National Resource for Proteomics and Pathways P41 funded by NCRR

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National Resource for Proteomics and PathwaysP41
funded by NCRR

• Philip Andrews, Director (UM)
• Russ Finley (WSU)
• Trey Ideker (UCSD)
• George Michailidis (UM)
• Curt Wilkerson (MSU)
• David States (UM)

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NCRR Proteomics, Glycomics, and Mass Spectrometry
Centers

• Proteomics Research Resource for Integrative
  Biology
• PNNL Richard Smith
• National Resource for Proteomics and Pathways
• University of Michigan Philip Andrews
• National Center for Glycomics and Glycoproteomics
• University of Indiana- Milos Novotny
• Integrated Technology Resource for Biomedical
  Glycomics
• University of Georgia- J. Michael Pierce
• Research Resource for Integrated Glycotechnology
• University of Georgia- James Prestegard
• Mass Spectrometry Resource for Biology and
  Medicine BU- Catherine Costello
• Bio-organic Biomedical Mass Spectrometry Resource
  UCSF Alma Burlingame
• National Resource for Mass Spectrometric Analysis
  of Biological Macromolecules Rockefeller
  University Brian Chait
• Resource for Biomedical and Bio-organic Mass
  Spectrometry Washington University- Michael Gross
• National Resource for Biomedical Accelerator Mass
  Spectrometry
• LLNL- Ken Turteltaub

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The Primary Goals of the NRPP

• Develop computational and bioinformatics tools
  for proteomics.
• Provide the datasets required to build predictive
  organismal models.
• Develop and prove technologies needed to produce
  proteomics data.

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NRPP Principal Technologies
YTH Protein Interactions
Informatics
NRPP Dissemination System
PRIME
Pull-downs Interactions
Cytoscape
Computational Tools
Data Sets
IM Browser
Organismal Models
Proteome Commons
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Protein Interaction Maps
Drosophila 6,935 nodes, 20,004 edges Giot et al.
(Curagen) Science, Dec 2003
Drosophila 737 nodes, 2,363 edges Stanyon et
al. Genome Biol., Dec 2004
Campylobacter jejuni 1,325 nodes, 11,484
edges Parrish,et al. unpublished
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C. jejuni Interaction Map

• 1,654 ORFs
• 1,477 cloned
• 336,000 assays
• 16,172 interactions
• 11,616 confirmed
• 2,829 high confidence

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Overlap with Reference Sets
Predicted interologs of E. coli reference
interactions
Freq. per 5,000 Random Interactions
Rate of overlap gtgt greater than expected by
chance Campy data enriched for true positives.
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Chemotaxis Signal Transduction Pathway Mapping
in C. jejuni
Cj0144
Cj0262c
Cj1110c
Cj0448c
Cj0951c
Cj0019c
CheW
Cj1670c
Cj0959c
CheV
CheA
CheY
Cj1012c
Cj1004
FliM
MotB
FliL
FliY
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Integrating Interaction Data

• Drosophila Gene and Protein Interactions Database

http//proteome.wayne.edu
Lana Pacifico
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Conserved Complexes

• PathBlast - Ideker

C. jejuni
E.coli
C. jejuni
yeast
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Expression Profiling

• Protein Expression Profiling
• PTM profiling
• Integration of mRNA expression data with
  interaction maps.

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Anthrax Infection, Human Lung 2001
Armed Forces Institute of Pathology, Dept of
Radiology
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B. anthracis Spore Germination Occurs Rapidly
germination
outgrowth
Does the proteomic profile change during
germination?
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The Abundance Ratios of Proteins Vary During
Germination
Protein distribution
Mean 1.00 St Dev .18
Protein distribution
Proteins degraded
Proteins synthesized
Mean 1.04 St Dev .21
2 min/0 min
Protein distribution
Mean 1.12 St Dev .32
7 min/0 min
17 min/0 min
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Heat Map Based on Standard Deviations
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Classification of 37 Proteins that Decrease
During Germination

