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Abstract:

While the genome provides the blueprint of gene products, proteins are the bricks and mortar of biology. Mass spectrometry (MS) is the core technology for the study of proteins, their post-translational modifications, and their interactions. Over the past decade, proteomics has been dominated by bottom-up MS that digests proteins into fragments and analyzes the resulting short peptides. Since information about intact proteins is lost during digestion, recent studies advocated top-down MS that analyzes intact proteins and gives rise to many computational challenges. While top-down MS researchers have made great progress, the algorithms for interpreting top-down MS data are still in their infancy. We describe computational challenges and combinatorial algorithms for the analysis of top-down MS data and show how they enable new biological applications.