Loading...
 
Last Update: Sept 26, 2014 (Final)

11th C-HPP Workshop, Segovia, October 9, 2014

A Guide To C-HPP Activities in Madrid and Segovia

CHPP world map updated on 9 September 2014


1. Introduction

  • During the past 8 months, we had many successful C-HPP scientific meetings in several places such as Busan (March 26, 2014), Sydney (July 30, 2014; by Mark Baker), and Bangkok (August 9, 2014). We are now in much better position to set out future plans and discuss all pending issues for our project in Madrid(external link) (Oct 5-8) and Segovia (Oct 9 see Appendix 5).
  • We are pleased to announce that Fernando Corrales has been approved to be a new PI for Chr 16 (termed General Coordinator) by the Spanish Granting Agency (The IP assembly of ProteoRed). He will assume the job previously hold by Juan Pablo Albar. In our PIC meeting in Madrid (Wed, Oct 8, 08:00-09:20, Room C), his role as PI for Chr 16 will be formally approved by PIC members.
  • Enclosed please find the updated version of workshop plans in Madrid (11th C-HPP Workshop) and Segovia (Joint HPP meeting). We hope all of you will sign up these two meetings where you will find many updated agenda on the future HPP development. In Madrid PIC meeting (on Wed), we will discuss few key pending issues as well as new plans for 2015 (Milano meeting June 23, 2015; JPR special issue publication, middle of 2015 etc.) (see Appendix 4 for details). If PI of any chromosome group is not available at the PIC meeting, please let us know his/her designator (voting right is given only to the confirmed representative) by Oct 1, 2014.
  • Most of this year’s C-HPP related meeting materials (presentation in ppt files) are available at the C-HPP wiki site(external link).

2. Tentative Schedule of the 11th C-HPP workshops in Madrid

Congress Venue:
Centro de Convenciones Norte, IFEMA Feria de Madrid, Avenida del Parten, 28042 Madrid(external link).
Tel. +34 902 22 15 15 for the website click here(external link).

C-HPP Activities from Sunday to Wednesday in Madrid

Updated on September 10, 2014


SUN, Oct. 5
10:00-16:00, Rm D
MON, Oct 6
8:00 - 9:20 Room C
TUES, Oct 7
8:00 - 9:20 Exhibit Hall
WED, SEPT 8
8:00 - 9:20 Room C
HPP General Investigators Meeting


(Chaired by Gil Omenn)


a. Overview of Progress,
b. Metrics, and Publications from the HPP
c. B/D-HPP Highlights,
d. C-HPP Highlights.
e. Update of HPP Metrics
f. Bioinformatics discussions and standardized re-analyses of major datasets of four major publications in 2014:
g. Discussion over working lunch about inter-relationships across HPP components and bioinformatics approaches.
h. Antibody and MS Resource Pillars
i. SSAB Panel, overview, strategic comments from SSAB members
j. Town Hall Meeting Open Forum – on B/D- and C-HPP Collaboration
k. Meeting of SSAB with l. HPP-EC for feedback.

Details in Appendix 1
C-HPP (Part 1)

● New Technology
(Chaired by Bill Hancock)


a. SRM measurement of missing proteins

b. RNA analysis, including predicting when transcript forms protein

c. Integration of RNA-Seq and proteomics

d. Approaches to ASV and SNV characterization such as down top MS, adoption of protein chemistry methods

e. Identification of protein families and sharing of specific data across chromosome families, integrated proteome browser

Details in Appendix 2
C-HPP (Part 2)

● Poster Session
(Chaired by Gyorgy Marko-Varga)


Poster Awards (Cash Prize and Award Certificate) will be given to


Total 10 Best Outstanding Poster Presenters


● It is required to load the poster no later than 5 pm, Monday. In addition to the C-HPP subjects (e.g., mapping missing proteins, ASV, PTM on each chromosome), any papers related to common technology or resources for C-HPP can also be presented. All eligible presenters should be one of the associated members of C-HPP consortium as of Sept 1, 2014.

Further Information in Appendix 3
C-HPP (Part 3)

● PIC Meeting
(Chaired by Young-Ki Paik)


● Topics: Metrics for success, elections, individual PI updates and Meeting Plans for 2015-2018


Details in Appendix 4

-------------------------

HPP Plenary Session

● 15:00 - 16:50 pm

Room A

--------------------------

Oct 9, Thursday

Segovia Meeting

Appendix 5



  • Special Note on the C-HPP Meeting
  • Duty assigned: Three co-chairs will share some workloads on the following sessions in Madrid.
- Young-Ki -Paik: Overall administrative affairs, organization of the scientific programs and PIC meeting (Part 3)
- Bill Hancock: New Technology Sessions (Part I), Liaise with HUPO (Activity Report at the Council)
- György Marko-Varga: Poster session (Part 2), Liaise with Madrid Organizer for poster settings and co-chair with Bill in Part 1.
- Peter Horvatovich (SG): Taking care of administrative affairs including contacts, meeting minutes, wiki and assistance to poster sessions and PIC meeting.

