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Time
SUNDAY (9/30/2018)

Pre-Congress Day

Time
THURSDAY (10/4/2018)

HPP Post-Congress Day
07:30–08:50
Room: Gardenia 2
B/D-HPP EC Meeting
Room: Banda Sea 2
C-HPP EC Meeting
08:15–08:30
Coffee
09:00–09:15
HPP Overview
Gil Omenn. Presentation is available here
(Room: Banda Sea 1)
08:30–9:30
What Exciting Prospects Lie Ahead?
Moderated by Rob Moritz, supported by Jennifer Watson 4-5 min presentations: Jenny van Eyk, Ileana Cristea, Ferdinando Cerciello, Jochen Schwenk, Chris Overall plus five more young investigators being identified: Lightning presentations with general participation.
09:15–10:15
HPP Reports (12 min each)
Chair: Gil Omenn

1. C-HPP (Young-Ki Paik). Presentation is available here.
2. B/D-HPP (Fernando J. Corrales). Presentation is available here.
3. Knowledge Base Pillar (Eric Deutsch & Lydie Lane). Presentation is available here
4. MS Pillar (Sue Weintraub). Presentation is available here.
5. Pathology Pillar (Dan Chan/Ed Nice)
9:30–12:10
HPP Town Hall Meeting
Deep Dive on HPP Goals, Strategy and Deliverables for the next 3 years, and Potential for Big International Translational Projects.
Chairs: Fernando Corrales & Young-Ki Paik

• 09:30-10:10 How can we accelerate identification of the remaining 2186 PE2,3,4 Missing Proteins? Siqi Liu, Eric Deutsch, Lydie Lane, Jochen Schwenk, Nino Bandeira, Chris Overall.
• 10:10-10:50 Identification and functional annotation of PTMs.
Chair: Alexey Nesvizhskii. Ultrafast Methods for Detection of PTMs (Alexey Nesvizhskii)
Results from the 96-phosphopeptide HPP sample community analysis (representative of MS Resource Pillar)
Roles of PTMs in Cardiovascular Disorders (Peggi Angel)
Proteogenomics; splice variants; proteoforms (Neil Kelleher). This presentation is available here.
10:15–12:00
Featured HPP Session
Chair: Mark Baker


1. C-HPP 2.0 Discussion (Chris Overall; 20 min). Presentation is available here.
2. B/D-HPP, Prioritization of Popular Proteins (Kun-Hsing Yu; 20 min)
3. Antibody Validation Initiative (52 min) (Jochen Schwenk, Mathias Uhlen (Peter Nilsson), Cecilia Lindskog Bergström, Heng Zhu, Lydie Lane, Cristina Al-Khalili Szigyarto)
• 10:50-11:30 Functional Studies: Protein-protein interactions; Single-Cell Analyses
How are protein-protein interaction data being incorporated by neXtProt for missing proteins and functionally unannotated proteins? (Lydie Lane)
Methods and applications of single-cell analyses of proteins (Bernd Bodenmiller)
• 11:30-12:10 Translational/Clinical Proteomics Strategies & Priorities
How can we more effectively incorporate proteomics in clinical research across many specialties? (Steve Pennington). This presentation is available here.
What lessons can be learned from international collaborations for Cancer Proteomics and applied for other disease categories? (Henry Rodriguez). This presentation is available here.
12:00–13:00
Lunch and Discussion.
12:10–13:10
Lunch, with HPP Senior Scientific Advisory Board Discussion Outline of Two-Year Strategic Plan for the HPP (Mark Baker). This presentation is available here
Lead Discussants: Cathy Costello, John Yates (Gil Omenn, moderator)
General Discussion
13:00–13:40
Round Table 1
Major Public DBs and MS Data Analysis

(Lydie Lane, Eric Deutsch)

Leaders of neXtProt, PeptideAtlas, and ProteomeXchange will highlight developments at each DB and invite comments and inquiries from end users.
13:00–14:00
Emerging Technologies for the HPP.
(Chairs: Rob Moritz and John Yates).
Using CRISPR/Cas9 genome-editing techniques to modify human iPSC and differentiated cells for Hemophilia B treatment (Bonghee Lee). This presentation is available here.
Proteogenomics: Revisiting human protein-coding genome annotation (Janne Lehtiö. This presentation is available here.
13:40–14:20
Round Table 2
Exploring the Undiscovered “Dark” Proteome

(Young-Ki Paik/Fernando Corrales)

• Accelerating progress to identify and annotate PE2-4 Missing Proteins
• Generating functional annotations for uPE1 Proteins
• Mobilizing/connecting C-HPP and B/D-HPP teams
14:00–15:00
What are the Grand Challenges for the Entire Field of Proteomics
Inspirational speaker: Mike Snyder. Presentation is available here.
General discussion
14:20–15:40
Two Breakout Sessions
B/D-HPP PI Meeting
(Banda Sea 1) and C-HPP PIC Meeting (Banda Sea 2)


B/D-HPP: Open session on Popular Proteins with specific presentations by the PIs of the following initiatives: Rheumatoid Diseases, PediOme, Glycoproteomics, Kidney/Urine-HPP, Diseasome
C-HPP: organizational and scientific strategies (PIs of C-HPP teams)
Part I: Report Session
Part 2: Business Session
Part 3: Election & Free Discussion

