De novo peptide sequencing is especially useful in theidentification of unknown proteins. A class of efficient modelson de novo peptide interpretation have been proposedrecently based on graph theory. However, majority of thegraph-based models convert each peak to multiple nodes inthe graph due to unknown ion types. This directly resultsin the decrease of the efficiency and accuracy of peptide sequencingalgorithms. To solve these problems, in this paperan ion transformation method is proposed to convert all theother type of ions to b-ions before the construction of spectrumgraph in the peptide sequencing. Experiments on boththe real QTof MS/MS data and the synthetic MS/MS datademonstrate that the proposed method reduces the size ofthe graph and improves the efficiency and accuracy of peptidesequencing algorithms.