  • 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: October 2014 till August 2016) who will assume the rest period of Juan Pablo Albar’s term (till Sep 9, 2016). We encourage you to send us the names of nominee for this position by Oct 1. Potential candidate may be from the European Region to maintain the balance between regions.


Election: The term of this new MAL will be those years left by Juan Pablo Albar (Oct, 2014–Sep 9, 2016). The following procedure is proposed for this election:
  • Oct 1, 2014: Closing nominations from PIC members
  • Oct 2, 2014: Verification of his/her candidacy by the C-HPP EC
  • Oct 8, 2014: Voting will take place during the PIC council meeting in Madrid


  • B/D-HPP related activities
    • Antibodies (also functions as an independent HUPO initiative)
    • Brain
    • Cancer
    • Cardiovascular
    • Diabetes
    • Epigenetic Chromatin
    • EyeOME
    • Glycoproteomics (also functions as an independent HUPO initiative)
    • iMOP (also functions as an independent HUPO initiative)
    • Kidney Urine
    • Liver
    • PediOME
    • Plasma
    • Stems Cells
    • Respiratory Disease B/D-HPP workshop. Program is availble here.

3. C-HPP Activity Report to HUPO Council:

As determined in the previous PIC meeting in Boston 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 these 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 at the ened of this year.

4. Segovia HPP Satellite and Town Hall Meeting in 2014 (see Appendix 5):

Bill’s Suggestions
Goal: To increase protein annotation (missing and orphan proteins so that B/D studies will be richer and more informative

Roundtable: bioinformatics covering the topics of the joint session. Goal is to drive consensus on the deposition of large proteomic data sets and acceptance into the data bases (PeptideAtlas, GPM.DB and Next prot). Discussion should include the framework of the 5 steps of acceptance of an individual laboratory results.
Rapid fire reports of each of the chromosome Pis.

Discussion of the integration of C-HPP and B/D HPP:
  1. A cross HPP effort to find the missing proteins (share information on sample sets, ensure deposition of data sets to ProteomeXchange, identify sources of rare sample sets, promote study of rare diseases,)
  2. Cross validation of proteomic results with antibody data in ProteinAtlas (analysis of protein families by unique peptide sequence or unique epitopes). Choose 3 protein families as test cases.
  3. Develop effective antibody capture reagents for the missing or orphan proteins, example collaboration between ProteinAtlas and Monash Ab facility
  4. How to generate data on protein interactions for the ‘orphan’ proteins.
  5. Most proteins are not mapped into protein pathways except by homology with well studied proteins. How can we proceed to expand our pathway knowledge?
  6. Targeted PTM analysis of the poorly characterized proteins

Back to the future, proteomics to protein chemistry
  1. The need for multiple enzyme digestions and top down MS for full sequence determination to characterize small changes in amino acid sequence (ASVs and SNVs). This will require good Ab capture reagents.
  2. Genome annotation in terms of protein expression/ common functions in a given genomic region

(see Appendix 5 for more details)

See you there soon!

Young-Ki, Bill and György
Co-Chairs, C-HPP
Peter, SG, C-HPP

The full HPP activity Guide to Madrid and Segovia si available in pdf format here.

Appendix 1

Agenda for HPP Investigators Meeting at HUPO2014

Madrid Congress (updated 9/8/14)

Sunday, October 5, 2014: 10:00 - 16:00 Rm D


10:00-10:10 Overview of Progress, Metrics, and Publications from the HPP
Gil Omenn, Chair, HPP, Univ. of Michigan, Ann Arbor, MI, US. This presentation is available here. The presnetation contains one other lecture of Gilbert Omenn presented at HUPO 2014 from slide 28.

