Post on 26-Mar-2022
2017 Human Proteome Project
* on behalf of and with thanks from the HPP community and human proteomics data contributors within and outside HUPO
Many Great HPP Outcomes Already• Consensus development of initiatives/streams/pillars model
• Collaborative building of Knowledgebase and data analysis pipeline (incl; ProteomeXchange, PRIDE, PeptideAtlas, neXtProt, etc)
• PE1-4 system created knowledge about proteins/families
• Created SRM Atlas, PASSEL (synthetic peptides ID/quantitation by targeted MS)
• Published 190+ specific manuscripts (w/ 5 JPR Special Issues)
• Launched C-HPP Missing Protein Challenge (MP50), uPE1 Challenge (CP50) and B/D-Popular Proteins for organ-specific research
• Launch/expansion HPA under aegis of Ab Pillar
• Built MS Pillar 96 phosphopeptides initiative
• Launched Pathology Pillar
1. Concentrate on HPP Science – Making a Difference – Focus on Impacta. Encourage PXD submissions globallyb. Support C-HPP move towards Chr teams + annotation + MP50 + CP50 challengesc. Consider joint C- and B/D-HPP Human Cell Type/Rare Tissues Proteomed. Consider Plasma Proteome Project v2e. Support proposed Pathology Pillar projectsf. Establish one additional MS Pillar Challengeg. Accelerate Ab Validation Strategy (Mathias)h. Consider if we should position iPOP/hPOP within HPPi. Consider development of a single “HPP knowledge portal”
Focusing on Higher HPP Impact
Human Proteome Project Goals
Complete the Human Proteome Parts List• Establish agreed, stringent and reliable communal standards for discovery of
the human proteome
• Identify > 1 protein product and as many as possible PTM, SNP and splice variants from the ~20,300 protein-coding human genes
• Discover the missing proteins and predict undetectable proteins
• Characterize the biology of all known proteins and proteoforms
Ensure proteomics adds value to understanding human biology• Position the human proteome in the context of function, biological networks,
interactions, pathways and other “omics”
• Stimulate use of popular proteins, SRM and Human Protein Atlases
• Impact clinical medicine and precision medicine (including pathology)
HUPO HPP – Pathology PillarMajor Goals
1. Identify opportunities for clinical unmet needs: Focus on
precision/personalized medicine, work with every HUPO
HPP initiative/project leaders
2. Translate proteomic discoveries into clinical use: FDA
clearance or approval, intended use, CLIA certification,
analytical and clinical validation/trial etc
3. Assist HPP projects with pathology expertise: Clinical
specimens, bio-banking, SOPs, QC, QA, guidelines,
pathology atlas etc
4. Liaise with international clinical/pathological organizations
for proteomic outreaches: IFCC, AACC, AACB, CAP,
RCPA, ESP etc
Build New Pathology Pillar(courtesy Pathology Pillar Co-chairs)
1. Outreach to pathology “colleges” (RCPA✓, CAP, ESP)
2. Establish HPP pathology requirements, build directory
of HUPO pathology personnel, skills and attract expertise
needed to accelerate precision medicine aspects of HPP
3. Initiate cross-disciplinary proteomics in pathology education program ✓
4. Develop guidelines, metrics and technologies
5. Ensure best-practice biobanking ✓
6. Build libraries of proteomic profiles of healthy/diseased tissues linked to
validated pathology histology/imaging
7. Launch and market HPP pathology projects demonstrating proteomics adds
value to genomics (e.g., ICPC (Cancer Moonshot) ✓, Missing Proteins
Challenge ✓)
8. Build/promote Human Protein Atlas “pathology” knowledge transfer ✓
✓ = underway
Liver Kidneyand urine
Immune-peptido
me
Brain
Cancer
Cardio-vascular
DiabetesEpigeneti
cchromati
nExtreme conditio
ns
EyeOME
Infectious
diseases
Modelorganism
sMitochond
ria
Glyco-proteomi
cs
Foodand
Nutrition
Toxicoproteomi
cs
Respiratory
Stemcells
Musculo-skeletal
Plasma
PediOme
Biology and Disease-driven
Human Proteome
Proteinaggregati
on
Pathology Will Support The BD-HPP
PRIDE PASSELMassIVE
PeptideAtlasHuman Protein
Atlas
Individual lab-based MS data
ProteomeXchange
neXtProt protein annotation & PE1-5 assignment
GPMDB, iPROX, JPROT, SWATH/DIA,MissingProteinPedia
Publications
+ +
HPP/neXtProt assures data integrity, quality and comprehensiveness
Other Ab data
Discuss/Communicate Challenges Capturing all MS, Ab and
other Data for PE1-5 Assignment
1. Focus on HPP Science – Making a Differencea. Encourage PXD submissions globallyb. Confirm C-HPP move towards Chr teams + annotation + MP50 + CP50 challenges (Chris)c. Consider joint C- and B/D-HPP Human Cell Type/Rare Tissues Proteome (Neil)d. Consider Plasma Proteome Project v2.0 (Sam)e. Build proposed Pathology Pillar projects; establish one additional MS Pillar Challengef. Accelerate Ab Validation Strategy (Mathias)g. Consider if we should position iPOP/hPOP within the HPP (Mike)h. Consider development of a single “HPP knowledge portal”
2. Have Good HPP Governance/Management in Placea. HPP EC leadership and SAB renewal/succession/gender equityb. HPP 5Yr “Future Human” HPP EC Workshop/s ----> “Future Human” 5Yr HPP Planc. HPP EC member responsibility/authority (addition to stream/pillar rep)d. My Personal HPP Sign-Up and Profile – everyone’s personal HPP profilee. Encourage ECR contributions across HPP
Where To next For the HPP ?
