HUPO 2015, September 27 - October 1, 2015, Vancouver, Canada

Final Circular: September 22, 2015. The pdf version is available here.

A Guide to the C-HPP Workshops in Vancouver

Introduction and Overview

• In 2015, the C-HPP consortium has begun its vibrant scientific activities around the globe. In addition to several local meetings, many relevant scientific topics on C-HPP have been discussed: USHUPO, 3/13-16 in Boston; KHUPO, 3/26-27 in Seoul; Y Chromosome Workshop 5/7/2015, Tehran, Iran; 12th C-HPP Workshop, 6/23, Milano, Italy.
• Peter Horvatovich, Secretary General of C-HPP Consortium, has made update on the wiki site where you can download some of slides presented in Milano workshop (see program at C-HPP Wiki).
• To maintain the momentum on these local or regional C-HPP activities, we are preparing for very exciting scientific festivals on the C-HPP in Vancouver. During the annual 2015 HUPO congress in Vancouver, we have a full package of scientific agenda which will certainly move our project forward as a key part of HUPO HPP (see ‘Summary of C-HPP Activities’ below and in Appendices 1-7). Please mark these schedules on your calendar.
• As we did last year, HPP leadership will also plan to host post-Congress HPP workshop (C-HPP + B/D-HPP + Resources Teams) to discuss all matters arising in the HPP research with deep and well-focused agenda (see Appendix 7). We are happy to inform you that there is already enthusiastic response to this post-congress meeting. We were told that the limited seat (~180) has almost been occupied by the registrants. However, we encourage you to visit the registration site here to check any seats available for you.
• The following workshops are now under organization among other HPP programs. We will make you update on each plan in the next circular around the middle of August.
• JPR Editorial Office (EIC, Bill Hancock) has initially received total 45 manuscripts for the C-HPP special issue. Due to some delays in review/revision process of some manuscripts, 25 accepted manuscripts will be published in JPR September issue and the remainder will be carried over in October issue. We appreciate all those editors involved in JPR SI publications.
  Editors for SI: Bill Hancock (EIC), Gil Omenn, Chris Overall, Eric Deutsch and Young-KI Paik.
  

• Special Note on the C-HPP Meeting
• Duty assignment: Three co-chairs and Secretary General will share some workloads on the following workshop sessions in Vancouver.
  • Young-Ki -Paik: Overall administrative affairs, organization of the scientific programs and PIC meeting.
  • Bill Hancock: Co-chairing HPP Keynote Session (with Gil Omenn) on Tuesday (9/29), New Technology Sessions (with Chris) on Thursday, Oct 1, 2015 (post-congress).
  • Lydie Lane: Poster session, Liaise with Vancouver Organizer (Grit Schoenherr, HUPO 2015 Program Manager and Chelsea Prangnell (HUPO) for poster settings.
  • Peter Horvatovich (SG): Taking care of administrative affairs including contacts, meeting minutes, wiki and assistance to poster sessions and PIC meeting.
• Peter Horvatovich, Secretary General of C-HPP Consortium, has made update on the wiki site where you can download some of slides presented in Milano workshop.
• Annual C-HPP EC meeting with Lunch. TBA. Agenda will be ready at the meeting.
  Participants: 3 co-chairs (Young-Ki Paik, Bill Hancock, Lydie Lane), Peter Horvatovich (SG), Chris Overall, Fernando Corrales, Fuchu He.
  

• C-HPP Executive Committee Meeting
  • Agenda: Overview of the programs, discussion topics in PIC meeting, election matters and other issues related to scientific missions.
  • Date and Time: TBA

HUPO 2015 Congress in Vancouver

HUPO 14^th World Congress Venue:
Vancouver Convention Centre
East Building
999 Canada Place
Vancouver, Canada
click here for website

HUPO Congress Scientific Programs at a Glance

Floor Map for C-HPP Workshop Lecture Rooms (11, 12, 18, 19)

Summary of C-HPP Activities in Vancouver (9/27/2015-10/1/2015)

Last updated: September 22, 2015

The program of "Proteomics Standards Initiative and ProteomeXchange Consortium" held on Tuesday 29 September 2015 is available here.

