Contents - Index - Previous - Next

Tutorial 06 -- Autofragment
In addition to manual fragmentations that you perform yourself, you can also choose to carry out an "Autofragmentation" of the molecule.  This will generate a list of every fragment that theoretically could be formed from the molecule by the breaking of all bonds in the compound, taken one or two at a time.  It is important to recognize that this list includes every possible fragment and does not necessarily imply that a listed fragment will retain a charge, or even be formed.

A structure must be present in the drawing window before autofragment is run.  If nicotine is not present at this time, please open it.


1  Click on the Analyze mode button at the lower left.  The label at the upper right should read Fragment.  Click Utilities | Autofragment or just click on the Toolbar button with a hammer icon on it.  A small window will open that contains some optional settings, and two command buttons: Start and Cancel.  If no structure is present in the drawing region, only Cancel will be available.

2  You can choose to generate only those fragments that can be formed by the breaking of a single bond in the compound, or those formed by either 1 or 2 bond breaks.  The latter is the default and will be used here.  There is also an option to 'Mark OE (odd electron) Ions' which will label each result in the list that is an odd electron fragment.  That option also is selected by default.

3  Click on the 'Start' button to carry out the autofragmentation.  As the molecule is fragmented, a completion bar will indicate the progress, although on modern computers the calculation usually occurs nearly instantaneously and no completion bar may appear.

4  When fragmentation of the molecule is completed, a new window termed Autofragmentation Results will open, containing a list of the fragment ions and several additional command buttons.  Since the 'Mark OE Ions' option was selected in step 2 above, each potential odd electron ion in the list will be indicated with a "dot+" symbol.  Clicking the Next button will display the mass of the next fragment in the list, and link it to the corresponding structure on the molecule by indicating the associated atoms with a superimposed markers.  You can move through the list by using Next, or show specific fragments by clicking on them in the list.

5  Select the (even electron) fragment with mass 147 from the list.  The structure will indicate that this fragment arises from the loss of the methyl group.  Click on the 'Mass Isotopes' button.  The Isotopic Profiler window will open and the profile for this fragment ion will be displayed.  You can adjust the options and recalculate this profile if desired as before.  Click the 'Close' button to close the IP window and return to Autofragment Results.

6  Select the 'Evaluate Fragments' button.  A new window will open with a brief list of possible fragment ions and/or likely losses.  Unlike the main list which is comprehensive, Evaluate generates and identifies a much more selective list of possible fragments and/or losses from the structure, including some major rearrangement ions such as McLafferty rearrangement products, tropyllium ions, trimethylsilanol,  etc.  Although Evaluate will attempt to identify realistic fragments and major rearrangement ions, it is far from inclusive and also may  generate some unreasonable possibilities for a given molecule.   These results from Evaluate should be regarded as simply an additional aid in identifying actual fragments from a structure.  If you click on 'Print', the results given in this window will be sent to the default printer.  Click 'Close' to close the window and return to Autofragmentation Results.

7  There are two additional command buttons on the Autofragment Results window: 'Print' and 'Compare Spectrum'.  Selecting Print will send a summary list of all unique masses, along with the number of entries for that mass in the list, to the default printer.  'Compare Spectrum'  accesses the Spectrum window and is used to compare the autofragmentation results from a structure with an observed mass spectrum.  This is covered in the next tutorial (Tutorial #7 - Spectrum).


Goto Tutorial #7

Return to QuickStart