Computing Post-translation Modification using FTMS

Post translational modifications (PTMs) discovery is an important problem in proteomic. In the past, people discover PTMs by Tandem Mass Spectrometer based on ‘bottom-up’ strategy. However, such strategy suffers from the problem of failing to discover all PTMs. Recently, due to the improvement in proteomic technology, Taylor et al. proposed a database software to discover PTMs with ‘topdown’ strategy by FTMS, which avoids the disadvantages of ‘bottom-up’ approach. However, their proposed algorithm runs in exponential time, requires a database of proteins, and needs prior knowledge about PTM sites. In this paper, a new algorithm is proposed which can work without a protein database and can identify modifications in polynomial time. Besides, no prior knowledge about PTM sites is needed.