiting Taiwan High Speed Rail. There is also bus back to Taipei which should be arranged by each participant. LOC will provide the shuttle bus from Fleur de Chine Hotel to THSR Taichung Station. The Shuttle Bus (transit between FDC hotel and Bus station)
    Schedule as follows: (A) 20:30, September 22 the Fleur de Chine Hotel -> THSR Taichung Station and (B) 17:45, September 23 the Fleur de Chine Hotel -> THSR Taichung Station

Appendix 6

Bioinformatics Hub at HUPO Congress 2016

Overview

The Bioinformatics Hub is a place where bioinformaticians gather together with three aims: (i) to provide their advice, knowledge, and support to anyone with a relevant question; (ii) to discuss current issues and challenges in proteomics informatics with the entire community; and (iii) to work on interesting, synergistic projects and to freely exchange tools, algorithms and know-how with each other, across all labs, seniorities and levels of experience. This will be achieved by specific sessions in the agenda. The Ask the Experts sessions (every day between 9h30 and 12h30) explicitly open the floor to anyone with a question, and leverages the combined experience and expertise of all Hub participants to answer those questions. The Special Interest Topic sessions address a current problem or issue in proteomics informatics in a short (max 20 min lecture), followed by an open, discussion of the topic by all participants, moderated by the organizers. The last type of session, the workshop style sessions, allow participants to work on synergistic topics of their choice, or to exchange know-how, tools and algorithms with the other participants. The Bioinformatics Hub will operate under an open door policy, and that anyone is free to walk in at any time and participate in the work or the discussions, ask a question of someone, or just listen in on what is going on! The bioinformatics hub is meant to be inclusive, low threshold, and aimed at knowledge exchange across all levels of experience.

Also note that representatives from the vendors are very much welcome to participate in the Hub, and typically are well-represented indeed. So your questions on vendor software can also be handled by the experts!

Sunday September 18:

  • 08h30-09h00: Arrival
  • 09h00-09h30: Introduction and concept by organizers
  • 09h30-10h00: Stand-up introductions
  • 10h00-12h00: Pitches: up to 15 minutes for anyone who wants to propose a topic to work on; a tool, library or approach that could be useful for someone; a problem they want address (during the meeting) and can use some help on; a currently neglected question that they think is important to the field; a tool that is currently missing and which they possibly would like to (help) develop
  • 12h00-13h00: Lunch break
  • 13h00-15h00: Pitches continued - Continued 15 minute pitches. These pitches are meant to create seed cores around which people can organize for the subsequent days' workshop sessions
  • 15h00-17h30: Split up into smaller groups and proceed workshop style


Monday September 19:

  • 08h30-10h00: Workshop style sessions
  • 09h30-12h30: Ask the Experts sessions
  • 12h30-13h30: Lunch break
  • 13h30-15h30: Special interest topic + discussion
  • 15h30-17h30: continue workshop style session


Tuesday September 20:

  • 08h30-10h00: Workshop style sessions
  • 09h30-12h30: Ask the Experts sessions
  • 12h30-13h30: Lunch break
  • 13h30-15h30: Special interest topic + discussion
  • 15h30-17h30: continue workshop style session


Wednesday September 21:

  • 08h30-10h00: Workshop style sessions
  • 09h30-12h30: Ask the Experts sessions
  • 10h30-12h30: Glycoproteomics Informatics (details below)
  • 12h30-13h30: Lunch break
  • 13h30-15h30: Special interest topic + discussion
  • 13h30-15h30: Glycoproteomics Informatics Ask the Experts session
  • 15h30-17h30: continue workshop style session


Pitches:

  • Glycoproteomics Informatics (Khoo Kayhooi)
  • HPP Data Interpretation Guidelines (Eric Deutsch)
  • Use of bioRXiv in Computational Proteomics (Eric Deutsch)


Special Planned Topics:

Glycoproteomics Informatics (Organizer: Khoo Kayhooi)

  • Wednesday 10h30-12h30: Glycoproteomics Informatics
    • Pospectus
    • Byonic
    • Pinnacle
    • (Team from China)
    • (Team from Korea)
    • Discussion
  • Wednesday 13h30-15h30: Glycoproteomics Informatics Ask the Experts session (Organizer: Khoo Kayhooi)

Appendix 7

Registration form for Fleur de Chine Hotel at Sun Moon Lake for accommodation for C-HPP workshop can be downloaded in pdf format from here.

Appendix 8

Brasil logo

16th C-HPP WORKSHOP in Commemoration with 100thAnniversary of Brazilian Academy of Science, RIO DE JANEIRO, BRAZIL,
DECEMBER 10 – 12, 2016

TRANSLATING THE CODE OF LIFE INTO PROTEINS AND DISEASES

Brazil Copa Cabana

1. Goals to Achieve

What does the 16th Workshop want to achieve?

  1. Celebrate the 100 years of The Brazilian Academy of Sciences during 2016. The workshop is already incorporated as an official scientific event of the Centennial Anniversary.
  2. Jointly discuss and integrate the Chromosome-centric Human Proteome and the Human Biology Diseases Projects. We hope that all groups will share their ideas on the benefits of the integrated studies of these two Human Proteome Projects.
  3. Present cutting-edge science on disease proteomics and mass spectrometry with impact on diseases and targeted medicine. Plans to invite frontier scientists are under way.
  4. Assessment and evaluation of the first Human Proteome Map.
  5. Other goals of the C-HPP 1st Phase not yet fully addressed are the pursuit of systematic ways for identification of proteoforms and complexes as well as cell & tissue localization
  6. Ask whether is there the need of a distinct data deposition for human proteoforms & complexes?
  7. Begin discussion of phase 2: validation. What actually does this mean? For instance, are we already validating protein existence as gene products when target techniques are used to identify missing proteins?
  8. Science has a strong impact on Society. We propose an open discussion with fellow scientists as well as lay citizens and media on the impact of the Human Proteome Project in our daily life.

2. Preliminary Agenda (Proposed by Rio Team)

  • Integration of the C-HPP with the other projects of Biology and Diseases
  • When would be ready for publication of the first HUPO Human Proteome Map.
  • Personal and Translational Medicine: seeds and fruits of The Human Proteome Project.
  • Are we ready for discussing the preparation of the 2nd Phase of the C-HPP (2018-2022)?
  • Communication with the Public: Deliverables to the public from the project?


*Details on the meeting plan will be available soon at HUPO Web and C-HPP Wiki.