Invited Talk: J. Eugene Lee: Ab measurement standardization, KRISS, Korea)
neXt-CP50: Resources
21st C-HPP Workshop in St. Malo
22nd C-HPP Workshop in St. Petersburg
Emerging issues
15:00–15:30
Session devoted to Gil Omenn’s Leadership of the HPP with Light Reception (Chair: Mark Baker).
15:40–17:00
Reception (everyone invited)
HUPO Council Meeting for HUPO Councilors
(Baker, Pennington, Overall, Weintraub, Martens, Hui Zhang, Lane)

Appendix 2

20th C-HPP Workshop, Appendix 2

Bioinformatics Hub at HUPO 2018

(Chairs: Eric Deutsch, Andy Jones)
Date: Sept 30-Oct 3, 2018
Venue: Poster Hall in Loews Royal Pacific


Programs are planned in the Bioinformatics Hub each day Sunday-Wednesday.
Sunday access the Bioinformatics Hub (Pacifica 11-12) via the side foyer (look for signs). Monday - Wednesday the hub will be open and accessible via the Poster-Exhibit Hall.

  • See Congress website for scheduled “pitches” and new approaches
  • MS Pillar 96-phosphopeptides standard assay results (Sue Weintraub)
  • “Stranded peptides” in silico approach to finding PE2-4 Missing Proteins combined with SRM Atlas spectral matches to validate missing proteins (Tadashi Yamamoto)
  • Computational predictions for uPE1 protein functional annotation with I-TASSER and COFACTOR (Gil Omenn)
  • Universal Spectrum Identifier (Eric Deutsch)
  • Bioinformatics Guidance for Use of Popular Proteins Research (Kun-Hsing Yu, Maggie Lam, Jenny van Eyk)

Consult the wiki for details: https://github.com/CompMS/Overview/wiki/HUPO-2018

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 is achieved by specific sessions in the agenda. The Ask the Experts sessions (every day between 16h00 and 17h00) explicitly open the space to all with questions, 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) presentation, 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 operates 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.
Hashtags for Twitter
#BioinformaticsHub #HUPO2018

Bioinformatics Hub Schedule:

Sunday September 30:

  • 08h30-09h00: Arrival
  • 09h00-9h30: Introduction and concept by organizers and stand-up introductions (Andy Jones et al.)
  • 9h30-12h00: Pitches: up to 15 minutes for anyone who wants to propose a topic to work on, for instance:
    • 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.
  • 13h00-17h45: Split up into smaller groups and proceed workshop style

Monday October 1:

  • 09h15-09h30: Arrival
  • 09h30-10h30: Special Interest Topic #1 - Analyzing the HPP MS Pillar 96-phosphopeptides standard assay results (Ulrike Kusebauch, Magnus Palmblad, Michael Hoopmann, Susan Weintraub)
  • 10h30-12h20: Special Interest Topic #2 - “Stranded peptides” in silico approach
  • 12h20-12h45: Lunch break
  • 12h45-13h45: Special Interest Topic #3 - Computational predictions for uPE1. Discussion will be provided by the group members and collaborators of Gilbert Omenn the I-TASSER and COFACTOR algorithms as demonstrated for Chromosome 17. Chromosome 17 team propose to expand this analysis to the full proteome and welcome queries and collaborations about the predictions and experimental follow-through. Poster of Chengxin Zhang et al. presented at the HUPO 2018 Congress in this topic is available here in pdf format.
  • 14h00-16h00: Special Interest Topic #4 - PSI/ProteomeXchange session
  • 16h00-17h00: Ask the Experts session

Tuesday October 2:

  • 09h15-09h30: Arrival
  • 09h30-10h30: Special Interest Topic #5 - How to handle exceptions to the HPP Guidelines
  • 10h30-12h20: Special Interest Topic #6 - How to handle exceptions to the HPP Guidelines (cont)
  • 12h20-12h45: Lunch break
  • 12h45-13h45: Special Interest Topic #7 - Bioinformatics Guidance for Use of Popular Proteins
  • 14h00-16h00: Special Interest Topic #8 - Free time (computational session)
  • 16h00-17h00: Ask the Experts session

Wednesday October 3:

  • 09h15-09h30: Arrival
  • 09h30-10h30: Special Interest Topic #9 - TBD
  • 10h30-12h20: Special Interest Topic #10 - TBD
  • 12h20 End. Exhibit hall teardown

Potential Pitches:

  • Analyzing the HPP MS Pillar 96-phosphopeptides standard assay results (Sue Weintraub)
  • “Stranded peptides” in silico approach to finding PE2-4 Missing Proteins (Tadashi Yamamoto)
  • Computational predictions for uPE1 protein functional annotation with I-TASSER and COFACTOR (Gil Omenn)
  • Universal Spectrum Identifier (Eric Deutsch)
  • Bioinformatics Guidance for Use of Popular Proteins Research (Kun-Hsing Yu, Maggie Lam, Jenny van Eyk)
  • How to handle exceptions to the HPP Guidelines for certain proteins (Eric Deutsch, Lydie Lane, Gil Omenn)
  • Ongoing work of the Proteomics Standards Initiative (Andy Jones)
  • Status and future work of the ProteomeXchange Consortium (Juan Antonio Vizcaíno)
  • Achieving universal implementation of data standards (Andy Jones)
  • Implementing the PSI Extended FASTA Format (PEFF) (Eric Deutsch)
  • JPR Annual Special Issue on Proteomics Informatics Tools (TBC)
  • Gathering evidence for translation of lncRNAs (Eric Deutsch)

Attending Organizers:

Other Confirmed Participants

  • All others are welcome!


Click here to go to the overview of C-HPP activities in HUPO 2018, Orlando.