For high-resolution tandem mass spectra, the determination of monoisotopic masses of fragment ions plays a key role in the\r\nsubsequent peptide and protein identification. In this paper, we present a new algorithm for deisotoping the bottom-up spectra.\r\nIsotopic-cluster graphs are constructed to describe the relationship between all possible isotopic clusters. Based on the relationship\r\nin isotopic-cluster graphs, each possible isotopic cluster is assessed with a score function, which is built by combining nonintensity\r\nand intensity features of fragment ions. The non-intensity features are used to prevent fragment ions with low intensity from\r\nbeing removed. Dynamic programming is adopted to find the highest score path with the most reliable isotopic clusters. The\r\nexperimental results have shown that the average Mascot scores and F-scores of identified peptides from spectra processed by our\r\ndeisotoping method are greater than those by YADA and MS-Deconv software.
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