Abstract: The method presented herein includes acquiring a mass spectrum of a molecule that includes mass spectrum peaks corresponding to a precursor ion and fragment ions. The method also includes identifying at least a portion of the fragment ions in the mass spectrum as corresponding to one or more monomer subunit ion of the precursor ion by appending one or more of the fragment ions to an inferable constituent to produce a topology building block. The topology building block is then stored in a candidate pool as corresponding to one or more of the monomer subunit ion if the combined mass of the inferable constituent and one or more of the fragment ions satisfy a first user-defined mass tolerance. One or more candidate topology of the precursor ion is then obtained by combining a plurality of the topology building blocks that satisfy a second user-defined mass tolerance for the precursor ion.

Abstract: The present disclosure includes systems and methods for performing a plurality of base statistical analysis on a dataset to yield multiple, different base statistics with respect to a first predetermined number of features. The dataset and the base statistics can be used to find a transformation that determines significant features while controlling a false discovery rate (FDR) to be below a target FDR threshold (?), wherein a second predetermined number of features are assumed to be independent from each other. Using the transformation, a composite index can be generated that represents a synthesis of the base statistics and a report can be generated that indicates at least the relative presence of the significant features in the dataset using the composite index.

Abstract: The method presented herein includes acquiring a mass spectrum of a molecule that includes mass spectrum peaks corresponding to a precursor ion and fragment ions. The method also includes identifying at least a portion of the fragment ions in the mass spectrum as corresponding to one or more monomer subunit ion of the precursor ion by appending one or more of the fragment ions to an inferable constituent to produce a topology building block. The topology building block is then stored in a candidate pool as corresponding to one or more of the monomer subunit ion if the combined mass of the inferable constituent and one or more of the fragment ions satisfy a first user-defined mass tolerance. One or more candidate topology of the precursor ion is then obtained by combining a plurality of the topology building blocks that satisfy a second user-defined mass tolerance for the precursor ion.

Abstract: The present disclosure includes systems and methods for performing a plurality of base statistical analysis on a dataset to yield multiple, different base statistics with respect to a first predetermined number of features. The dataset and the base statistics can be used to find a transformation that determines significant features while controlling a false discovery rate (FDR) to be below a target FDR threshold (?), wherein a second predetermined number of features are assumed to be independent from each other. Using the transformation, a composite index can be generated that represents a synthesis of the base statistics and a report can be generated that indicates at least the relative presence of the significant features in the dataset using the composite index.

Abstract: Reference resolution may be modeled as an optimization problem, where certain techniques disclosed herein can identify the most probable references by simultaneously satisfying a plurality of matching constraints, such as semantic, temporal, and contextual constraints. Two structures are generated. The first comprises information describing one or more referring expressions and describing relationships, if any, between the one or more referring expressions. The second comprises information describing one or more referents to which the one or more referring expressions might refer and describing relationships, if any, between the one or more referents. Matching is performed, by using the structures, to match a given one of the one or more referring expressions to at least a given referent.