MassSpec is designed to help you eliminate the time-consuming and error-prone methods of correlating structure fragments to peaks observed in a mass spectrum.

Use the Tools Palette to build your structure and MassSpec then generates a database of fragments resulting from bond cleavages up to three at a time.Enter a mass number from your spectrum or from the list the program generated and the program shows the fragments it has identified, and highlights them on your structure one at a time.
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Enter a mass number from your spectrum or from the list the program generated and the program shows the fragments it has identified, and highlights them on your structure one at a time.

The program also displays information on isotope peaks, peaks arising from the gain or loss of one hydrogen, and relative isotopic abundances (M+1...M+20) for all non-isotopic fragments.

Structures with a molecular weight of 9999 or less may be entered.

MassSpec recognizes masses resulting from the McLafferty rearrangement. This function operates recursively so that it produces masses arising from all possible rearrangements taken one, two, and three at a time. It will also operate on the so-called "McLafferty + 1" rearrangement.

If you work with proteins, an extended database replaces the standard elemental database with a table containing the appropriate names and masses of amino acid residues. Instead of drawing a polypeptide structures you can enter the three letter designation. A utility program is included for creating additional databases for specific research.