10:20-10:40 B/D-HPP Highlights, priority protein lists by disease, Clinician- Scientist initiative, Workshops plan
  • Ruedi Aebersold, ETH Zurich, Switzerland. This presentation is available online in pdf format here.
  • Jennifer van Eyk, Cedars-Sinai Health System, Los Angeles, CA, US
With Discussion

10:40-11:00 C-HPP Highlights, Busan and Bangkok workshops, Congress workshops
  • Young-Ki Paik, Chair, C-HPP Initiative, Yonsei Univ., Seoul, Korea. This presentation is available here.
  • William S. Hancock, Co-Chair, Northeastern Univ., Boston, MA, US
With Discussion

11:00-11:55 Update of HPP Metrics: neXtProt (9/14), PeptideAtlas (8/1/14) & GPMdb
Moderator: Gil Omenn
Bioinformatics discussions and standardized re-analyses of major datasets of four major publications in 2014:
  • Kim et al (Pandey lab, PXD000561(external link))
  • Wilhelm et al (Kuster lab, PXD000865(external link))
  • Guo et al (Mirzaei lab with various proteolytic enzymes), and TCGA datasets
Comments
  • Amos Bairoch & Lydie Lane, SIB, Geneva, Switzerland
  • Eric Deutsch, Inst. Systems Biology, Seattle, WA, US. Presenation of Eric Deutsch on MRMAtlas is available here. Presenattion of Eric Deutsch on Peptide Atlas is available here.
  • Akhilesh Pandey, Johns Hopkins & Bangalore; Bernhard Kuster, TUM, Munich; Henry Rodriguez, Bethesda

12:00-12:50 Discussion over working lunch about inter-relationships across HPP components and bioinformatics approaches
Moderator: William S. Hancock

13:00-13:30 Antibody and MS Resource Pillars
Cross-validation with Ab and MS approaches including MRM based Quantitation for HPP
  • Emma Lundberg, SciLifeLab, Stockholm, Sweden
ProteomeAnalyzer Project
  • Bruno Domon, Centre Sante’ Clinical Proteomics Center, Luxembourg. This presenation is available here.

13:30-14:00 SSAB Panel, overview, strategic comments from SSAB members
Moderator: Mike Snyder, Stanford Univ., Stanford, CA, US
  • Cathy Costello, Boston Univ, Boston, MA, US, Matthias Mann, Max Planck, Munich, Germany, Kate Rosenbloom, Univ of California Santa Cruz/ENCODE, US

14:00-16:00 Town Hall Meeting Open Forum – on B/D- and C-HPP Collaboration
Co-Chairs: Ruedi Aebersold and Young-Ki Paik

Part 1. Integrated Data Management
“Priority Proteins”/”Popular Proteins”, including PTMs, Splice Isoforms, SNPs/SAAPs, for specific diseases; use of SRM peptides, spectral libraries, and SRMAtlas
  • Jennifer Van Eyk, Ruedi Aebersold, Eric Deutsch and B/D Teams
ProteomeExchange experience: PDX identifiers and release of data on acceptance, uploading large data sets
Proteogenomics/RNA Seq, Integrated ‘Omics analyses
  • Gyorgy Marko-Varga, Lund Univ., Sweden, Jennifer Harlow, Kate Rosenbloom, Michael Snyder (ENCODE)

Part 2. Biological Impact of Missing Proteins on C-HPP and B/D-HPP Research
Updates from neXtProt on the missing and orphan proteins
  • Lydie Lane and Amos Bairoch, SIB, Switzerland. This presentation is available here.
A Strategy for Bioinformaticians to take a deep dive on Chr-specific Missing Protein lists (as discussed in Bangkok C-HPP workshop)
  • William S. Hancock, Co-Chair, C-HPP Consortium , Gyorgy Marko-Varga, Co-Chair, C-HPP Consortium

Timing of JPR special issue and standardization of data bases for publication metrics: What is the best theme and date (middle of 2015) for this special issue?

Part 3. Opportunities to explore collaborations within and between B/D-HPP and C-HPP

4:00-5:00 Meeting of SSAB with HPP-EC for feedback
Mike Snyder and SSAB Group

Appendix 2

C-HPP Meeting (Part 1): New Technology

Monday, October 6, 2014: 08:00 - 09:20 Rm C


Chaired by Bill Hancock

Invited Speakers: Confirmed as of 9/8/2014
Robert Moritz; Christoph Borchers; Ravi Sirdeshmukh; Siqi Liu; Gyorgy Marko-Varga

a) SRM measurement of missing proteins (8.05 to 8.20), Christoph Borchers, Rob Moritz, Ulrike Yassene, Alex Archakov. This presenation is available here.

b) Integration of RNA-Seq with proteomics, control of when transcript forms protein (8.25 to 8.45), Siqi Liu, Carol Nillsson , Ravi Sirdeshmukh

c) Approaches to ASV and SNV characterization (8.50 to 9.05), Gil Omenn, Akhilesh Pandey

d) Identification of protein families, integrated HPP browser (9.05 to 9.20), Lydie Lane, Dong Li, Ed Nice.Presentation of Lydie Lane and Dong li Lydie and Dong.pdf. Presenation of Ed Nice on "Antibody-Based Strategies for Detection of Missing Proteins" here.

