Bioinformatics at NIAID-Biodefense Bioinformatics at NIAID-Biodefense Proteomics Administrative Proteomics Administrative

Resource CenterResource Center

Peter McGarvey Ph.D.

Senior Bioinformatics Scientist, Project ManagerProtein Information Resource (PIR)Georgetown University Medical Center

NIAID Biodefense Proteomics ProgramNIAID Biodefense Proteomics Program

• 7 Proteomics Research Centers: Identifying Targets for Therapeutic Interventions “..discovering targets for potential candidates for the next generation of vaccines, therapeutics, and diagnostics”

• Administrative Resource Center: Support research centers, public distribution of results and protocols

..establish a Scientific Advisory Group, Interoperability Working Group and promote awareness of the project so scientists worldwide can utilize these resources.

o Social & Scientific Systems

o PIR, Georgetown University Medical Center

o Virginia Bioinformatics Institute, Virginia Tech

o Biodefense & Emerging Infections Research Resource Repository

Administrative Resource ActivitiesAdministrative Resource Activities

• Project Management (SSS)– Meetings and Communications– Web Portal

• Scientific Coordination (PIR/VBI)– Scientific Advisory Working Group (SWG)– Interoperability Working Group (IWG)

• Data Infrastructure (VBI/PIR)– Proteomic Database: Storage and Retrieval (VBI)– Data Management and Analysis Tools (PIR/VBI)– Integrated Protein Knowledge System (PIR)

1. Albert Einstein College of Medicine (PI - George Orr)T. gondii, C. parvum

2. Caprion Pharmaceuticals (PI - Eustache Paramithiotis)B. abortus

3. Harvard Institute of Proteomics (PI - Joshua LaBaer)V. cholerae, B. anthracis

4. Myriad Genetics (PI - Jerry Lanchbury)B. anthracis, Y. pestis, F. tularensis, Vaccinia

5. Pacific Northwest National Laboratory (PI - Richard Smith)S. typhimurium, S. typhi, Vaccinia, Monkeypox

6. Scripps; Burnham Institute (PI - Peter Kuhn)SARS CoV

7. University of Michigan (PI - Philip Hanna)B. anthracis

• Mass Spectrometry:– LC-MS/MS– LC-FTICR

• Bio-arrays and Y2H: – Affymetrix Arrays– Protein Arrays– Random & Directed Y2H

Screens– 1-D & 2-D Gels

• Structural Proteomics: – High resolution NMR/X-

ray crystallography

• Other Experimental Data: – RNAi & KO data– ORF clones for complete

proteomes– Mutant proteins – Antibody Screens– Phagocytosis mapping

using fluorescence– Protein localization

information, EM

• Methodology: – Sample Prep Methodology– Experimental protocols– Novel technologies

Proteomic DataProteomic Data

Administrative Center Progress to dateAdministrative Center Progress to date

• Scientific Working Group (SWG)• Outside experts to advise the project

• Interoperability Working Group (IWG)• Adopt MIAPE/MIAME and community standards.• Adopt relevant ontologies

• Prototypes for Web Interfaceso SSS – www.proteomicsresource.orgo PIR – pir.georgetown.edu/proteomicso VBI - proteinbank.vbi.vt.edu/bprc

• Documentation: Use Cases > Req. >> Design• Outreach – What are your suggestions?

SSS – www.proteomicsresource.orgVBI - proteinbank.vbi.vt.edu/bprc PIR – pir.georgetown.edu/proteomics

• Sophisticated Text Searches• Customizable Information Matrix • Report Retrieval

1. UniProtKB Protein Report1. UniProtKB Protein Report2. iProClass Protein Report2. iProClass Protein Report3. BioThesaurus Name Report3. BioThesaurus Name Report4. PIRSF Family Report4. PIRSF Family Report5. UniRef50 Cluster Report5. UniRef50 Cluster Report

• Links Proteins in Experimental Data

12 43

5

Master CatalogMaster Catalog

Complete Proteome ToolComplete Proteome Tool

CUPID CUPID CCore and ore and UUnique nique PProtein rotein IdIdentification systementification system

AcknowledgementsAcknowledgementsPIR – Georgetown University

– Cathy Wu

– Peter McGarvey

– Hongzhan Huang

– Raja Mazumder

– Darran Natale

– Zhang-Zhi Hu

– Xin Yuan

– Baris Suzek

Virginia Bioinformatics Institute

– Bruno Sobral

– Jeff Chen

– Oswald Crasta

Social & Scientific Systems

– Margaret Moore

– Terry Brennan

– Paula Yadvish

National Institute of Allergy & Infectious Diseases (NIAID/NIH/DHHS)

– Kimberly Stemple

– Joseph Breen

• END