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National Resource for Proteomics and Pathways P41 funded by NCRR

NCRR Proteomics, Glycomics, and Mass Spectrometry Centers. Proteomics Research Resource for Integrative Biology PNNL

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National Resource for Proteomics and Pathways P41 funded by NCRR

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    1. National Resource for Proteomics and Pathways P41 funded by NCRR Philip Andrews, Director (UM) Russ Finley (WSU) Trey Ideker (UCSD) George Michailidis (UM) Curt Wilkerson (MSU) David States (UM)

    2. 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

    3. 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.

    4. NRPP Principal Technologies

    5. Protein Interaction Maps All interaction detected by yeast two-hybrid screening. 1 large, 69 small components. Largest single data set yet obtained. Random baits used. Covers nearly half of proteome. 1 large, 6 small components. Second largest data set, independently obtained, baits focused on a function, useful to compare with this data. 1 large, 2 small components. New data, protoeome-screening for a bacterial pathogen, widest coverage for an organism yet. Concerned about how we view and use this data.All interaction detected by yeast two-hybrid screening. 1 large, 69 small components. Largest single data set yet obtained. Random baits used. Covers nearly half of proteome. 1 large, 6 small components. Second largest data set, independently obtained, baits focused on a function, useful to compare with this data. 1 large, 2 small components. New data, protoeome-screening for a bacterial pathogen, widest coverage for an organism yet. Concerned about how we view and use this data.

    6. C. jejuni Interaction Map 1,654 ORFs 1,477 cloned ~336,000 assays 16,172 interactions 11,616 confirmed 2,829 high confidence

    7. Overlap with Reference Sets

    9. Integrating Interaction Data Drosophila Gene and Protein Interactions Database

    10. Conserved Complexes PathBlast - Ideker

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

    12. Anthrax Infection, Human Lung 2001

    18. Time Course Profiles A549 cell response to TGFbeta

    19. 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)

    20. 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.

    21. 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)

    22. 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.

    23. 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

    26. 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

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

    29. https://dfs/proteomecommons.org/

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