International Conference on Intelligent

Biology and Medicine (ICIBM 2012)

April 22-24, 2012, Nashville, TN, USA


Introduction to Proteome Informatics
April 22, 2012


1:00 PM    Identifying proteins through LC-MS/MS
David Tabb
  • Generating tandem mass spectral collections through analytical chemistry
  • Identifying peptide matches through database search algorithms
  • Thresholding peptide-spectrum matches to a specified False Discovery Rate
  • Assembling parsimonious protein lists via bipartite graphs
    1:50 PM Break
    2:00 PM    Comparing proteomes and recognizing protein modifications
    David Tabb
  • Differentiating cohorts by protein spectral counts
  • Monitoring batch effects and proteomics quality control
  • Detecting post-translational modifications
  • Controlling false discoveries and localizing modifications
    2:45 PM Break
    3:00 PM    Building customized protein databases from RNA-Seq data
    Xiaojing Wang
    3:30 PM    Enhancing miRNA target identification through proteomics
    Qi Liu
    4:00 PM    Relating protein modification to gene expression changes
    Bing Zhang
    4:30 PM Questions and Answers
    4:50 PM    Adjourn


    Identifying proteins and post-translational modifications (PTMs) from tandem mass spectrometry data depends heavily on an ecosystem of algorithms that has emerged during the last decade. This workshop introduces major elements of the protein and PTM identification pipeline and describes strategies for comparative proteomics. The second half describes techniques to address biological questions through integrating proteomic data with genomic data. The content is designed to be accessible to computer scientists and bioinformaticists who have not previously worked with proteomics data sets.


    David L. Tabb, Ph.D., is an associate professor of Biomedical Informatics at Vanderbilt University. He has developed algorithms for protein identification since 1996, when he began graduate school in the Laboratory of John Yates. He contributes bioinformatics expertise for two National Cancer Institute programs in proteomics: the Clinical Proteomics Technology Assessment for Cancer and the Early Detection Research Network.

    Bing Zhang, Ph.D., is an assistant professor of Biomedical Informatics and Cancer Biology at Vanderbilt University. His previous training includes both Bioinformatics and Molecular Genetics and Genomics. His group develops and applies systems biology approaches to the study of complex diseases, with a focus on cancer. His research interests include modeling and analysis of biological networks, biological data exploration and integration, and translational bioinformatics.

    Qi Liu, Ph.D., is a postdoctoral research associate in Dr. Bing Zhang’s group at Vanderbilt University. She joined Dr. Zhang’s group in 2011 with a Ph.D. degree in bioinformatics. Her current research focuses on the elucidation of post-transcriptional regulation mechanisms through the integration of high-throughput genomic and proteomic data.

    Xiaojing Wang, Ph.D., is a postdoctoral research associate in Dr. Bing Zhang’s group at Vanderbilt University. She joined Dr. Zhang’s group in 2010 with a Ph.D. degree in bioinformatics. She develops bioinformatics tools that utilize proteomic data to facilitate the functional interpretation of genomic variations.