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Compare
Compare is a button that will appear at the bottom of the Spectrum window if Spectrum has been called from Autofragment. That is, the Compare button will only be visible if you have first created or loaded a structure and carried out an autofragmentation, and then clicked on the 'Compare Spectrum' button on the Autofragment Results window.
When you click on the Compare button, MSC will examine the Autofragmentation list and the current spectrum for common ions, and each matched ion in the spectrum will be redrawn in red to provide a visual indication of the degree of agreement. This comparison includes the molecular ion (and isotopes) in addition to the reported autofragmentation masses, but does not include fragment mass isotopes. Note that the presence of a 'match' only indicates common mass (within the range specified by the number of H transfers allowed), and, of course, cannot confirm the identity or even necessarily the elemental composition of the ion. Following a comparison, a Summary item will appear on the Spectrum menu -- see the topic below for more information.
When Compare is available,an additional option termed 'Hydrogen Transfers' will be indicated near the bottom of the Spectrum window: If this option is active, either 1 or 2 H transfers will be allowed in the comparison depending on the value selected. If Hydrogen Transfers is active when Compare is initiated, spectrum ions will match autofragment masses if they are within n amu of the target mass where n = the number of transfers allowed, thus enabling the detection of fragments that have undergone one (or two) H transfers.
Summary