Thursday, April 25th: Sixue Chen – “Redox proteomics and metabolomics of guard cell immunity and CO2 response”

226 Weill Hall. 2PM – 3PM

Light refreshments will be served.

Dr Chen joins us from the University of Mississippi, where he is a professor and the chair of the Department of Biology.

Pathogen infection and other environmental stresses have posed grand challenges to crop production and food security. Stomatal pores are major entry points of bacteria pathogens.How stomatal guard cells respond to pathogen invasion and other environmental factors(e.g., rising CO2) is an important question. Recently, we have reported a new redox proteomics method called cysTMTRAQ that combines two types of isobaric tags, isobaric tag for relative and absolute quantification (iTRAQ) and cysteine tandem mass tag (cysTMT) in one experiment. The method not only enables simultaneous analysis of cysteine redox changes and total protein level changes, but also allows determination of bona fide redox modified cysteines in proteins through correction of protein turnover. This technology has recently been applied to discover potential redox proteins in stomatal guard cells in response to a 22-aa peptide (flg22) of Pseudomonas syringae. cysTMTRAQ revealed 677 proteins containing cysteines with cysTMT labels, and 57 showing significant redox changes after flg22 treatment. As CO2 levels affect stomatal immunity, we studied CO2 signaling using metabolomics. A new signaling pathway involving jasmonic acid was discovered.

Thursday, March 28th: Alexey Nesvizhskii – “FragPipe: A comprehensive computational platform for proteomics”

226 Weill Hall, 2pm-3pm

Light refreshments will be served.

Dr Nesvizhskii joins us from the University of Michigan, where he is the Professor of Bioinformatics, Computational Medicine, Pathology and is the Director of the Proteomics Resource Facility.This event is sponsored by the Cornell University Department of Computational Biology.

Dr. Nesvizhskii presented:

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.

Thursday, February 22nd : Yonghao Yu – “Targeting Protein Poly-ADP-Ribosylation for the Development of Next Generation PARP Inhibitors”

226 Weill Hall, 2pm-3pm

Light refreshments will be served.

Dr. Yu joins us from Columbia University Irving Medical Center, where he is a professor in the department of Molecular Pharmacology and Therapeutics.

Thursday, November 9th : Savas Tay – “Understanding and modeling signaling networks by single-cell proteomics”

226 Weill Hall, 2pm-3pm

Thursday, October 26th : Jacob Geri – “Photocatalytic Proximity Labeling”

Biotechnology Building Auditorium G01, 9:30am – 10:30am

Breakfast will open at 9am!