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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 by liquid chromatography in mass spectrometry analysis. Results: We formulate the top-down HomMTM spectral identification problem as the minimum errordoi:10.1186/s12859-018-2273-4 pmid:30367573 fatcat:wh7iarat4ngejpnc2gw45ohhwa