Alphabet Projection of Spectra

In
the metabolomics, glycomics, and mass spectrometry of structured
small molecules, the combinatoric nature of the problem renders a
database impossibly large, and thus de novo analysis is necessary.
De novo analysis requires an alphabet of mass difference values used
to link peaks in fragmentation spectra when they are different by
a mass in the alphabet divided by a charge. Often, this alphabet is
not known, prohibiting de novo analysis. A method is proposed that,
given fragmentation mass spectra, identifies an alphabet of m/z differences that can build large connected
graphs from many intense peaks in each spectrum from a collection.
We then introduce a novel approach to efficiently find recurring substructures
in the de novo graph results.