PhD Seminar • Bioinformatics • NeoMS: Identification of Novel MHC-I Peptides with Tandem Mass Spectrometry

Please note: This PhD seminar will take place online.

Shaokai Wang, PhD candidate
David R. Cheriton School of Computer Science

Supervisor: Professor Bin Ma

The study of immunopeptidomics requires the identification of both regular and mutated MHC-I peptides from mass spectrometry data. For the efficient identification of MHC-I peptides with either one or no mutation from a sequence database, we propose a novel work-flow: NeoMS. It employs three main modules: generating an expanded sequence database with a tagging algorithm, a machine learning-based scoring function to maximize the search sensitivity, and a careful target-decoy implementation to control the false discovery rates (FDR) of both the regular and mutated peptides.

Experimental results demonstrate that NeoMS both improved the identification rate of the regular peptides over other database search software and identified hundreds of mutated peptides that have not been identified by any current methods. Further study shows the validity of these new novel peptides.

To attend this PhD seminar on Zoom, please go to https://uwaterloo.zoom.us/j/93694715579?pwd=dHlmMXN2Mnc1N1FjRjlyMTRqVkpwUT09.