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Training & Protocols

Workshops

No workshops are currently scheduled.

Past Workshops

  • "Data Extraction and Analysis for LC-MS Based Proteomics" - February 22, 2009
    In 2009 we presented a short course at US HUPO, discussing label-free quantitative proteomics, AMT tag databases, and downstream data analysis using LC-MS analysis platforms. The topics discussed included

    • Overview of Label-Free Quantitative Proteomics
    • Feature discovery in LC-MS datasets
    • Biological Application of the AMT tag Approach

    These topics were chosen to educate researchers about some of the latest developments in high throughput LC-MS analysis, while also presenting aspects to consider when design large-scale experiments and extracting biological knowledge from large-scale experiments. We also described several informations tools and algorithms, most of which are available on the OMICS distribution site
    PDF slides (7.9 MB) PDF Icon

  • "Data Extraction and Analysis for LC-MS Based Proteomics" - March 16, 2008
    In 2008 we presented an updated and expanded short course at US HUPO, discussing various aspects of label-free quantitative proteomics using LC-MS analysis platforms. The topics discussed included

    • Overview of Label-Free Quantitative Proteomics
    • Feature discovery in LC-MS datasets
    • PEPPeR, GenePattern and Real-world examples

    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. In addition, several informatics tools and algorithms were described, many either open-source or freely available in the Software & Tools section of the OMICS distribution site.
    PDF slides (6.5 MB) PDF Icon

  • "Data Extraction and Analysis for LC-MS Based Proteomics" - March 5, 2007
    This short course at US HUPO discussed 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 can be used for higher-throughput proteomics. The topics discussed included 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 increasing 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 are either open-source or freely available in the Software & Tools section of the OMICS distribution site.
    PDF slides (5.2 MB) PDF Icon

  • "Separations and Mass Spectrometry Applied to Proteomics and the Informatics Challenges" - April 1, 2005
    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.

  • Resource Workshop: "Quantitative Proteomics Applied to Cellular Function" - June 8, 2004
    David Camp, Associate Director of the Resource, chaired this session of the 2004 Northwest Symposium for Systems Biology. This session focused on the evolution of quantitative proteomics that represents an area of rapid technological development with new approaches capable of characterizing the global protein complement in specific tissues or cells to identify transient and dynamic protein roles associated with cellular function.

Proteomics