Identifying Peptide Mass Spectra by Library Searching

by
Barbara Frewen

A widespread proteomics procedure for characterizing a complex mixture of proteins combines tandem mass spectrometry and database search software to yield mass spectra with identified peptide sequences. The same peptides are often detected in multiple experiments, and once they have been identified can be used for future identifications. We present a method for collecting previously identified tandem mass spectra into a reference library which is used to identify new spectra. Query spectra are compared to references in the library to find the ones that are most similar. A dot product metric is used to measure the degree of similarity. The query spectrum is assigned the sequence of the reference spectrum to which it is most similar. With our largest library, the search of a query set found 91\% of the identifications that could be made with a database search. A second experiment demonstrates that queries acquired on an LCQ ion trap mass spectrometer can be identified with a library of references acquired on an LTQ ion trap mass spectrometer. The dot product similarity score provides good separation of correct and incorrect identifications.

Advised by Bill Noble

CSE 403
Wednesday
February 8, 2006
3:30 - 4:20 pm