Appendix 1

Sunday, Sept 27, HPP General Investigators’ Meeting, Room: 11

9:00 Gil Omenn: Overview and Metrics. This presentation in pdf format is available here.
9:20 Young-Ki Paik: C-HPP highlights. This presentation in pdf format is available here.
9:40 Jennifer van Eyk: B/D-HPP highlights
10:00 Eric Deutsch & Lydie Lane: PeptideAtlas and neXtProt 2015 updates. The presenation of Lydie Lane is available here, while the presentation of Eric Deutsch is available here. Both presentations are in pdf format.
10:20 Mathias Uhlen & Emma Lundberg: Human Protein Atlas 2015. The presentation in pdf format is available here.

Bill Hancock, Chris Overall, Eric Deutsch, Young-Ki Paik, Gil Omenn.

• Ulrich Eckhard (Univ. of British Columbia, Vancouver, Canada): Recent Progress on TAILS N-terminomics. This presentation is available in pdf format here.
• Pengyuan Yang (Fudan Univ., Shanghai, China): Finding missing proteins from epigenetically manipulated human cell lines.
• Ping Xu (BPRC, Beijing, China): Special enrichment strategies for missing proteins.
• Peter Horvatovich (Univ. of Groningen, Groningen, The Netherlands): In vitro transcription/translation system: a versatile tool. This presentation is available here.

Breakout session 1: C-HPP working session with lunch, led by Young-Ki Paik (Rm 18). See Appendix 1A.
Breakout session 2: B/D-HPP working session with lunch, led by Jennifer van Eyk & Fernando Corrales (Rm 19)
Members of the resource pillars will go to these breakouts.

Proposed Crowd-Sourcing Project on Plasma Proteome Variation, a multiplex SRM/SWATH-MS analysis of priority proteins in HUPO Volunteers (Micheal Snyder)
Initial comments from Senior Scientific Advisory Board (Snyder et al). Presentation of Micheal Snyder is avilable here in pdf format.

Charles Pineau (France, presentation is available here), Siqi Liu (China, presentation in pdf format is available here), Ghasem Salekdeh (Iran), Cecilia Lindskog (Sweden)

YuJu Chen (Taiwan), Takeshi Tomonaga (Japan), Akhilesh Pandey (USA), Mathias Uhlen, (Sweden); Lead Discussant: Alexey Nesvizhskii

20 morning B/D-HPP and C- HPP workshops (M-T-W); Mon lunchtime C-HPP Bioinformatics workshop, Tues Early Career Researchers session, Tues lunchtime C-HPP PI mtg, Tues HPP Congress scientific session, post- Congress HPP Next Steps Thursday Workshop.

Appendix 1A

Agenda for the C-HPP Break-out Session

Part I: Opening Stimulatory Talk: New ideas for missing protein study?

11:30 Use of mouse peptides/tissues for validation of human missing proteins
Christoph H. Borchers, University of Victoria - Genome British Columbia Proteomics Centre

11:45 Q & A

Part II: Update on the C-HPP Restructuring Initiative

11:50 Introduction & Guidance for Group Discussion

11:50 Introduction & Guidance for Group Discussion

12:00 Group Discussion with Lunch
Common agenda to be discussed at each group
Examples: (The followings are just minimum number of items to be discussed)

1. Organization, Designate discussion leader (spokesperson) within each group
2. Goal Setting (year 2016; 2017): -Qualitative and quantitative ways
3. Strategy for coordinated research within group
   1. Sharing reagents (clones, ab, assay) and resources (blood, tissues, cell lines)

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Appendix 2

HC-HPP Poster Session (Exhibit Hall)

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: 7:30 - 09:00, Monday, Sept 28%%%Chromosomes #Odd Numbers (1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21)
Session 2: 16:00 - 17:30, Monday, Sept 28%%%Chromosomes #Even Numbers (2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, X, Y, Mito) and Related Technologies.