Appendix 3

C-HPP Meeting (Part 2): Poster Session

Tuesday, October 7, 2014: 08:00 - 09:20 Exhibit Hall


  • Chaired by Gyorgy Marko-Varga
  • Evaluation Team: TBA
  • Poster Awards (Cash Prize and Award Certificate) 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 for C-HPP can also be presented. All eligible presenters (first authors or senior authors) should be one of the members (PI, co-PI or participating members) of C-HPP consortium as of Sept 1, 2014.
  • Each presenter needs to load the poster no later than 5 pm, Monday. In addition to the C-HPP, Any papers related to common technology or resources can be presented.
  • Gyorgy Marko-Varga will organize the evaluation committee and scoring sheet for selection of the winners.
  • Presentation Times:
08:00-08:40: Group A: Chromosome 1-12

08:40-09:20: Group B: Chr 13-22, X, Y and Related Technologies (bioinformatics, MS, Ab, reagents etc.)
  • There will be additional time for presentation if necessary. Chair will notify this info.

List of posters
  • P-NN4: 1-GPA (Integrated GlycoPeptid Analyzer): High-throughput MS Platform for Automated N-glycoproteome Analysis Applicable to Human Proteome Project, Heeyoun Hwang, Gun Wook Park, Jin Young Kim, Ju Yeon Lee, Hyun Kyoung Lee, Ki Na Yun, Mi Hee Cheon, Hoi Keun Jeong, Eun Sun Ji, Kwang Hoe Kim, Young Hee Ahn , Yong-Sam Kim, Jeong Heon Ko, Jae-Han Kim, Hyun Joo An, Young-Ki Paik, Jong Shin Yoo.
    1-GPA (Integrated GlycoPeptid Analyzer) : High-throughput MS Platform for Automated N-glycoproteome Analysis Applicable to Human Proteome Project, Heeyoun Hwang
  • P-NN3: Mining Missing Membrane Proteins from Lung Cancer Tissues and Cell lines, Baby Rorielyn T. Dimayacyac-Esleta, Reta Birhanu Kitata, Wai-Kok Choong, Chia-Feng Tsai, Hsin-Yi Wu, Yi-Ju Chen, Ting-Yi Sung, Yu-Ju Chen
    Mining Missing Membrane Proteins from Lung Cancer Tissues and Cell lines, Baby Rorielyn T. Dimayacyac-Esleta, Reta Birhanu Kitata, Wai-Kok Choong, Chia-Feng Tsai, Hsin-Yi Wu, Yi-Ju Chen, Ting-Yi Sung, Yu-Ju Chen
  • P-NN2: Missing Protein Family on Human Chromosome, Fan Zhong, Yang Zhang, Pengyuan Yang, Fuchu He
    Missing Protein Family on Human Chromosome, Fan Zhong, Yang Zhang, Pengyuan Yang, Fuchu He
  • P-253: Revisiting the Identification of Canonical Splice lsoforms through Integration of Functional Genomics and Proteomics Evidence from the Chromosome 17 Human Proteome Project, Hongdong Li, Rajasree Menon, Gilbert S. Omenn, Yuanfang Guan
    Revisiting the Identification of Canonical Splice lsoforms through Integration of Functional Genomics and Proteomics Evidence from the Chromosome 17 Human Proteome Project, Hongdong Li, Rajasree Menon, Gilbert S. Omenn, Yuanfang Guan
  • P-932: Disecting Chromosome 16 proteome, Fernando J. Corrales, Concha Gil, Francisco Blanco, Manuel M. Sanchez del Pino, Jesus Vazquez, Javier Munoz, Enrique Santamaria, Felix Elortza, Eliandre Oliveira, Francese Canals, Alberto Pascual-Montano, Jesus, M. Arizmendi, Josep Marla Estanyol, Silvia Barcel, Irene Orera, M. Gonzalez-Barderas, Jaime Sancho, Fernando Vivanco, Manuel Fuentes, Eduard Sabido, Joaquim Abian, Juan P. Albar
    Disecting Chromosome 16 proteome, Fernando J. Corrales, Concha Gil, Francisco Blanco, Manuel M. sanchez del Pino, JesUs V;izquez, Javier Mu~oz, Enrique Santamaria, F
  • P-929: CAPER 3.0: a scalable cloud-based pipeline for the data-intensive analysis of proteomic datasets, Shuai Yang, Hongli Diao, Honglei Li, Xinlei Zhang, Dong Li, Fuchu He
    CAPER 3.0: a scalable cloud-based pipeline for the data-intensive analysis of proteomic datasets, Shuai Yang, Hongli Diao, Honglei Li, Xinlei Zhang, Dong Li, Fucbu He
  • P-?: Approaching the Organellar Brain Proteome to Understand the Molecular Basis of Schizophrenia, Erika Velasquez, Fabio CS Nogueira, Livia Goto, Magno Junqueira, Andrea Schmitt, Daniel Martins de Souza, Gilberto B. Domont
