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C-HPP Workshop Bioinformatics, August 9, 2014

Final Circular (last updated 7/8/2014).

CHPP logo

The International Consortium of the Chromosome - Centric Human Proteome Project

10th C-HPP Workshop in Bangkok, Thailand


Proteome Data Management and Identification of Missing Proteins


Photo SiMR Building
Bangkok CHPP Workshop flyer

1. Purpose and Goals of 10th C-HPP Workshop

A. Why do we need this workshop?
Given the recent publication of a large dataset for the HPP in Nature (Pandey lab and Kuster lab: Congratulations to both teams!), data management (verification, validation, peptide level confidence with FDR <1% etc.) became the central issue of the community. As to be expected claims based such large data sets generate issues, such as what information is deposited in ProteomeXchange, the amount of meta-data available for each sample and the availability of MS/MS spectra in the case of novel protein identifications. To keep momentum going after the Busan workshop, which laid out the future direction of the C-HPP development, we are now in a very crucial position to tackle all those pending issues associated with data managements in the course of missing protein identification that should be done in more standardized and coordinated manner. An important discussion will be on the validation process in which a protein identification goes from a laboratory result to an accepted publication to acceptance by PeptideAtlas and GPMDB and is finally included in neXtProt. The organizing committee members propose that this meeting would have a regional flavor but get international chromosome teams together to work on data management which deals with data deposition and curation.

We hope this meeting will bring all those people who are working large databases together and share a common issue as to how each group can provide up-to-date information on each chromosome. For example, the dataset A is the list of missing proteins, from which we have already lot of information but the goal would be to look at the other datasets and see if it is possible to get information in the same way for the missing proteins. The best thing would be to organize a roundtable discussion to address these questions and discuss which information is possible to get from the currently available resources and what is need to be done in the future to get those information. It is quite obvious for us to resolve these issues through this workshop.

B. What things to be achieved through this workshop?
1) Proteomic Dataset: How can we make those deposited data through ProteomeXchange or published data available for the consortium members? Even though many groups wish to share the deposited data, but the process is not so easy. For example, some of data deposited to PDX is not accessible to those annotators (e.g., Eric Deutsch at the PeptideAtlas, Lydie Lane at NexProt, or Ron Beavis at GPMDB).
- What can we do for such inaccessible datasets in the public DB?
- Do we need to ask people to place a link with PXD identifier on the Wiki in order to see which chromosome team placed which datasets online (for sharing)?

2) Proteogenomic Dataset: We have even more difficulties to get access or deposit proteogenomic dataset which include RNAseq and other types of genetic data. Where are other types of data deposited and how they can be linked together? We definitely need to establish some versatile programs to handle these datasets.

3) Enhanced Connections: Although a local upload site is fine, connection from outside to the uploading site seems problematic which may be due to the internet speed going through the national firewall for sending large dataset. Therefore our goal is to figure out how make this connection faster and accessible. For example, we should make the connections faster between a local server and ProteomeXchange server.

Thus, we would like to welcome all of you to sign up this meeting and join us in the active discussion of all data management issues.

2. Outline of Meeting

Title: 10th C-HPP Workshop in Bangkok, Thailand.
Date & Time: August 9, 2014, 08:30- 18:30
Venue: SiMR Building, Siriraj Hospital, Mahidol University, 2 Wanglang Road (formerly Prannok Road), Bangkok, Thailand
Organizing Committee:
- Convener: William S. Hancock
- Program Coordinator: Young-Ki Paik),
- Administrator: Peter Horvatovich
- Local Host: Visith Thongboonkerd
Theme: "Proteome Data Management and Identification of Missing Proteins"
This workshop is open to all C-HPP PIs and their co-workers and will serve as a link between the two to keep the C-HPP activities more interactive.
Funding Support: This workshop is kindly supported by:
- Faculty of Medicine Siriraj Hospital, Mahidol University
- The Thailand Research Fund (TRF)
Transportation: A shuttle service (kindly supported by Faculty of Medicine Siriraj Hospital, Mahidol University), to and from the workshop venue, will be provided only at Miracle Grand Convention Hotel. Please wait at the hotel lobby on August 9th, and the shuttle will depart at 7:00 am sharp (Breakfast at the hotel starts at 6:00 am).
Administration: All matters related to letter of invitation, workshop venue, and accommodation will be handled by the local host, Prof. Visith Thongboonkerd.

3. Scientific Program (final version, updated 7/8/2014)

Note: This program will be updated from time to time at www.c-hpp.org, http://thehpp.org,(external link), hupo.org, wiki site(external link).