• 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 10 Best Outstanding Poster Presenters based on the merits of contents, 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).
• All posters need to be loaded on the board between 19:30-21:00 pm, Sunday. At least one author is required to be in attendance at the poster for the entire duration of the designated session to be qualified for Young Investigators’ Award (Session 1: 07:30-09:00, Session 2: 16:00-17:30
• Posters should be prepared according to the guideline set by HUPO Congress organizer. Poster Presentation Guidelines (see details here)
  • The maximum poster size is: 4’ x 4’. Poster Boards will be Velcro and Push Pin compatible.
  • All Posters will be displayed in the Exhibit Hall at the Vancouver Convention Centre, East Building.
  • Keep illustrations and text simple, remember that one must be able to read it from a distance.
    • Setup hours: Sunday, September 27 – 19:30 – 21:00 (during Welcome Reception)
    • Take down hours: Wednesday, September 30 by 16:30; any posters not removed by 16:30 will be discarded by management.

Poster Printing Guidelines: It is important to set up your slide to a size that is proportional to the printed size of the poster. In PowerPoint, go to Page Setup and select Custom. Fill in the proper width and height.
The following printed poster sizes are available:
48 inches (w) x 48 inches (h) – square
48 inches (w) x 24 inches (h) – landscape
24 inches (w) x 24 inches (h) – square

Maximum poster size: each poster can be a maximum size of 48 inches wide x 48 inches high. Fonts – Choose two fonts at most, nothing cursive. Stick to sans-serif fonts for legibility: Arial and Helvetica are recommended. If you wish to use a serif font, we recommend Times New Roman (Windows) or Times (Macintosh).
Excel Charts – You can paste Excel charts into PowerPoint: from Excel, select your chart and Copy, then in PowerPoint, Paste the chart where you want it to appear. For detailed instructions, please click here.
Word Text – insert a text box into your PowerPoint slides, copy the text from your Word document and paste it into the textbox in your slide.
Image Files – To add image file, select “Insert”>”Picture”. Images should be good quality and appear clear and sharp on your screen. Since they will be enlarged for printing, we recommend that images are set to a resolution of 300 dpi.
Backgrounds – For legibility and viewing ease, we suggest that you keep your backgrounds simple and avoid using dark colors.

Abstract provided for the poster are available here.

The winner of the poster award are:
Amr Elguoshy (Chr X)
Ekaterina Mostovenko (Chr 19)
Concha Gil (Chr 16)
Mauricio Ronci (Mito)
Young-In Kim (Chr 9)
Jin-Young Cho (Chr 13)
Gilberto Domont (Chr 15)
Qidan Li (Chr 1, 8, 20)
Weiming Zhang (Chr 1, 8, 20)

Dong Yang (Chr 1, 8, 20)

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Appendix 3

HPP Bioinformatics Workshop

Date: Monday, Sept 28, 2015
Time: 13:15-14:15
Location: Room: 12
Orgnizer: Eric Deutsch

In this workshop, the current and future HPP data guidelines will be discussed. The goal of the workshop is to understand where the existing guidelines have served the HPP well and poorly, and discuss a proposed set of new guidelines, specifically in the context of advancing confident detections of missing proteins. Each subtopic will be introduced separately, followed by discussion by the workshop participants. Full audience participation is encouraged. The major subtopics include: current HPP data guidelines, data deposition in ProteomeXchange, the 1% protein-level FDR requirement, manual inspection of extraordinary claims, consideration of alternate explanations of the data, use of synthetic reference peptides, and the use of SRM to confirm shotgun results.

Presentation of Eric Deutch on "Enhancing Novel Claim Reporting Guidelines" is available in pdf here.

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Appendix 4

C-HPP Principal Investigator Council Meeting

PIC Members Invited to This Meeting (as of August 1, 2015).

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), 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), Charles Lee and Akhileshi Pandey (Chr 22), Tadashi Yamamoto (Chr X), Ghasem Hosseini Salekdeh (Chr Y), Andrea Urbani (Mito).