    Approaching the Organellar Brain Proteome to Understand the Molecular Basis of Schizophrenia, Erika Velasquez, Fabio CS Nogueira, Livia Goto, Magno Junqueira, Andrea Schmitt, Daniel Martins de Souza, Gilberto B. Domon
  • P-915: GenomewidePDB v 2.0: Update on the transcriptomic and proteomic expression data with alternatively spliced products layered in a genome-wide manner, Seul-Ki Jeong, Keun-Na, Jong-Sun Lim, William S. Hancock, Young-Ki Paik.
    GenomewidePDB v 2.0: Update on the transcriptomic and proteomic expression data with alternatively spliced products layered in a genome-wide manner, Seul-Ki Jeong, Keun-Na, Jong-Sun Lim, William S. Hancock, Young-Ki Paik
  • P-906: Chromosome 18: Master Proteome, Russian consortium
    Chromosome 18: Master Proteome, Russian consortium
  • P-903: The Mitochondrial Human Proteome Project - MT-HPP, Italian consortium
    The Mitochondrial Human Proteome Project - MT-HPP, Italian consortium
  • P-NN1: Easy Omics Annotation - A platform of Integrative analysis of large proteomics data set, Chinese Human Chromosome Proteome Consortium
    Easy Omics Annotation - A platform of Integrative analysis of large proteomics data set, Chinese Human Chromosome Proteome Consortium
  • P-923?: Chromosome X, Japaneese Chromosome Consortium
    Chromosome X, Japanese Chromosome Consortium
  • P-937: Missing proteins in Chromosome 16 Spanish HPP, Manuel Fuentes , Felipe Clemente, Maria Luisa Hernaez, Maria Gonzalez-Gonzalez, Noelia Dasilva , Fernando Corrales, Juan Pablo Albar, Concha Gil
    Missing proteins in Chromosome 16 Spanish HPP, Manuel Fuentes , Felipe Clemente, Maria Luisa Hernaez, Maria Gonzalez-Gonzalez, Noelia Dasilva , Fernando Corrales, Juan Pablo Albar, Concha Gil
  • P-936: Transcriptomic profiling towards the localization of the missing proteins, Elizabeth Guruceaga, Fernando J Corrales, Victor Segura
    Transcriptomic profiling towards the localization of the missing proteins, Elizabeth Guruceaga, Fernando J Corrales, Victor Segura
  • P-935: Subcellular fractionation enhances Chromosome 16 Proteome Coverage, Chormosome 16 Consortium
    Subcellular fractionation enhances Chromosome 16 Proteome Coverage, Chormosome 16 Consortium
  • P-934: Targeting proteins of chromosome 16, Leticia Odriozola, Nuna Colome, Francese Canals, Maria L Hernaez, Felipe Clemente, Concha Gil, Patricia Fernandez, Cristina Ruiz, Irene Orera, Silvia Barcelo, Miguel Marcilla, Severine Gharbi, Fernando Vivanco, Eduard Sabido, Eva Perez, Manuel M Sanchez del Pino, Joaquin Fernandez, Juan P Albar, Fernando J Corrales.
    Targeting proteins of chromosome 16, LetiCia Odriozola, Nuna Colome, Francese Canals, Maria L Hernaez, Felipe Clemente, Concha Gil, Patricia Fernandez, Cristina Ruiz, Irene Orera, Silvia Barcelo, Miguel Marcilla, Severine Gharbi, Fernando Vivanco, Eduard Sabido, Eva Perez, Manuel M Sanchez del Pino, Joaquin Fernandez, Juan P Albar, Fernando J Corrales.
  • P-914: Development of improved subcellular fractionation procedures of the placental membrane proteins for discovering disease biomarkers and missing proteins, ''Seul-Ki Jeong, Keun-Na, Jong-Sun Lim, William S. Hancock, Young-Ki Paik".
    Development of improved subcellular fractionation procedures of the placental membrane proteins for discovering disease biomarkers and missing proteins, Seul-Ki Jeong, Keun-Na, Jong-Sun Lim, William S. Hancock, Young-Ki Paik
  • P-938: The Chromosome 19 Strategy to Characterize Novel Proteoforms and Missing Proteins Using ENCODE Resources, C.L.Nilsson, E. Mostovenko, C.F. Lich5, K. Ruggles, D. Fenyö, R.A. Kroes, S. Hober, Á. Végvári, M. Rezeli, P.E. Andrén, E.P. Sulman, F.F. Lang, M. Fuentes, E. Carlsohn, J.R. Moskal, J.A. Opsahl, F.S. Berven, T.E. Fehniger, G. Marko-Varga
    This poster in pdf format can be downloaded here.