• 8 Small acid soluble proteins-required to protect
  DNA in the spore
• 7 Spore coat proteins-5 known and 2 new
• 1 Spore protease
• 8 small hypothetical proteins (lt10 kDa)
• 6 conserved hypothetical proteins (gt10 kDa)
• 7 misc known proteins

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Small Acid Soluble Protein BAS0493 Identification
of Cleavage Sites



1 MSKKQQGYNKATSGASIQSTNASYGTEFATETNVQAVKQANAQSEAKK
AQA 51

52 SGASIQSTNASYGTEFATETDVHAVKKQNAQSAAKQSQSSSSNQ
end



Tryptic peptides
GPR protease
Alt trypsin site
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Time Course ProfilesA549 cell response to TGFbeta
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Proteome Informatics

• Open Source code (most efficient approach for
  Proteomics)
• Standardized on Java
• IO Framework, MS Expedite, Data Extractor,
  various modules
• Proteome Commons- Open Source site
• The PC Dissemination System (DFS)

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Interactions with other NCRR Centers.

• PNL- Richard Smith
• Proteome Commons
• DFS collaborations in progress
• Software development- coordination of efforts.
• North Dakota INBRE- Donald Sens
• Training, Bioinformatics infrastructure
• UCSF- Burlingame
• PRIME Protein Prospector
• DFS- planned.

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Proteome Commons

• Services
• One stop for most proteomics Open Source tools
• Data sets to develop and test new algorithms
• Code development tools (versioning, Subversion)
• Proteomics news and announcements
• Distributed File System (The DFS)

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Data Sharing and Publishing Challenges and
Solutions

• Bandwidth/file transfer rates.
• New journal guidelines ask for data access.
• The vanishing webserver syndrome.
• There are some file and annotation standards and
  efforts to develop more.

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DFS

• Peer-to-Peer (P2P) Distributed File System
• Open, simple, cross-platform protocols
• e-Commerce-grade encryption makes it appropriate
  for scientific research (allows peer-review and
  traceability)
• It can easily grow to accommodate very large
  amounts of data and users
• Commodity hardware! 0.37 per GB storage

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Current Status

• 16 TB over 13 servers (46 TB online in June)
• 1 BioChem, 8 NRPP, 1 ISB, 1 MSU, 1 UC Davis, 1
  UNC
• 1.3 terabytes of MS/MSMS data (all public data
  available).
• Docs, tools, code, credits and more
  http//www.proteomecommons.org/dev/dfs
• Data sets
• TheGPM, PNNL, Aurum, QqTOF vs QSTAR, sPRG ABRF
  2006, HUPO PPP
• PeptideAtlas, OPD

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Acknowledgements

• Collaborators
• Curt Wilkerson
• Brett Phinney
• Eric Deutsch
• Joshua Adkins
• Richard Smith
• Al Burlingame
• Janine Maddock
• Venkat Keshamouni

• NRPP
• Xuequn Chen
• Jayson Falkner
• Brian Maso
• Panagiotis Papoulias
• Gary Rymar
• Eric Simon
• John Strahler
• Peter Ulintz
• Donna Veine
• Angela Walker

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Pathway/Network BLASTRoded SharanSilpa
SuthramRyan KelleyPeter UetzRichard
Karp Genetic interactionsRyan Kelley Functional
orthologsSourav BandyopadhyayRoded
Sharan Transcriptional pathwaysChen-Hsiang
YeangCraig MakScott McCuineChris WorkmanTommi
Jaakkola
CytoscapeBenno SchwikowskiChris SanderAnnette
AdlerLeroy HoodGary BaderEthan CeramiKei
OnoNerius LandysRyan KelleyChris
WorkmanMelissa ClineRichard BonneauRowan
ChristmasIliana Avila-CampilloAllan
KuchinskyAditya Vailaya
Funding NCRR, NIGMS, NSF Packard Fellowship
Unilever Websites www.pathblast.org
www.cytoscape.org
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DFS Home

• https//dfs/proteomecommons.org/

Project funded by NCRR