Additional Invitees:

Co-PIs of each Chromosome team, Members of C-HPP EC & SSAB, Amos Bairoch, Emma Lundberg, Eric Deutsch, Christoph Borchers and *Designated New PI candidates: Peter Horvatovich (for Chr 5), Ed Nice (for Chr 7): We will warmly welcome those additional designated New PI candidates for chromosome teams other than Chr 5 and 7.
Agenda (tentative).

1. Welcome Remarks
2. Election of the C-HPP Co-Chair Representing ‘America’ (North and South)
3. Discussion and Approval of C-HPP Restructuring Plans (see attached Appendix 6)
4. Discussion and Approval of the New PI candidates who will replace the current PIs (Chr 5, Chr 7, possibly more from Sunday 27th Break-out session) who will start their terms from January 1, 2016.
5. 2016 Plans:

• 14^th C-HPP Workshop in Shanghai, China (early Summer, 2016)
• JPR SI publication plans (Bill Hancock)
• Initiation of Cross-Chromosome Works and more.

6. Open discussion on how to further stimulate C-HPP Activities

Presenation of Young-Ki Paik in pdf format is available here.

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Appendix 5

Proposal for Restructuring C-HPP Teams to Stimulate Scientific Activity of Individual Teams and Cross-Chromosome Studies

1. Aims

• To stimulate activity of each team and work performance of chromosome-based proteomics research in a cooperative manner, resulting in more credible and reproducible results.
• To improve efficiency and make a closer working relationship between chromosome teams and their resource pillar towards completion of the scientific goals.
• To make a strong research focus of chromosome teams using the advanced proteomics platform technologies and resources, enabling secure research funding.

2. Why we need restructuring?

• As the technology in proteomics research and large scale competitive publications came out recently, it was necessary for us to closely re-examine the direction of ongoing projects and C-HPP teams’ operation to ensure we continually are at upfront in the studies of Chromosome-based proteomics.
• At the juncture of a half past in Phase I (2012.9-2018.9), the C-HPP leadership felt that some changes in our working structure and consortium operation are necessary as the strong demands on better corporation between teams are emerging, making necessary to develop a team approach to achieve our scientific goals.
• It is also noticed that at present there exist some differences among the consortium teams with respect to research productivity (e.g., publications to JPR special issues, 2013-2015), efficiency of collaborations, level of secured funding and team management. Thus, to improve the current situation, leadership of C-HPP and HPP had an informal meeting in Milano, Italy (June 25, 2015) and they came up with an idea on restructuring the current C-HPP teams.
• C-HPP leadership felt that the structural changes need to be done stepwise without disturbing overall organization. This new move will give us a golden opportunity to reshape the leadership (PI) of our individual chromosome teams, if necessary, and build new team networks to achieve our scientific goals.

3. Expected Outcomes

• 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.
• 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. For instace, 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 restructured team, 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.

Proposed Action Items by Each Team

Step 1: Each PI of chromosome team may consult his/her team members first and discuss what type of changes would enhance their current operation as well as collaboration to achieve their goals. If this step goes well, then they proceed to step 2.
Step 2: Each team will identify potential new members (e.g., PI, co-PIs, supportive groups, associate members etc.) and partner(s) and start contacting them by email or phone calls before the Vancouver Sunday (Sept 27) workshop. If necessary, they can seek some advice from the C-HPP co-chairs.
Step 3: C-HPP will hold a Break-out session from 11:30 to 13:30 at Room 18, Sunday, Sept 27, in Vancouver Convention Center. In this meeting, they can freely exchange their view on this proposal for their own team development and the potential benefits from this restructuring effort, and each PI reports the outcomes from this discussion to whole group at the meeting. More specifically, 13:30“Interaction with SSAB and Reports from Breakout Sessions (led by Mike Snyder). We also would like to encourage all teams to establish team’s long-term plans (2015.9-2018.9, Phase I and 2018.9-2022.9, Phase II) including the research funding.

Step 4: All decisions made at this meeting will be reported to C-HPP EC and also be ratified by PIC members at PIC meeting on Tuesday, 13:15-14:15, at Room 12. Although this will conclude the debate on the restructuring plan, we will continue to put our all efforts to improve our organizational operation to accomplish our scientific goals throughout the project period (till Sept 10, 2022).