  • P-NN5: Unified Human Proteome Browser Initiative, Mark Baker, Fuchu He, Ed Nice, Young-Ki Paik, Ping Xu, Ian Smith, Anthony Beitz, Dong Li, SebasKan Barney, Cuixa Chen, Lihong Diao, Rob Goode, Zechi Huang, Honglei Li, Simon Yu, Xinlei Zhang
    This poster in pdf format can be downloaded here.

Details to prepare the posters
Posters display (Madrid Congress)
Posters will be displayed from Monday, October 6th 09:00 to Wednesday,
October 8th 18:15 hours in the poster area.

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.

At least one author is required to be in attendance at the poster for the entire duration of the panel sesion.

Posters should fit on 90 cm wide x 120 cm high poster boards (view sample below).

Poster display format

Push-pins will be provided. Each poster will be identified with a number. This number corresponds to the number printed in the program for your presentation.

The success of the poster session depends on the ability of the viewers to readily understand the material. Observe the following guidelines in the preparation for your poster session.
    • Prepare all poster material ahead of time;
    • Keep the presentation simple;
    • Do not mount materials on heavy board because these may be difficult to keep in position on the poster board;
    • Prepare a visual summary of the research with enough information to stimulate interested viewers rather than a written research paper. Use bulleted phrases rather than narrative text;
    • Prepare distinct panels on the poster to correspond with the major parts of the presentation. For example, consider including a panel for each of the following: Introduction, methods, results, conclusions, and references;
    • Number each panel so that the reader can follow along in the order intended.
    • Ensure that all poster materials can be read from three feet away. We suggest an Arial font with bold characters. Titles and headings should be at least 1 inch high. DO NOT use a 12 point font.
    • Prepare a title board for the top of the poster space indicating the title and author(s). The lettering for this title should be no less than 1.5 inches high.

Appendix 4

C-HPP Meeting (Part 3) Principal Investigator Council Meeting

Wednesday, October 8, 2014: 08:00 - 09:20 Rm C


Chair: Young-Ki Paik

PIC Members Invited to This Meeting (as of August 1, 2014)
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 (Mit) (*subject to approval by Spanish Granting Authority and PIC meeting).

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. Welcome and Formal Approval of new Chr 16 PI: Dr. Fernando Corrales, Spain
  2. Open discussion on how to further stimulate
  3. Election of the C-HPP EC member-at-large
  4. 2015 C-HPP workshop plans
  5. 2015 JPR Special Issue on thematic topics with publication timing may possibly be explored.
  6. Organization Matters
(*order of the topics is subject to change depending on the priority; Your inputs on the agenda list are highly appreciated)

Appendix 5

C-HPP Logo Segovia

Efforts to Accelerate the HUPO Human Proteome Project

Final Program

To the memory of Juan Pablo Albar

Photo of Juan Pablo Albar

Thursday, 9 October, 2014; 09:00-17:00; Venue: in Segovia

(Final, 9/26/2014)



Bus departing Madrid for Segovia will be provided for all participants who register in advance. For details, go to here(external link).

08:45-09:10 Coffee and Welcome
Fernando Corrales, Concha Gil
Young-Ki Paik, Bill Hancock, Jennifer Van Eyk, Tadashi Yamamoto, Pierre Legrain, Gil Omenn

09:10-10:00 Common Reagents and Resources for HPP Networks

09:10-09:35 A Tissue-Based Map of the Human Proteome: Cross-Validation of HPA antibody data with MS, RNA-Seq and Other Publicly Available Data; Ulrika Qundos, (SciLife Lab, Sweden). Shortened version of this presenation in pdf format is available here.

09:35-09:45 Develop Effective Antibody Capture Reagents for the Missing or Orphan Proteins and for Characterization of Proteoforms of Well-Known Proteins; Collaboration between ProteinAtlas and Monash Monoclonal Ab Facility, Ed Nice (Monash University, Australia). This presentation is available here.