1. Focus on HPP Science – Making a Differencea. Encourage PXD submissions globallyb. Confirm C-HPP move towards Chr teams + annotation + MP50 + CP50 challenges (Chris)c. Consider joint C- and B/D-HPP Human Cell Type/Rare Tissues Proteome (Neil)d. Consider Plasma Proteome Project v2.0 (Sam)e. Build proposed Pathology Pillar projects; establish one additional MS Pillar Challengef. Accelerate Ab Validation Strategy (Mathias)g. Consider if we should position iPOP/hPOP within the HPP (Mike)h. Consider development of a single “HPP knowledge portal”
2. Have Good HPP Governance/Management in Placea. HPP EC leadership and SAB renewal/succession/gender equityb. HPP 5Yr “Future Human” HPP EC Workshop/s ----> “Future Human” 5Yr HPP Planc. HPP EC member responsibility/authority (addition to stream/pillar rep)d. My Personal HPP Sign-Up and Profile – everyone’s personal HPP profilee. Encourage ECR contributions across HPP
3. Improve/Ease HPP Team Reporting Requirementsa. Continue current HPP Reporting (annual metrics/guidelines manuscripts, HUPO Council report, HUPO EC
monthly reports, HUPOST, social media)b. Build Human Proteome Reference Library (HPRL capturing C-, B/D-, pillar activity through PubMed IDs)c. Possibility of a one-off HPP “Future Human” Decadal Report (?HUPO2020 Stockholm?)
Where To next For the HPP ?
Human Proteome References
immunology
braineye
diabetes
cardiovascular
cancer
plasma
PSI
liver
rheumatic disorders
pediatrics
kidney/urine
metricsguidelinesneXtProt
Chrs1-22, Mt, X, Y
MP-50 (missing proteins)
CP-50 (uPE1s)
29425503
28949146
28508355
26872682
26549206
26331911
25845585
25676247
25418211
24903697
24804578
24753468
24274931
24167090
24108682
23341065
23341064
22609191
22290803
22045679
21796782
21717571
21063951
20514650
21137003
18466049
18452233
18384107
18338822
18283670
18283666
18256214
17964607
17922513
17907274
17610211
17340642
16967475
16927433
16927432
16927431
16927428
16927427
16927420
16912976
16912975
16912974
16912973
16912972
16912971
1
2
3
4
5
24211518
24261998
24304897
28938075
23701512
22930569
21850651
21692344
21468943
21063952
19782775
19235168
19131327
19053147
18793429
21136733
16608429
16400715
16104060
16104058
16104057
16104056
16052627
16052625
16052624
16052623
16052621
16052619
16052618
16047310
16047309
16041672
16041671
16038022
16038021
15502245
15188391
15061371
Construct The Human Proteome Reference Library
1. Focus on HPP Science – Making a Differencea. Encourage PXD submissions globallyb. Confirm C-HPP move towards Chr teams + annotation + MP50 + CP50 challenges (Chris)c. Consider joint C- and B/D-HPP Human Cell Type/Rare Tissues Proteome (Neil)d. Consider Plasma Proteome Project v2.0 (Sam)e. Build proposed Pathology Pillar projects; establish one additional MS Pillar Challengef. Accelerate Ab Validation Strategy (Mathias)g. Consider if we should position iPOP/hPOP within the HPP (Mike)h. Consider development of a single “HPP knowledge portal”
2. Have Good HPP Governance/Management in Placea. HPP EC leadership and SAB renewal/succession/gender equityb. HPP 5Yr “Future Human” HPP EC Workshop/s ----> “Future Human” 5Yr HPP Planc. HPP EC member responsibility/authority (addition to stream/pillar rep)d. My Personal HPP Sign-Up and Profile – everyone’s personal HPP profilee. Encourage ECR contributions across HPP
3. Improve/Ease HPP Reporting Requirementsa. Continue current HPP Reporting (annual metrics/guidelines manuscripts, HUPO Council report, HUPO EC
monthly reports, HUPOST, social media)b. Build Human Proteome Reference Library (HPRL capturing C-, B/D-, pillar activity through PubMed IDs)c. Possibility of a one-off HPP “Future Human” Decadal Report (?HUPO2020 Stockholm?)
