Similarity search and posttranslational modifications in tandem mass spectra

Tandem mass spectrometry is a fast and modern method for determining protein and peptide sequences from an “in vitro” sample. A mass spectrometer outputs mass spectra, which are utilized for sequences identification. The successful methods for mass spectra interpretation are based on search in databases of already known or predicted protein sequences. Since the amount of protein sequences in the databases grows exponentially, couple of indexing approaches have been proposed to speed up the identification of the sequences corresponding to the mass spectra. However, many of these approaches do not (or poorly) support interpretation of the spectra contaminated with posttranslational modifications (PTMs), which in real-world conditions occur very often. We propose a promising method for dealing with PTMs in mass spectra, including efficient similarity search employing metric indexing. In this paper, we generalize a previously proposed method based on the parametrized Hausdorff distance (dHP), which can be used as a coarse filter for any other database-based mass spectra interpretation method.