08:30-08:50 Welcome & Opening Remarks
Moderator: Visith Thongboonkerd, Mahidol Univ., Bangkok, Thailand
Siriraj Hospital VDO Presentation
Dean, Faculty of Medicine Siriraj Hospital, Mahidol University
Chair, HUPO C-HPP Consortium (Young-Ki Paik)

08:50-09:40 Session 1: Introduction and Opening Talk
Chair: Visith Thongboonkerd, Mahidol Univ., Bangkok, Thailand
Part A'': Briefings on the C-HPP Progress (10 min each)
  • Update & Future Plans on the C-HPP Publications in 2014 and 2015, Bill Hancock, Co-Chair of the C-HPP Consortium & Editor-in-Chief, JPR, Northeastern University, Boston, MA, USA. Presentation in pdf format is avalable here.
  • Update on the Bio-banks within the HPP, Peter Horvatovich, Secretary General, C-HPP (for Gyorgy Marko-Varga). Presentation in pdf format is avalable here.

Part B'': Opening Invited Talks 9 (30 min)
  • Integrative Proteo-Genomic Analysis of Early Onset Gastric Cancer, Sanghyuk Lee, Dept. of Life Science, Ewha Womans Univ., Seoul, Korea

09:40-10:25 Session 2: Invited Talks on "Progress on the Proteogenomics/Transcriptomic Data Productions" (Invited Talks, 15 min each) Part I
Chair: Bill Hancock, Co-Chair, C-HPP Consortium, Editor-in-Chief of JPR, Northeastern University, Boston, MA, USA
  • Looking for missing proteins: an enlightenment from the analysis of free-mRNA and RNC-mRNA data, Siqi Liu, Beijing Genome Institute, Shenzhen, China. The pdf version of this presenation is available here.
  • Integration of ENCODE, Human Body Map and Proteomics Data in a Devoted Dashboard board, Victor Segura, CIMA, University of Navarra, Pamplona, Spain. This presentation in pdf format is available here.
  • Progress of high coverage proteomics study on C-HPP in China, Ping Xu, BPRC, Beijing, China. The pdf version of this presentation is available available here.

10:25-10:45 Coffee Breaks

10:45-11:30 Session 3: Invited Talks on "Progress on the Proteogenomics/Transcriptomic Data Productions" (Invited Talks, 15 min each) Part II
Chair: Bill Hancock, Co-Chair, C-HPP Consortium, Editor-in-Chief of JPR, Northeastern University, Boston, MA, USA
  • Proteogenomic analysis of the human chromosome 9-encoded genes, Je-Yoel Cho, Seoul Natl Univ., Seoul, Korea
  • Comprehensive characterization of a liver tissue and HepG2 cells transcriptoproteome for human chromosome 18, Andrey Lisitsa, Institute of Biomedical Chemistry of Rus. Acad. Med. Sci., Russia. This presentation in pdf format is available here.
  • Human Y Chromosome Proteome Project: 2014 update, Ghasem Hosseini Salakdeh, Royan Institute for Stem Cell Biology and Technology, Tehran, Iran. This presentation in pdf fromat is available here.

11:30-12:30 Session 4: Strategy for Identifying Missing Proteins. Part I (15 min each)
Co-Chairs: Mark Baker, HUPO President-elect, Macquarie Univ., Sydney, Australia and Ping Xu, BPRC, Beijing, China
  • Metrics and strategy for identifying missing proteins, Gil Omenn, Chair, HPP EC, Univ. of Michigan, Ann Arbor, USA. The pdf version of this presentation is available here.
  • A Combined strategy for Identifying missing proteins, Young-Ki Paik, Chair, C-HPP Consortium, Yonsei Univ., Seoul, South-Korea. The revised version of this presenation is available here.
  • Identification of missing proteins by profiling of specific tissues and cell lines, lessons learnt in the hunt for olfactory receptors located on chromosome 17 and identification of potential co-expression events, William S. Hancock, Co-Chair, C-HPP Consortium. The presenation in pdf format can be downaloaded from here.

12:30 - 13:30 Lunch

13:30-15:00 Session 5: Strategy for Identifying Missing Proteins. Part II (15 min each)
Co-Chairs: Mark Baker, HUPO President-elect, Macquarie Univ., Sydney, Australia and Ping Xu, BPRC, Beijing, China
  • Sydney Inaugural HPP Missing Proteins Workshop Report, Mark Baker, President-elect HUPO (Chr 7 PI). This presentation is available in pdf format here.
  • Identification of Missing Proteins in Aggregated Proteins Qing-Yu He, Jinan University, Guangzhou, China. The pdf version of this presentation is available here.
  • Missing proteins hidden in the membrane proteome Yu-Ju Chen, Institute of Chemistry, Academia Sinica , Taipei, Taiwan. The pdf version of this presentation is available here.
  • To conquer the last hard-core of missing proteome, Pengyuan Yang, Fudan Univ., Shanghai, China. The pdf version of this presentation is available here.
  • Size of master proteome expressed by single chromosome in different tissues and cells. If there are missing master proteins in proteome? Alex Archakov, Institute of Biomedical Chemistry of Rus.Acad.Med.Sci., Russia. This presentation in pdf format is available here.

