Data and Bioinformatics Tools at the NIAID Proteomics Resource Center

1
Data and Bioinformatics Tools at the NIAID
Proteomics Resource Center P. B. McGarvey1, H.
Huang1, J. Zhang1, R. Mazumder1, Y. Chen1, B.
Sobral2, S. Cammer2, M. Moore3, and C. H. Wu1. 1
Protein Information Resource (PIR) 2 The
Virginia Bioinformatics Institute (VBI) 3 Social
Scientific Systems, Inc. (SSS)
Abstract The National Institute for Allergy
and Infectious Diseases (NIAID) has created a
biodefense proteomics program to identify targets
for potential vaccines, therapeutics, and
diagnostics, for agents of concern in
bioterrorism. The program funds seven Proteomics
Research Centers (PRCs) and a Resource Center
charged with developing the bioinformatics
infrastructure for public dissemination of the
PRC data and reagents. Administering such a
program presented unique challenges as large and
heterogeneous proteomic data have to be
integrated for knowledge discovery. The Project
Catalog currently contains the results from mass
spectrometry, microarray, protein interaction,
protein structural studies and genomic cloning
experiments on a diverse set of pathogens.
The system supports data mining and analysis
functions and consists of a website portal
(www.proteomicsresource.org) with summary
information on the project and the data and
reagents available, the Master Protein Directory,
a searchable protein knowledge system that
integrates proteins identified by the PRCs with
functional and pathway information from over 90
databases including the Proteomics Data Center,
which houses underlying experimental results from
the project, visualization tools and allows data
downloads in HUPO PSI formats for additional
analysis. Availability of the data in an
integrated system with analytical tools allows
comparative analysis at many levels, including
the pathway and single protein level. Here we
illustrate how analysis of proteins involved in
the Vibrio cholerae colonization pathway reveals
that homologs of many of these proteins are
present in other pathogens being studied within
the Biodefense Proteomics Project and how
information on these proteins and reagents can be
found using the resources of the Center. Studies
of bacterial virulence genes and their regulatory
systems across different taxa can be useful in
better understanding these organisms and aid in
finding proteins that might be potential targets
for intervention.
2 Project Catalog Summary View Summarizes
information on identified proteins, literature,
experimental results, and protocols currently
available. http//www.proteomicsresource.org/Resou
rces/Catalog.aspx

• 4 Batch Retrieval on Family Classification.
• Retrieval on PIRSF IDs gave 98 proteins from 3
  organisms 3 centers. Othologs and Paralogs.
  Pfam, Interpro other classifications available.
• 18 from an MS/MS study of the Salmonella
  typhimurium by Pacific Northwest National
  Laboratories.
• 10 from Microarray Studies of the Bacillus
  anthracis Life Cycle by University of Michigan.
• 9 from Clones of the Bacillus anthracis Proteome
  by Harvard Institute of Proteomics. (7 overlap
  with microarray study).
• 68 from Clones of Vibrio cholerae Proteome by
  Harvard Institute of Proteomics.

3 Master Protein Directory Search Searching
KEGG Pathways for cholera colonization finds
that all 29 proteins in the pathway exist as full
length clones from Harvard. The Pathway or
UniProtKB records can be viewed and clones
ordered from repositories.
5 Experimental Results and Visualizations
Available In the Proteomics Data Center
1 Participating Institutions and Organisms

• Albert Einstein College of MedicineT. gondii, C.
  parvum
• Caprion Pharmaceuticals B. abortus
• Harvard Institute of Proteomics V. cholerae, B.
  anthracis
• Myriad Genetics B. anthracis, Y. pestis, F.
  tularensis, Vaccinia
• Pacific Northwest National Laboratory S.
  typhimurium, S. typhi, Vaccinia, Monkeypox
• ScrippsSARS CoV
• University of Michigan B. anthracis

6 Download Results in Community Formats
The Immune Epitope Databaseand Analysis Resource
(IEDB)
Acknowledgements Study supported by National
Institutes of Allergy and Infectious Disease NIH
Contract HHSN266200400061C
7 Links to Related Resources IEDB shows several
of the pathway proteins contain immunogenic
epitopes.