CIP@Cornell is delighted to host Dr. Alexey Nesvizhskii, Professor of Bioinformatics, Computational Medicine and Bioinformatics, Pathology, and Director of the Proteomics Resource Facility​​​​​​ at the University of Michigan. This event is sponsored by the Cornell University Department of Computational Biology. Light refreshments will be served.

Dr. Nesvizhskii will present:

FragPipe: A comprehensive computational platform for proteomics

I have been fascinated with the subject of the “dark proteome” since my entry in the field of proteomics in 2001. What are all those spectra that we cannot identify in a typical proteomics experiment, and how do we design efficient computational strategies to move beyond standard analyses. To this end, we have created a highly efficient peptide indexing algorithm and implemented it in an ultrafast peptide identification tool MSFragger, which has become the engine behind our widely used FragPipe computational platform. MSFragger have empowered new strategies for faster and more sensitive identification of biologically or chemically modified peptides. I will describe recent computational advances and applications of our algorithms, including methods for the identification of N- and O-linked glycopeptides, labile PTMs, as well as collaborative studies in the areas of single-cell proteomics and chemical proteomics. I will illustrate the power of our algorithms for the analysis of large-scale proteomics and immunopeptidomics datasets. I will also provide an overview of the various quantification workflows (DIA, TMT, LFQ-MBR) available in FragPipe supporting analysis of data across all major instrument platforms.