A New Approach to Protein Identification

Abstract. Advances in tandem mass-spectrometry (MS/MS) steadily increase the rate of generation of MS/MS spectra and make it more computationally chal-lenging to analyze such huge datasets. As a result, the existing approaches that compare spectra against databases are already facing a bottleneck, particularly when interpreting spectra of post-translationally modified peptides. In this paper we introduce a new idea that allows one to perform MS/MS database search... without ever comparing a spectrum against a database. The idea has two compo-nents: experimental and computational. Our experimental idea is counter-intuitive: we propose to intentionally introduce chemical damage to the sample. Although it does not appear to make any sense from the experimental perspec-tive, it creates a large number of “spectral pairs ” that, as we show below, open up computational avenues that were never explored before. Having a spectrum of a modified peptide paired with a spectrum of an unmodified peptide, allows one to separate the prefix and suffix ladders, to greatly reduce the number of noise peaks, and to generate a small number of peptide reconstructions that are very likely to contain the correct one. The MS/MS database search is thus reduced to extremely fast pattern matching (rather than time-consuming matching of spectra against databases). In addition to speed, our approach provides a new paradigm for identifying post-translational modifications.