A graph-based approach for proteoform identification and quantification using top-down homogeneous multiplexed tandem mass spectra

Abstract Background Top-down homogeneous multiplexed tandem mass (HomMTM) spectra are generated from modified proteoforms of the same protein with different post-translational modification patterns.They are frequently observed in the analysis of ultramodified proteins, some proteoforms of which have similar molecular weights and cannot be well separated DMSO+ALOE VERA by liquid chromatography in mass spectrometry analysis.Results We formulate the top-down HomMTM spectral identification problem as the minimum error k-splittable Shoes flow problem on graphs and propose a graph-based algorithm for the identification and quantification of proteoforms using top-down HomMTM spectra.Conclusions Experiments on a top-down mass spectrometry data set of the histone H4 protein showed that the proposed method identified many proteoform pairs that better explain the query spectra than single proteoforms.