4. Develop Wonderful HPP Marketing Toolsa. Develop HPP Marketing Plan (part HPP 5Yr Future Human Plan)b. HPP Logo Competitionc. Build & publish an interactive HUPO/HPP/Proteomics Timelined. Continue building marketing materials - TEDX/plenaries/ECR advances in proteomics/HPRL
Where To next For the HPP ?
https://hupo.org/What-is-Proteomics
Reinvigorate HPP Marketing Through both HUPO IAB and Marketing C’ttees
Official HPP logo?
Create an Interactive Web-based Past/Future HPP Timeline(thanks to Young-Ki Paik, Pierre Legrain & others)
1. Focus on HPP Science – Making a Differencea. Encourage PXD submissions globallyb. Confirm C-HPP move towards Chr teams + annotation + MP50 + CP50 challenges (Chris)c. Consider joint C- and B/D-HPP Human Cell Type/Rare Tissues Proteome (Neil)d. Consider Plasma Proteome Project v2.0 (Sam)e. Build proposed Pathology Pillar projects; establish one additional MS Pillar Challengef. Accelerate Ab Validation Strategy (Mathias)g. Consider if we should position iPOP/hPOP within the HPP (Mike)h. Consider development of a single “HPP knowledge portal”
2. Have Good HPP Governance/Management in Placea. HPP EC leadership and SAB renewal/succession/gender equityb. HPP 5Yr “Future Human” HPP EC Workshop/s ----> “Future Human” 5Yr HPP Planc. HPP EC member responsibility/authority (addition to stream/pillar rep)d. My Personal HPP Sign-Up and Profile – everyone’s personal HPP profilee. Encourage ECR contributions across HPP
3. Improve/Ease HPP Team Reporting Requirementsa. Continue current HPP Reporting (annual metrics/guidelines manuscripts, HUPO Council report, HUPO EC
monthly reports, HUPOST, social media)b. Build Human Proteome Reference Library (HPRL capturing C-, B/D-, pillar activity through PubMed IDs)c. Possibility of a one-off HPP “Future Human” Decadal Report (?HUPO2020 Stockholm?)
4. Develop Wonderful HPP Marketing Toolsa. Develop HPP Marketing Plan (part HPP 5Yr Future Human Plan)b. HPP Logo Competitionc. Build & publish an interactive HUPO/HPP/Proteomics Timelined. Continue building marketing materials - TEDX/plenaries/ECR advances in proteomics/HPRL
5. Address Key Questions Fearlessly - Would HPP Funding Bring Greater Impacta. Discuss current/future HPP funding options and evaluate feasibility of “Pinnacle Challenges” (Steve)
Where To next For the HPP ?
Baxter International
Bill & Melinda Gates Foundation
Brocher Foundation
Burroughs Wellcome Fund
Carnegie Corporation
Chiang Ching-kuo Foundation
Department of Energy
EarthWatch Institute
Fulbright Program
German Academic Exchange Service (DAAD)
Humboldt Foundation
National Institutes of Health
National Science Foundation (NSF)
North Carolina Biotechnology Center
NSF Office of International Science and Engineering
Marie Curie Actions Research Programme
Rockefeller Foundation
US Agency for International Development (USAID)
US Department of Agriculture (USDA)
US National Institute of Food and Agriculture (NIFA)
US Department of State
World Bank
Various Collaborative National Agencies
Should/Could we Apply for Full/Focused HPP FundingUnlikely as Climbing Mons Huygens (Tallest Mountain on Moon)
https://www.humancellatlas.org/