Non-metric similarity search of tandem mass spectra including posttranslational modifications

In biological applications, the tandem mass spectrometry is a widely used method for determining protein and peptide sequences from an “in vitro” sample. The sequences are not determined directly, but they must be interpreted from the mass spectra, which is the output of the mass spectrometer. This work is focused on a similarity-search approach to mass spectra interpretation, where the parameterized Hausdorff distance (dHPdHP) is used as the similarity. In order to provide an efficient similarity search under dHPdHP, the metric access methods and the TriGen algorithm (controlling the metricity of dHPdHP) are employed. Moreover, the search model based on the dHPdHP supports posttranslational modifications (PTMs) in the query mass spectra, what is typically a problem when an indexing approach is used. Our approach can be utilized as a coarse filter by any other database approach for mass spectra interpretation.