The invention relates to the scanning and representation of daughter ion spectra for the purpose of determining the structural characteristics of parent ions in ion traps. The invention consists of combining all or selected daughter and granddaughter spectra of a parent ion over several generations in one combined descendants spectrum. This combined descendants spectrum can be depicted as a graphic or a list. The references to origin can be plotted on the combined descendants spectrum. For biopolymers, where the loss of fragments can be identified due to their mass, the names or abbreviations of lost molecule fragments can be entered. The criteria for selection of the spectra can be predefined; in this way, the spectra can be depicted and even scanned automatically.

Methods for determining the chemical structures, substructures and/or ionic structural arrangements of unknown or partially structurally characterized compounds from mass spectrometric data are disclosed. The methods of the invention are directed to elucidating the molecular structures of compounds by identifying the structures of ions generated from those compounds through the use of tandem mass spectrometry and subsequently conducting a library search of structurally characterized tandem product spectra from known ions for specific matches. The collective structural information and/or alternative structural candidates are then constructed from the determined ion structures and other structural characteristics using a structure generator and/or a structure assembly and/or a structure reduction system. The structure or substructure determination process can be continuously improved by adding additional data, e.g., information obtained from molecules previously structurally characterized using this method.