09:45-10:00 Develop and Facilitate Utilization of Common Bio-Banking Samples; Gyorgy Marko-Varga (Lund Univ., Sweden) and Henry Rodriguez (NCI, USA)

10:00-11:45 Defining Highly Informative Sets of Proteins for Studies of Specific Diseases: Moving from HPP Focus on the Missing Proteins to the 80% Known Proteins

10:00-10:10 Analysis of Consecutive Islet Protein Data Sets for Understanding Obesity-Associated Type 2 Diabetes Mellitus; Peter Bergsten for Diabetes-HPP (Uppsala Univ, Sweden)

10:10-10:20 The Proteome-wide SRM Resources: Peptides, Spectral Libraries, PASSEL Database; Robert Moritz and Eric Deutsch (ISB, USA). This presentation is available here.

10:20-10:30 Report on HPP Inter-Laboratory Performance with SRM/MRM Assays; Christoph Borchers (Univ. Victoria, Canada)

10:30-10:40 Extended SWATH Library that makes >10,000 Human Proteins Precisely Measurable; George Rosenberger (ETH Zurich, Switzerland). This presentation in pdf format is available here.

10:40-11:30 Popular Proteins, Quantitative Assays, Functional Networks and Pathways
10:40-10:55 Peipei Ping, CV-HPP, Heart and Vascular Diseases
10:55-11:10 Fuchu He, CN-HLPP: Liver Diseases
11:10-11:20 Hui Zhang or Ruth Huttenhain, Cancer-HPP: Cancers
11:20-11:30 Tadashi Yamamoto, HKUPP: Kidney Diseases. This presenation is available in pdf format here.
11:30-11:45 Bridging from the Proteomics Research Community to the Clinic: The ProteomeAnalyzer Project of the B/D-HPP: Robust, Moderate Cost, High Throughput; Bruno Domon (Luxembourg). This presenation is available here.

11:45-13:00 Combined C-HPP + B/D-HPP Studies of Proteome Biology and Disease

11:45-12:05 Demonstration of Joint Efforts on MS-based Automated PTM Analysis and Biological Characterization of Brain Proteins and Glioblastoma; Jong Shin Yoo, (KBSI, Korea) and Young-Mok Park (HBPP, Korea). This presentation in pdf format is available here.

12:05-12:20 Demonstration of Utilizing Combined Resources and Technologies from B/D-HPP and C-HPP to Search for Cancer Biomarkers; Gyorgy Marko-Varga of Chr 19 (Lund Univ.), Hui Zhang, Chair, Cancer-HPP (Johns Hopkins, US)

12:20-12:40 Management of RNA Seq Data for Mapping Isoforms (C-HPP) and Characterizing Biological Functions (with B/D-HPP); Ravi Sirdeshmukh (Bangalore, India)

12:40-13:00 Combined Tools for Characterizing Membrane-Embedded Missing Proteins with Disease Implications (AO-HUPO Membrane Proteome Initiative); Takeshi Tomonaga (National Institute of Biomedical Innovation) and Yu-ju Chen of Chr 4 (Taipei, Taiwan). Takeshi Tomonaga presentation's is available here.

1300-1400 Lunch

14:00-15:30 Data Resources, Data Standards, and Common Informatics Tools

14:00-15:00 Panel Discussion: Update on HPP Metrics for High-Confidence Protein Identifications and Missing Proteins combining PeptideAtlas, GPMdb, neXtProt, Human Protein Atlas and including major 2014 datasets
Chair/Moderator: Amos Bairoch (neXtProt, SIB, Switzerland)
Panelists: Lydie Lane (neXtProt, SIB, Switzerland), Eric Deutsch (PeptideAtlas, ISB, USA), Ulrika Qundos (Human Protein Atlas, SciLife Lab, Sweden), Alberto Pascual-Montano (Spain), and Fernando Corrales (Spain), representative of IHPB Working Group

Discussion Topics:

  • Reinforcement of Policies on Dataset Deposition with ProteomeXchange, Stringent Protein FDR thresholds, and Reanalysis with Standardized PeptideAtlas and GPMdb Pipelines
  • Creation of the Integrated HUPO Human Proteome Browser, or IHPB (Caper, TPB, Genome-wide PDB). Working group for this new project compromised of Ed Nice, Fuchu He, Ping Xu, Ian Smith, Mark Baker, Anthony Beitz, Dong Li, Young-Ki Paik. This presentation is available here.
  • Recognition of Reasons Proteins can be Hard to Detect: restricted tissue expression, low abundance, high hydrophobicity or basicity, embedded in membranes, low MW, members of highly homologous protein families
  • neXtProt update by Lydie Lane. This presenation is available here.
  • Update on neXtProt metrix by Amos Bairoch is available here.
  • PeptideAtlas Metrics and Update by Eric Deutsch. This presenation is available here.
  • Proteogenomics Dashboard for the Human Proteome Project presented by Alberto Pascual-Montano. This presentation is available here.
  • Computational Mass Spectrometry Initiative presented by Shoba Ranganathan. This presentation is available here.

