Riptide: fast protein identification from mass spectrometer data

Abstract

The biotechfirm target discovery incorporated (TDI) has developed a relatively fast and inexpensive method for protein identification. The final step in their approach involves an algorithm to deduce the terminal amino acid sequence of an unknown intact protein from its fragmentation mass spectrum. TDI's web-published algorithm was taken as a starting point for further research. The algorithm Riptide was developed that matches the output of TDI's algorithm, but demonstrates a 193X speed improvement on a 6-deep sequencing.