a method and system for searching for an optimal sequence of subunits from among possible sequences of subunits . a described embodiment provides for evaluating each possible subunit sequence of a biopolymer with respect to a mass spectrum produced by ionizing and fragmenting the mass - tagged biopolymer in order to determine the most probable subunit sequence of the biopolymer . however , unlike in the currently practiced , permutations - based methods , an efficient combinations - based search is used to hierarchically partition all possible subunit sequences , and to assign maximum subunit - sequence rankings to the partitions , in order to computationally efficiently extract the most probable subunit sequence .