This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Accessibility of advanced proteomics technologies to the biomedical community is a longer-term goal of the Research Center. This information transfer is made possible by the NCRR website (full details on website on page 22 of the Research Progress Report) and the hosting of workshops and tutorials. Since the establishment of our NCRR program, we have organized two NCRR workshops and participated in six short courses/tutorials. A Short Course titled, """"""""Data Extraction and Analysis for LC-MS Based Proteomics"""""""" was given at the U.S. HUPO meeting in San Diego, CA in February 2009. This is the third consecutive year that the PNNL NCRR informatics team has presented this invited course. The course covered several aspects of quantitative proteomics using LC-MS analysis platforms, including an overview of quantitative approaches and software tools available to the community, considerations for experimental design, feature discovery in LC-MS datasets, and statistically sound analysis of identified peptides and proteins. These topics were aimed at informing researchers about the issues to consider when designing LC-MS experiments, while also describing the general approaches used for extracting information content from LC-MS data. The 15 people in attendance each received a data disk (DVD) with the software installers for proteomics software developed at the Center, plus the example data used to prepare the presentation. A Short Course titled, """"""""Data Extraction and Analysis for LC-MS Based Proteomics"""""""" was given at the U.S. HUPO meeting in Bethesda, MD in March 2008. The course covered several aspects of quantitative proteomics using LC-MS analysis platforms, including a comparison of the approaches and software tools available to the community, considerations for experiment design, feature discovery in LC-MS datasets, and statistically sound analysis of identified peptides and proteins. These topics were aimed at informing researchers about the issues to consider when designing LC-MS experiments, while also describing the general approaches used for extracting information content from LC-MS data. The ~35 people in attendance received a data disk (DVD) with the software installers for proteomics software developed at PNNL, plus the example data used to prepare the figures shown in the presentation. A Short Course titled, """"""""Data Extraction and Analysis for LC-MS Based Proteomics"""""""" was given at the U.S. HUPO meeting in Seattle, WA in March 2007. The course was intended to educate the U.S. proteomics community and discuss the use of two different LC-MS data extraction and analysis platforms to demonstrate how high mass measurement accuracy mass spectrometry and high resolution liquid chromatography could be applied for higher-throughput proteomics. The topics presented include 1) LC-MS feature extraction, 2) experimental design and analysis of large LC-MS datasets, and 3) identification and characterization of peptides and proteins using LC-MS. These topics were aimed at getting increased information content from LC-MS experiments both within customized and commercially available LC-MS systems. A number of informatics tools and algorithms were described, many of which are either open-source or freely available at the NCRR website. A DVD was also distributed to attendees with software installers and demo data. A Special Interest Subgroup titled, """"""""Managing the Data Explosion in Systems Biology"""""""" was held at the American Society for Cell Biology (ASCB) Meeting in San Diego, CA in December 2006. The following abstract summarizes the Special Interest Subgroup at the ASCB meeting entitled: New technologies in genomics, proteomics, and quantitative imaging are producing enormous amounts of data that promise to revolutionize biology in the upcoming decades. To realize this potential, however, new approaches must be developed to manipulate, integrate and analyze the large datasets that these technologies can generate. Otherwise, the trees will continue to obscure the forest. This subgroup brought together investigators with an interest and expertise in managing and analyzing large, heterogeneous datasets with the intent of building systems-level models of cellular functions. The state of the art was discussed and possibilities for community collaborations outlined. A Tutorial titled, """"""""Apples and Oranges: Integrating Disparate Data Sets to Understand Complex Cellular Function"""""""" was presented at the American Society for Cell Biology (ASCB) Meeting in San Francisco, CA in December 2005. The following abstract summarizes the tutorial presentation: Systems biology requires the integration of many types of data to understand complex cell processes. Unfortunately, it is currently very difficult to connect disparate data sets. This tutorial provided an overview of software-based approaches to handle heterogeneous data sets, such as proteomics and microarray data. The intent was to discuss the different approaches that are being used, the limitations and advantages of different solutions and where to find help. There will be three areas of discussion: 1) starting with good data, 2) linking data sets, 3) how to find patterns in the data. Both commercial and open source software packages will be discussed, although the emphasis will be on the latter, in particular CCE and Cytoscape. A NCRR Workshop titled, """"""""Separations and Mass Spectrometry Applied to Proteomics and the Informatics Challenges"""""""" was planned and executed at PNNL in conjunction with a Proteome Society Meeting hosted by PNNL in April 2005. The following is a description that emphasizes the focus of the workshop: Among the issues confronting the proteomics community, few may be as important as those covered in this workshop. Specifically, we covered both data dissemination standards as well as open source software tools that help analyze that data. Data standards are vital to the growing collaborative nature of large scale proteomics studies in that they will allow multiple institutions located in diverse areas to share the results of instrumental analyses without the requirement that many separate analysis software tools be broadly distributed amongst those groups. Further, standardized formats will simplify publication of analyzed data, fostering rigorous peer review of results and new analysis tool development. Indeed, open source data analysis tool development, wherein the software that enables discovery science as applied to proteomics becomes available to all institutions for use and improvement, was the second major issue covered during the workshop. Rather than requiring collaborators to simply trust the results that stem from black-box style analysis tools, open source software allows any institution to examine, validate, and ultimately, improve these tools when and where appropriate. Lastly, open source tools provide a more solid foundation upon which exciting discoveries may rest. This workshop brought together some of the preeminent individuals working in these areas in an interactive environment to both present their findings and discuss the implications and future directions of these important issues. A Tutorial titled, """"""""Mass Spectrometry-based Quantitative Proteomics for Cell Biology"""""""" was presented at the American Society for Cell Biology (ASCB) Meeting in Washington D.C. in December 2004. The following abstract summarizes the tutorial presentation: The effective integration of proteomics data into cell biology studies requires both identification and quantification of the proteins. Mass spectrometry combined with high-resolution liquid chromatographic separations of fractionated or enriched peptide samples represents a highly efficient approach to peptide identification and quantitation. This tutorial will focus on the application of quantitative proteomic strategies (stable isotope labeling and absolute quantitation) in combination with recently developed sample fractionation and enrichment methodologies, including automated protein complex isolation and cell fractionation. The tutorial will include a presentation of the analysis methods for interpreting quantitative proteomics data and their application to analyzing cellular responses to exogenous stimulation. A NCRR Proteomics Workshop titled, """"""""Quantitative Proteomics Applied to Cellular Function"""""""" was held in conjunction with the 2004 Northwest Symposium for Systems Biology at PNNL in June 2004. The focus of the workshop was on the evolution of quantitative proteomics. The goals of the workshop were (1) to educate researchers to the utility of the application of quantitative proteomics to understanding cellular function;(2) to stimulate possible new collaborations between the presenters, participating scientists, and the Research Center;and (3) to increase the awareness of the scientific community to the NCRR Biomedical Technology Research Center at PNNL.
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