Parameters: Algorithms described in this manuscript have parameters that must be prescribed by the user. Predicted molecular masses as well as their classification scores depend on these parameters. Table summarizes the parameter values employed for examples in this manuscript, as well as the range of feasible values for all parameters. Optimizing these parameters for various application areas will lead to improved performance. 1 Must be an integer value. Values are presented assuming similarity match factors are computed between 0 and 999 as described in this manuscript.