15:00-16:00 Session 6: Practical aspects of individual data management (60 min)
Co-Chairs: Peter Horvatovich, Secretary General of the C-HPP Consortium, University of Groningen, Netherlands and Andrey Lisitsa, Institute of Biomedical Chemistry RAMS, Moscow, Russia

Special Invited Spekaer (Skype): Juan Antonio Vizcaino, EMBL-EBI, Hinxton, Cambridge, UK. The presentation in pdf is available here.

Part A. Proteomic Dataset with PXD
Q1. How to make deposited through ProteomeXchange or published data available for the consortium members as well as public DB managers (GPMDB, neXtProt, PeptideAtlas and ProteinAtlas)?
Q2. What can we do for such inaccessible datasets in the public DB?
Q3. Do we need to ask people to place a link with PXD identifier on the Wiki in order to see which chromosome team placed which datasets online (for sharing)?
Q4. Sharing any experience with public databases (PeptideAtlas?, ProteinAtlas? ProteomeXchange? GPMDB? neXtProt?)?

Part B. Proteogenomic Dataset:
Q1. How to make easy access to or deposit proteogenomic dataset which include RNAseq and other types of genetic data.
Q2. Where are these types of data deposited and how they can be linked together?
Q3. Other issues?

Part C. Difficulties in Connections:
Q1. How to make the connections between local server and central DBs much faster and accessible (e.g.. local server and ProteomeXchange)
Q2. Strategy for Data sharing within HPP: What are the bottlenecks or obstacles?
Q3. Partnering with B/D-HPP teams: What is the full list of active teams with their research interests and resources?
Q4. Integration with the overall HPP plan: How?
Q5. Share information about sample sets analyzed
Q6. Sharing reagents such as antibodies, expression vector clones, cell lines etc,
Q7. Disease/biology collaborations based on pathways, gene sets or amplicons

16:00-16:20 Coffee Breaks

16:20-17:50 Session 7: Roundtable Discussion on “Problems and Solutions for the Large Dataset Validations”
Co-Chairs: William S. Hancock (Co-Chair of C-HPP EC & Editor-in-Chief of JPR, Northeastern University, Boston, MA, USA) and Gil Omenn (Chair of HPP EC, University of Michigan, Ann Arbor, MI, USA)
Panelists (Country Representatives):
Mark Baker (Australia)
Siqi Liu (China)
Ghasem Hosseini Salakdeh (Iran)
Tadashi Yamamoto (Japan)
Jong Shin Yoo (Korea)
Peter Horvatovich (Netherlands)
Andrey Lisitsa, (Russia)
Victor Segura (Spain)
Visith Thongboonkerd (Thailand)
Yu-Ju Chen (Taiwan)
Ravi Sirdeshmukh (India)
Terence Poon (Hong Kong)
Maxey Chung (Singapore)

Part A: What are the most burning issues?
Q1. Proof of validity of a large dataset available in the public DB: Production, Repository, Exchange, Quality, Reproducibility (e.g., the protein identifications with higher rate of false discovery than the C-HPP consensus methods.).
Q2. How to make major analytical assessments of the large datasets to be incorporated into well annotated data resources (GPMDB, PeptideAtlas, neXtProt, ProteinAtlas).
Q3. How to make corrections if the spectra do not support assignments?
Q4. How well the definition of datasets are suited to store and provide information from already data resources/infrastructure (GPMDB, Nextprot, proteomeXchange etc) and if information is not present, what resources are available to implement these needs. Role of Wiki and individual groups in Data and Information management/sharing.

B. Potential Solutions-Standard Protocols Adopting a Multi-level Data Validation (proposed by William S. Hancock)
  1. Individual scientists’ laboratory data using accepted practices and submit data to ProteomeXchange.
  2. Work is reviewed and accepted (or not) by a high impact journal and published (work now has published status).
  3. MS data is reviewed by PeptideAtlas and/or GPMDB if OK theidentification is labeled as provisional (correct word?).
  4. Final step where neXtProt accepts the identification along with other data such as sample curation.
  5. The same process is followed for tissue expression studies where the final arbitrator is ProteinAtlas.

