Applied Seminar: An integer programming model for the de novo analysis of tandem mass spectrometry data
3:10pm, Webster Hall B12
Abstract Tandem mass spectrometry is the standard technique used for the identification of peptides derived from mixtures of proteins. The information obtained consists of sequential mass-to-charge ratios of the peptide (called the spectrum) as it fragments along the peptide backbone. Traditionally, this spectrum (of an unknown peptide) is compared with known spectra derived from genomic databases. On the other hand, a de novo methodology attempts to find an amino acid sequence that would produce this spectrum, without referring to an archive of sequences. In this talk, I will present an integer optimization model for the de novo sequencing problem. This is work that is (very much) in progress.