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Appendix 6

HPP Keynote Session, 14:30 - 16:20; Room 11, Tues, Sept 29

• The Progress and Challenges of the HUPO Human Proteome Project - Gilbert Omenn, USA. The presentation in pdf format is available here.
• Strategic Points for Dealing with Missing Protein Mapping in the C-HPP - Young-Ki Paik, South Korea. The presentation in pdf format is available here.
• Controlling False Discovery Rates (FDRs) in Genome-Wide Proteomics Datasets - Juergen Cox, Germany.
• How Does an Extra Chromosome 21 Modulate the Quantitative Human Proteome? - Yansheng Liu, Switzerland.
• Mining Missing Proteins Base on the Transcriptomics and Proteomics to the Individual Testis Tissues - Qidan Li, China.
• Call for a Testis-Epididymis Proteome Project - Charles Pineau, France.
• Refining the Human Proteome: Analyzing Human Tissues by RNA-Seq, Proteomics and Antibodies - Hannes Hahne, Germany.
• Urinary Proteins Originating Uniquely from Each Nephron Segment - Tadashi Yamamoto, Japan.
• Detection of Chromosome 16 Missing Proteins - Spanish HPP - Concha Gil, Spain. The presentation in pdf format is available here.

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Appendix 7

Post-Congress HPP Next Steps Workshop Program

Oct 1, Thursday: Post-Congress HPP Workshop Day (Ticketed session)

Location: SFU Harbour Centre, Joseph and Rosalie Seagal Centre, 515 West Hastings Street
Registration fee: 50 CAD/Light refreshments and lunch included.
Co-Chairs: Gil Omenn, Jennifer van Eyk & Young-Ki Paik

Selected workshop presentations from C- HPP and B/D-HPP (lightning style, 4 min + question) (chairs Jenny van Eyk & YK Paik).

Protein existence levels PE 2,3,4) and novel proteins (attributed to pseudogenes, lncRNAs, PE5 protein entries

• Lessons from multiple HPP groups and JPR manuscripts and Monday Bioinformatics Workshop (Eric Deutsch)
• Validation of claims of detecting missing and novel proteins (Alex Nesvizhskii, Juergen Cox, Jong Shin Yoo)
• Searching for and credibly identifying OR proteins (Tress, Gowda, Deutsch, Beavis)
• More stringent guidelines established by PeptideAtlas & neXtProt (Lane)
• Realization that some predicted proteins will not be detectable by mass spectrometry; should we adjust the denominator? (Corrales, Ulrike Kusebauch)

Aebersold,van Eyk, Borchers: How to assist HPP investigators and the broad community to utilize these advances from the B/D-HPP? How to improve the workflows, especially for low-abundance proteins and complex tissues?

With informal discussion

multiple presenters and active discussion

13:00 C-HPP (Paik, Hancock, Lane, He, Archakov, Chen):
Emphasis on cross-chromosome collaborations (based on the Proposed Clustering Plans discussed on Sunday Lunch Time)-examples:

• In Vitro Transcription/Translation (IVTT) platform involving Chr 5, 10, 15, 16, 19
• Membrane proteins: 4 (Taiwan), 7 (Australia/NZ), 18 (Russia), Mito (Italy); 3 and X (Japan), Chinese teams Chr 1, 8, 20; Korean teams: Chr 9, 11, 13

14:00 B/D-HPP
van Eyk, Aebersold, EC, and B/D team leaders:

• Popular proteins/priority proteins (Borchers)
• Cancer B/D (Zheng, Kinsinger)
• Selected other B/D teams
• Early Career Researchers: mentoring and manuscript competition
• Physician-scientists initiative
• New technologies: oxidation in vivo, unnatural amino acids, iPSCs/organs on a chip, Bio-banking

Lundberg, Uhlen, Snyder: tissue proteome; knock-down initiative collaborations with mass spectrometry

Domon, Moritz, Aebersold: Computational MS (conference in Germany end of August); Cross-linking and MS (new initiative)

All, including SAB members

Fletcher Room must be vacated.

In nearby room.

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