17:50-18:20 Session 8: Amended Version of Long Term Plans and Deliverables
Co-Chairs: Young-Ki Paik (Chair of C-HPP EC, YPRC, Yonsei University, Seoul, Korea) and William S. Hancock (Co-Chair of C-HPP EC & Editor-in-Chief of JPR, Northeastern University, Boston, MA, USA)
*Drafted version of updated long-term plans and milestones along with HPP community: Free Discussion following the presentation of plan. (Based on the feedbacks given by KC-HPP (Chr 9, 11, 13), Juan Pablo Alba (Chr 16), Mark Baker (Chr 7), Alex Archakov (Chr 18), Jerome Garin & Yves Vandenbrouck (Chr 14) and Lydie Lane & A. Bairoch (Chr.2); Reflection of the recent Nature papers on the milestones
  • Future Plans and Perspectives for the C-HPP
    • 11th C-HPP Workshop Plans in Madrid 2014 (Oct 5-8, Oct. 9 Segovia)
    • 12th C-HPP Workshop Plans in Milano 2015 (June 23-24, 2015)
    • 13th C-HPP Workshop Plans in Vancouver (Sept 26-30, 2015)
    • 14th C-HPP Workshop Plans in Shanghai (Spring, 2016) (TBA)
    • 15th C-HPP Workshop Plans in Taipei (Sept 18-22, 2016)
    • 16th C-HPP Workshop Plans in Tehran, Iran (Spring, 2017) (TBA)
    • 17th C-HPP Workshop Plans in Dublin, Ireland (Sept 2018) (TBA)

18:20-18:30 Conclusions: William S. Hancock
Co-Chair of C-HPP EC & Editor-in-Chief of JPR, Northeastern University, Boston, MA, USA

18:30-21:30 Dinner
Sponsored by Sponsored by Faculty of Medicine Siriraj Hospital, Mahidol University

The end of workshop

4. Excursion: August 10, 2014, a Half Day Tour:

Complimentary to all participants.
Kindly supported by Faculty of Medicine Siriraj Hospital, Mahidol University.

Tentative Program:

10:30-12:00 Vimanmek Mansion

The tour should be ended no later than 13:00 and the shuttle will send all back to Miracle Grand Convention Hotel. A lunch box will be served on the shuttle bus.
Please wait at the hotel lobby on August 10th, and the shuttle will depart at 7:15 am sharp.
Those who plan to travel after the tour can check-out on August 10th and leave luggage on the shuttle bus during the tour.
After the tour, there will be another complimentary shuttle to go directly to Suvarnabhumi International Airport. Please register for the shuttle on Aug 9th during the workshop.

5. Acknowledgements

The organizing committee would like to thank for kind contributions (congress materials and other supports) from:
  • AB SCIEX
  • Bruker Daltonics
  • Bio-Rad Laboratories, Inc.

6. Confirmed Participants

Alessio SoggiuUniversity of Milan, Milan, Italy
Alexander ArchakovInstitute of Biomedical Chemistry RAMS, Moscow, Russia
Andrey LisitsaInstitute of Biomedical Chemistry RAMS, Moscow, Russia
Anil K. MadugunduInstitute of Bioinformatics, Bangalore/Karnataka, India
Fuchu HeBeijing Proteome Research Center, Beijing, China
Ghasem Hosseini SalekdehRoyan Institute, Tehran, Iran
Gilbert S. OmennUniversity of Michigan, MI, USA
Haidan SunBeijing Institute of Genomics, Beijing, China
Je-Yoel ChoSeoul National University, Seoul, Korea
Jin-Young ChoYonsei Proteome Research Center, Seoul, Korea
Jong-Shin YooKorea Basic Science Institute, Daejon, Korea
Ju-Wan KimYonsei Proteome Research Center, Seoul, Korea
Kyung-Hoon KwonKorea Basic Science Institute, Cheongju, Chungbuk, Korea
Mark S. BakerMacquarie University, NSW, Australia
Maxey ChungNational University of Singapore, Singapore
Pengyuan YangFudan University, Shanghai, China
Peter HorvatovichUniversity of Groningen, Groningen, the Netherlands
Ping Xu BeijingProteome Research Center, Beijing, China
Qing-Yu HeJinan University, Guangzhou, China
Quanhui WangBeijing Institute of Genomics, Beijing, China
Ravi SirdeshmukhInstitute of Bioinformatics, Bangalore, India
Sanghyuk LeeEwha Womans University, Seoul, Korea
Savita JayaramInstitute of Bioinformatics, Bangalore/Karnataka, India
Seul-Ki JeongYonsei Proteome Research Center, Seoul, Korea
Siqi LiuBeijing Institute of Genomics and BGI-Shenzhen, China
Soo-Youn LeeSamsung Medical Center, Seoul, Korea
Tadashi YamamotoNiigata University, Niigata, Japan
Terence C.W. PoonChinese University of Hong Kong, Shatin, Hong Kong
Tong WangJinan University, Ghangzhou, China
Victor SeguraCenter for Applied Medical Research (CIMA), Pamplona, Spain
Visith ThongboonkerdSiriraj Hospital, Mahidol University, Bangkok, Thailand
William S. HancockNortheastern University, Boston, MA, USA
Young-Ki PaikYonsei University, Seoul, Korea
Yu-Ju ChenInstitute of Chemistry, Academia Sinica, Taipei, Taiwan