1. Bioinformatics at NIAID-Biodefense Proteomics Administrative Resource Center Peter McGarvey Ph.D. Senior Bioinformatics Scientist, Project Manager Protein Information Resource (PIR) Georgetown University Medical Center

3. NIAID 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. oSocial & Scientific Systems oPIR, Georgetown University Medical Center oVirginia Bioinformatics Institute, Virginia Tech oBiodefense & Emerging Infections Research Resource Repository

4. Administrative 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)

5. 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

6. 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 Data

8. Administrative 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 Interfaces oSSS – www.proteomicsresource.orgwww.proteomicsresource.org oPIR – pir.georgetown.edu/proteomicspir.georgetown.edu/proteomics oVBI - proteinbank.vbi.vt.edu/bprcproteinbank.vbi.vt.edu/bprc Documentation: Use Cases > Req. >> Design Outreach – What are your suggestions?

9. SSS – www.proteomicsresource.orgwww.proteomicsresource.org VBI - proteinbank.vbi.vt.edu/bprcproteinbank.vbi.vt.edu/bprc PIR – pir.georgetown.edu/proteomicspir.georgetown.edu/proteomics

10. Sophisticated Text Searches Customizable Information Matrix Report Retrieval 1. UniProtKB Protein Report 2. iProClass Protein Report 3. BioThesaurus Name Report 4. PIRSF Family Report 5. UniRef50 Cluster Report Links Proteins in Experimental Data 12 4 3 5 Master Catalog

12. Complete Proteome Tool

13. CUPID Core and Unique Protein Identification system

14. Acknowledgements PIR – 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

15. END