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Training & Protocols

Workshops

  • July, 2013
    The Mass Spectrometry Special Interest Group (MS-SIG) is holding a symposium in Berlin Germany featuring prominent researchers in the field of proteomics, including Jurgen Cox, Oliver Kohlbacher, Olga Vitek, and others. This one day symposium, which occurs just prior to the ISMB/ECCB 2013 conference, will have two sessions on:

    • Protein identification/modification/quantification
    • Data integration & Proteomics applications in biology and medicine

    For more information, please see the Special Interest Group Flyer plus also the ISMB Special Interest Group Meetings page and the MS-SIG 2013 website.

Past Workshops

  • MS-SIG: Computational Challenges in High-Throughput Proteomics - July 14, 2012
    The Mass Sepctrometry Special Interest Group (MS-SIG), held a symposium in Long Beach, CA featuring prominent researchers in the field of proteomics, including Richard D. Smith, Michael MacCoss, Olga Vitek, Alexey Nesvizhskii, and Bobbie-Jo Webb-Robertson. This one day symposium, occurred just prior to the ISMB 2012 Conference, which focused on:

    • Label vs. label-free protein quantification
    • Proteomics applications in biology and medicine

    For more information, please see the ISMB Special Interest Group Meetings page.

  • "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

  • "Managing the Data Explosion in Systems Biology" - December 2006
    This tutorial presented at the American Society for Cell Biology (ACSB) meeting in San Diego, CA 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.

  • "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.
    See Article

  • "Apples and Oranges: Integrating Disparate Data Sets to Understand Complex Cellular Function" - December 2005
    This tutorial presented at the American Society for Cell Biology (ACSB) meeting in San Francisco, CA provided an overview of software-based approaches to handle heterogeneous data sets, such as proteomics and microarray data. The tutorial promoted discussion on different approaches that are being applied, the limitations and advantages of different solutions, and where to find help.

  • "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.

  • "Mass Spectrometry-based Quantitative Proteomics for Cell Biology" - December 2004
    This tutorial presented at the American Society for Cell Biology (ACSB) meeting in Washington D.C. focused on the application of quantitative proteomics strategies in combination with recently developed sample fractionation and enrichment methodologies, including automated protein complex isolation and cell fractionation.

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