15:00-15:30 Panel Discussion: Focus on PTMs, ASVs, Protein Interactions, protein and glycan chemistry

Chair/Moderator: Cathy Costello (Boston Univ, USA)
Panelists: Bill Hancock (Northeastern Univ, USA), Hisashi Narimatsu (Research Center for Medical Glycoscience at AIST, Japan), Naoyuki Taniguchi (RIKEN Advanced Science Institute, Japan), Gil Omenn (Univ. Michigan, USA)

Presentation of Hisashi Narimatsu on "Glycoproteomics" is available here.

15:30-17:00 Town Hall Meeting on Future Directions of the HPP
Everyone in the proteomics community is warmly invited to actively participate. We welcome a broad discussion about the development, integration, and wide application of C-HPP, B/D-HPP and Technology Pillars.

  • How to make proteomics an essential component of “functional genomics” and integrated ‘omics research?
  • How to connect with investigators not part of HPP, including clinical investigators, pathologists, geneticists, biologists?
  • How to emphasize characterizing the biology of the many proteoforms of known proteins, while sustaining the effort to complete the parts list?
  • How to assist and mobilize less active teams in both B/D-HPP and C-HPP consortium?
  • How to accelerate HPP development through coordination between B//D-HPP, C-HPP, and Resource Pillars?
  • What should be the focus of the next J Proteome Research C-HPP/HPP Special Issue for mid-2015?

Conclusions and Perspectives
Cathy Costello, Pierre Legrain, Mark Baker, HUPO Presidents
Gil Omenn, Chair, HPP Consortium

Presentation of Mark Baker is available here.

17:30-19:30 Segovia City Tour

20:30-23:00 Dinner

Organizers (2014 Post-Congress Workshop in Segovia)

Organizations: PROTEORED and HUPO HPP Consortium
Fernando Corrales, Pamplona, Spain
Concha Gil, Madrid, Spain
Gil Omenn, Chair, HUPO HPP Consortium*
Tadashi Yamamoto, Chair, HUPO Initiative Committee
Young-Ki Paik and Bill Hancock, Chair and co-Chair, C-HPP Consortium
Ruedi Aebersold and Jennifer van Eyk, Co-Chairs, B/D-HPP Consortium

For more information, please contact Lola Segura mdsegura@proteored.org

Interested participants are invited to register here(external link) (required). Segovia is located approximately one-hour from Madrid (by train or bus). Transportation TO Segovia on Wednesday evening (October 8) will be provided for all registered participants (by bus). Participants are responsible for their own hotel room Wednesday (Oct 8) and/or Thursday (Oct 9).
(* This information is available as wel on http://www.hupo2014.com/newtrends.html(external link).)

Annoncement of Lola Segura regarding Segovia C-HPP Workshop on 7 October 2014

Transportation will be provided (bus) from the Feria de Madrid (Main Conference location) to Segovia (50 min-1h) October 8 evening, as well as coffee and lunch breaks, dinner and a guided City tour (October 9). The remaining expenses of two hotel nights, dinner October 8 and travel back to Madrid by high speed train (35 min, 20 €) should be arranged by each attendee individually. More information about venue and transportation can be found in the website of the workshop: ProteoRed(external link)

BUS DEPARTURE: Bus departure is scheduled on 8th October at 20:30h from Hotel Pullman.
However, there will be a Meeting Point at 20:15h at the North Gate of the convention center (Registration Area) to guide the attendees to the buses.

Best regards,

Lola Segura

Transportation Info
  • From Madrid: Bus departing Madrid for Segovia will be ready for all participants who signed up for Segovia meeting. More detailed info will be available later.
  • From Segovia to Madrid: The participants can select either Bus or Train for returning to Madrid. Unless otherwise, the participants are responsible for their own arrangement of hotel and one way transportation (from Segovia to Madrid). For those invited speakers, there may be separate information as to transportation from/to Madrid/Segovia when the local organizers send them a letter of invitation. This is subject to change.
Segovia transportation time table 1

Segovia transportation time table 2