PRIME (PaRtition of Ion types of tandem Mass spectra)is a software for identification of b and y ions in tandem mass spectra, a key challenging problem in de novo sequencing. PRIME utilizes a feature that ions of the same and different types follow different mass-difference distributions to separate b from y ions correctly. We have formulated the problem as a graph partition problem.A linear integer-programming algorithm has been implemented to solve the graph partition problem rigorously and efficiently.
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B. Yan, Y. Qu, F. Mao, V Olman, Ying Xu,
PRIME: A Mass Spectrum Data Mining Tool for De Novo Sequencing and PTMs Identification
Journal of Computer Science and Technology